Miracle-dz/UniFAR-FTUs huggingface dataset:
The SMART Platform: early experience enabling substitutable applications for electronic health records

Objective The Substitutable Medical Applications, Reusable Technologies (SMART) Platforms project seeks to develop a health information technology platform with substitutable applications (apps) constructed around core services. The authors believe this is a promising approach to driving down healthcare costs, supporting standards evolution, accommodating differences in care workflow, fostering competition in the market, and accelerating innovation. Materials and methods The Office of the National Coordinator for Health Information Technology, through the Strategic Health IT Advanced Research Projects (SHARP) Program, funds the project. The SMART team has focused on enabling the property of substitutability through an app programming interface leveraging web standards, presenting predictable data payloads, and abstracting away many details of enterprise health information technology systems. Containers—health information technology systems, such as electronic health records (EHR), personally controlled health records, and health information exchanges that use the SMART app programming interface or a portion of it—marshal data sources and present data simply, reliably, and consistently to apps. Results The SMART team has completed the first phase of the project (a) defining an app programming interface, (b) developing containers, and (c) producing a set of charter apps that showcase the system capabilities. A focal point of this phase was the SMART Apps Challenge, publicized by the White House, using http://www.challenge. gov website, and generating 15 app submissions with diverse functionality. Conclusion Key strategic decisions must be made about the most effective market for further disseminating SMART: existing market-leading EHR vendors, new entrants into the EHR market, or other stakeholders such as health information exchanges.
Journal of Neuroengineering and Rehabilitation Open Access Exoskeletons and Orthoses: Classification, Design Challenges and Future Directions

For over a century, technologists and scientists have actively sought the development of exoskeletons and orthoses designed to augment human economy, strength, and endurance. While there are still many challenges associated with exoskeletal and orthotic design that have yet to be perfected, the advances in the field have been truly impressive. In this commentary, I first classify exoskeletons and orthoses into devices that act in series and in parallel to a human limb, providing a few examples within each category. This classification is then followed by a discussion of major design challenges and future research directions critical to the field of exoskeletons and orthoses.
Genomic and Physiological Analysis of Carbon Storage in the Verrucomicrobial Methanotroph “Ca. Methylacidiphilum Fumariolicum” SolV

“Candidatus Methylacidiphilum fumariolicum” SolV is a verrucomicrobial methanotroph that can grow in extremely acidic environments at high temperature. Strain SolV fixes carbon dioxide (CO2) via the Calvin–Benson–Bassham cycle with methane as energy source, a trait so far very unusual in methanotrophs. In this study, the ability of “Ca. M. fumariolicum” to store carbon was explored by genome analysis, physiological studies, and electron microscopy. When cell cultures were depleted for nitrogen, glycogen storage was clearly observed in cytoplasmic storage vesicles by electron microscopy. After cessation of growth, the dry weight kept increasing and the bacteria were filled up almost entirely by glycogen. This was confirmed by biochemical analysis, which showed that glycogen accumulated to 36% of the total dry weight of the cells. When methane was removed from the culture, this glycogen was consumed within 47 days. During the period of glycogen consumption, the bacteria kept their viability high when compared to bacteria without glycogen (from cultures growing exponentially). The latter bacteria lost viability already after a few days when starved for methane. Analysis of the draft genome of “Ca. M. fumariolicum” SolV demonstrated that all known genes for glycogen storage and degradation were present and also transcribed. Phylogenetic analysis of these genes showed that they form a separate cluster with “Ca. M. infernorum” V4, and the most closely related other sequences only have an identity of 40%. This study presents the first physiological evidence of glycogen storage in the phylum Verrucomicrobia and indicates that carbon storage is important for survival at times of methane starvation.
Inbreeding Alters Activities of the Stress-Related Enzymes Chitinases and β-1,3-Glucanases

Pathogenesis-related proteins, chitinases (CHT) and β-1,3-glucanases (GLU), are stress proteins up-regulated as response to extrinsic environmental stress in plants. It is unknown whether these PR proteins are also influenced by inbreeding, which has been suggested to constitute intrinsic genetic stress, and which is also known to affect the ability of plants to cope with environmental stress. We investigated activities of CHT and GLU in response to inbreeding in plants from 13 Ragged Robin (Lychnis flos-cuculi) populations. We also studied whether activities of these enzymes were associated with levels of herbivore damage and pathogen infection in the populations from which the plants originated. We found an increase in pathogenesis-related protein activity in inbred plants from five out of the 13 investigated populations, which suggests that these proteins may play a role in how plants respond to intrinsic genetic stress brought about by inbreeding in some populations depending on the allele frequencies of loci affecting the expression of CHT and the past levels of inbreeding. More importantly, we found that CHT activities were higher in plants from populations with higher levels of herbivore or pathogen damage, but inbreeding reduced CHT activity in these populations disrupting the increased activities of this resistance-related enzyme in populations where high resistance is beneficial. These results provide novel information on the effects of plant inbreeding on plant–enemy interactions on a biochemical level.
SURVEY AND DIVERSITY OF INTERTIDAL MOLLUSCSALONG THE COAST OFVERAVAL (GUJARAT), ARABIAN SEA

The 1.6 km long rocky coastal stretch with 90 mt. vertical exposure during lowest low tide shown rich biological diversity. The study carried out in belt transect method to study abundance and density of intertidal macrofauna from Sept-2015 to Aug-2016. The zone was divided into 3 zones viz. Zone-1 (0-30mt), Zone-2 (30-60mt), and Zone-3 (60-90mt). The one square meter quadrate having 10 X 10 cm sub quadrates were employed along the line transact at every 10 mt intervals on the intertidal region perpendicular to the shoreline starting from highest high watermark to lowest low water mark at the time of the study. The highest density of organisms found at Zone-2, followed by Zone-3 and Zone-1. The coast exhibited the presence of 31 species of molluscs. It is also observed that the most abundant and year-round species observed was Patella radiate followed by Turbo intercostalis, Chiton granoradiatus, Rinoclavissinensis and Cerithiumspp. The shellfishes like Hexaplexendivia, Pyrene versicolor, Anadara Spp. , Murex tribulus and Chicoreusramosus shown rare availability at almost all the level.
In-vitro efficacy of different antibiotics used in the treatment of bacteria isolated from bovine mastitis in South Khartoum

Mastitis is the most important disease in dairy farms worldwide causing significant economic losses. Sixty milk samples were collected from mastitic cows and submitted to the laboratory for further bacteriological examinations, Staphylococcus spp. (45%), Bacillus spp. (22.5%), Enterobacter spp. (14.5%), Pseudomonas spp. (8%), Acinobacter spp (5%) and Micrococcus spp (5%) were found in bacteriological examination of all milk samples. Staphylococcus aureus was the most prevalent among Staphylococci isolates (45%), followed by Staphylococcus intermedius (22%), Staphylococcus warneri (11%), Staphylococcus hyicus (11%), Staphylococcus chromogenes (11%) and Staphylococcus lentus (11%) Also Bacillus spp were found to be: Bacillus alvei (40%) Bacillus thermophilus (20%), Bacillus coagulans (20%) and Bacillus firmus (20%). Sensitivity tests were conducted using 12 different antibiotics including Tetracycline and Gentamicin. The sensitivity was determined for each antibiotic by using disc diffusion technique according to Kirby–Bauer method. The isolated bacteria were highly sensitive to Ciprofloxacin, Ifovluxtsen, Linezolid, Gentamicin and they were found to be resistant to Cloxacillin, Cephalexin, followed by Tetracycline, Lincomycin. Roxithromycin. This study showed that the most causative agent of mastitis in south Khartoum is Staphylococcus aureus. Hygienic practices procedure in dairy farm must be sustainable to reduce this disease and to be aware about the suitable antibiotics to be used using antibiotic sensitivity test. The present study was designed to investigate the sensitivity of different antibiotics against bacteria isolated from suspected mastitic cows in dairy farms in south Khartoum, Sudan. Keywords: Staph. aureus, Bacillus, Antibiotics, Mastitis, Ceprofloxacin, Sensitivity.
Estimating the effect of COVID-19 on mental health: Linguistic indicators of depression during a global pandemic

This preliminary analysis uses a deep LSTM neural network with fastText embeddings to predict population rates of depression on Reddit in order to estimate the effect of COVID-19 on mental health. We find that year over year, depression rates on Reddit are up 50% , suggesting a 15-million person increase in the number of depressed Americans and a $7.5 billion increase in depression related spending. This finding suggests that utility in NLP approaches to longitudinal public-health surveillance.
Infertility among iron industry workers

Occupational exposures in different industries may pose serious health impacts. A number of epidemiological studies have focused on the association of occupational exposures and adverse health effects. The need of the hour is to focus on the reproductive health of workers engaged at different jobs in varied industries. Increasing environmental as well as occupational exposures have led to serious effects on the reproductive health of workers and have also endangered the life of future generations. The present paper highlights the impact of occupational exposures on iron industry workers. Future health based researches are recommended so as to assess the impact of occupational exposures on reproductive capabilities of workers.
Search My Favorites by Color: Fashion Parsing through Color Classiﬁcation

This paper investigates using computational color naming approach that mapping pixel values from fashion images to standardized color names. Current commercialized solutions are all based on vendor-generated linguistic tags such as "red sweater", "black jeans" putting into the HTML meta data, and letting user perform text searches based on those tags. In this work, we consider using a convolutional neural network (CNN) and softmax activation to classify the color of fashion images. Since the color naming only focused on ROI (region of interest) in the image, we use Region-based convolutional neural network (R-CNN) to focus on pixels within the detected boxes as the training input, and use softmax for classiﬁcation and learn the fashion colors. More speciﬁcally, we adopt the Mask R-CNN with the Semantic Segmentation approach to adapt to the fashion images. This approach can let users ﬁlter their favorite fashions by a standardized color naming without the help of linguistic color tags from the online images.
Generating Probability Distributions for Future Stock Prices

This project explores the efﬁcacy of using softmax to generate detailed probability distributions for future stock prices. Our ﬁndings show that such a model can generate realistic price probability distributions, with a MSE loss of 0.0815 when predicting among a set of 10 price change ranges. These results build on top of our other experimental ﬁndings with various deep learning models
Object Localization of Concentrated Animal Feeding Operations

We modify an object detector based on Yolov3 to detect concentrated animal feeding operations from high-resolution satellite images. We focus on optimizing the Mean Average Precision (MAP) at an Intersection-Over-Union threshold of IOU t = 0 . 1 . We show speciﬁc techniques and hyper-parameters tuned to achieve a MAP@0.1>0.9. We compute saliency maps to visualize what the model is learning and draw conclusions from both exercises as future steps to scale our detector.
End-to-End Lung Cancer Diagnosis on Computed Tomography Scans using 3D CNN and Explainable AI

Lung cancer is one of the most common malignant neoplasms all over the world. It accounts for more cancer deaths than any other cancer. It is increasingly being recognized in hospitals all across the globe. With the increasing prevalence of smoking, Lung cancer has reached epidemic proportions. Thus, we propose a 3D-CNN-based model [6] that uses a patient’s Computed Tomography scans to detect nodules and check for malignancy. We intend to add an explainable aspect to the result since the central problem of such models is that they are regarded as black-box models, and they lack an explicit declarative knowledge representation [9]. This calls for systems enabling to make decisions transparent, understandable and explainable.
Repurposing a Relighting Network for Realistic Compositions of Captured Scenes

Multi-view stereo can be used to rapidly create realistic virtual content, such as textured meshes or a geometric proxy for free-viewpoint Image-Based Rendering (IBR). These solutions greatly simplify the content creation process compared to traditional methods, but it is difficult to modify the content of the scene. We propose a novel approach to create scenes by composing (parts of) multiple captured scenes. The main difficulty of such compositions is that lighting conditions in each captured scene are different; to obtain a realistic composition we need to make lighting coherent. We propose a two-pass solution, by adapting a multi-view relighting network. We first match the lighting conditions of each scene separately and then synthesize shadows between scenes in a subsequent pass. We also improve the realism of the composition by estimating the change in ambient occlusion in contact areas between parts and compensate for the color balance of the different cameras used for capture. We illustrate our method with results on multiple compositions of outdoor scenes and show its application to multi-view image composition, IBR and textured mesh creation.
Operating point selection in multiple access rate regions

We study the selection of the rate allocation in multiple access channels (MAC). We consider MACs with different rate regions. Namely, we investigate the polytope rate regions, convex non-polytope rate regions, and non-convex rate regions. Different operating points of the rate region possess different properties in terms of efficiency, fairness, stability, etc. Our goal is to provide guidelines for the choice of an operating point using the above-mentioned criteria. We use two methodological approaches: fairness function approach leading to an optimal system operation point and game theoretic approach leading to an equilibrium point. In particular, we use games with correlated constraints. All fairness concepts and normalized Nash equilibrium produce the same rate allocation in the case of a MAC with polytope rate region. In the case of MACs with convex non-polytope and non-convex rate regions this property does not hold and behavior becomes much more various. In the case of some non convex rate regions the max-min fair allocation may even not exist.
Implanted reuptake-deficient or wild-type dopaminergic neurons improve ON l-dopa dyskinesias without OFF-dyskinesias in a rat model of Parkinson's disease

OFF-l-dopa dyskinesias have been a surprising side-effect of intrastriatal foetal ventral mesencephalic transplantation in patients with Parkinson's disease. It has been proposed that excessive and unregulated dopaminergic stimulation of host post-synaptic striatal neurons by the grafts could be responsible for these dyskinesias. To address this issue we transplanted foetal dopaminergic neurons from mice lacking the dopamine transporter (DATKO) or from wild-type mice, into a rat model of Parkinson's disease and l-dopa-induced dyskinesias. Both wild-type and DATKO grafts reinnervated the host striatum to a similar extent, but DATKO grafts produced a greater and more diffuse increase in extra-cellular striatal dopamine levels. Interestingly, grafts containing wild-type dopaminergic neurons improved parkinsonian signs to a similar extent as DATKO grafts, but provided a more complete reduction of l-dopa induced dyskinesias. Neither DATKO nor wild-type grafts induced OFF-l-dopa dyskinesias. Behavioural and receptor autoradiography analyses demonstrated that DATKO grafts induced a greater normalization of striatal dopaminergic receptor supersensitivity than wild-type grafts. Both graft types induced a similar downregulation and normalization of PEnk and fosb/Δfosb in striatal neurons. In summary, DATKO grafts causing high and diffuse extra-cellular dompamine levels do not per se alter graft-induced recovery or produce OFF-l-dopa dyskinesias. Wild-type dopaminergic neurons appear to be the most effective neuronal type to restore function and reduce l-dopa-induced dyskinesias.
Intensity of Nematode Infection in Children Aged 3 to 5 Years Living in Mukuru Kwa Njenga Slum Settlement, Nairobi, Kenya

Background The burden of nematode infections is high mostly in children below 5 years old, with clinical manifestations ranging from mild to painful symptoms due to severe infections that end up suppressing the immune system of the infected children. The occurrence of these infections is highest in areas of extreme poverty. This study evaluated the intensity of nematode infections and assessed the status of deworming in children aged 3 to 5 years living in Mukuru slum settlement, Nairobi County, Kenya. Methodology. A total of 172 children aged between 3 and 5 years were sampled across the 5 major villages of Mukuru Slum settlement: Kwa Njenga, Vietnum, Wapewape, Kwa Reuben, and Motomoto. Community health workers administered questionnaires on the deworming history of children. Stool samples were collected, macroscopically examined, and microscopically analysed using Kato-Katz technique to assess the intensity of infection. The intensities of nematode infections were expressed as eggs per gram (epg) of faeces. Results The point prevalence of nematode infection among the 98 children in the 1st sampling was 25.5% with a mean infection intensity of 5424 epg, whereas among the 74 children sampled in 2nd sampling, 47.3% had nematode infection with a mean infection intensity of 12384 epg. The average nematode infection for the 172 participants was 34.9% with a mean intensity of 17808 epg. The highest number of children infected with nematodes was in the village of Wapewape where 34 participants were examined and 36.3% were infected with a mean intensity of 3216 epg. Kwa Reuben and Vietnum villages had the same prevalence values of 32.4% where 34 participants in each village had a mean intensity of 3624 epg and 4512 epg, respectively. In both samplings, more than 80% of children had been dewormed more than 6 months prior to the study. Ascaris lumbricoides was the only species of intestinal nematodes identified to be present in the stool samples of children in this study, whereas Trichuris trichiura and hookworm infections were found to be absent. The intensity of infection was not dependent on age or gender.
DeepBreath: An Automated Chest X-Ray Diagnostic Tool

Chest x-rays are one of the most widely used radiological examinations for diagnosing and detecting various thoracic diseases. Developing a tool that can help radiologists achieve more accurate diagnoses could have tremendous beneﬁts for under-resourced hospitals and clinics. In this paper, we present various deep learning models trained to detect for the presence of 14 different observations from both lateral and frontal chest x-ray scans. From the explored architectures, the DenseNet-169 [1] model performed the best, achieving a test accurracy of 86%
Effects of Yoga on Mental and Physical Health: A Short Summary of Reviews

This report summarizes the current evidence on the effects of yoga interventions on various components of mental and physical health, by focussing on the evidence described in review articles. Collectively, these reviews suggest a number of areas where yoga may well be beneficial, but more research is required for virtually all of them to firmly establish such benefits. The heterogeneity among interventions and conditions studied has hampered the use of meta-analysis as an appropriate tool for summarizing the current literature. Nevertheless, there are some meta-analyses which indicate beneficial effects of yoga interventions, and there are several randomized clinical trials (RCT's) of relatively high quality indicating beneficial effects of yoga for pain-associated disability and mental health. Yoga may well be effective as a supportive adjunct to mitigate some medical conditions, but not yet a proven stand-alone, curative treatment. Larger-scale and more rigorous research with higher methodological quality and adequate control interventions is highly encouraged because yoga may have potential to be implemented as a beneficial supportive/adjunct treatment that is relatively cost-effective, may be practiced at least in part as a self-care behavioral treatment, provides a life-long behavioural skill, enhances self-efficacy and self-confidence and is often associated with additional positive side effects.
Combination of heat shock protein 90 and focal adhesion kinase inhibitors synergistically inhibits the growth of non-small cell lung cancer cells

Discovery of effective drug combinations is a promising strategy to improve patient survival. This study explores the impact of heat shock protein 90 (Hsp90) inhibition in combination with focal adhesion kinase (FAK) inhibitor on the growth of non-small cell lung cancer cells (NSCLC cells). Our data show that 17-N-Allylamino-17-demethoxygeldanamycin (17-AAG), a well-studied Hsp90 inhibitor, synergized with FAK inhibitor, PF-573228, on the growth inhibition of NSCLC cells. This combination effect was confirmed using additional chemically distinct Hsp90 inhibitor, STA-9090, which is currently undergoing phase 3 clinical evaluation. Co-treatment of NSCLC cells with Hsp90 and FAK inhibitors significantly enhanced the inhibition on long-term colony formation compared to that with single agent. Inhibition of FAK exacerbated the G2 cell cycle arrest and annexin-V apoptotic staining induced by 17-AAG. Further mechanistic studies revealed that the combination of Hsp90 and FAK inhibitors reduced the activity of canonical proliferative and survival Akt-mTOR signaling, and increased pro-apoptotic caspase activation. Interestingly, FAK inhibition alone induced feedback activation of pro-survival Erk signaling, which was abrogated by co-treatment with Hsp90 inhibitors. Both Hsp90 and FAK inhibitors are undergoing clinical evaluation. Our studies suggest the tandem of Hsp90 and FAK inhibitors may provide an effective treatment option for NSCLC patients.
CD4:CD8 ratio in children with perinatally acquired HIV‐1 infection†

In adults with horizontally acquired HIV infection, an inverted CD4:CD8 ratio is associated with persistent immune activation, size of HIV reservoir and predicts an increased risk of non‐AIDS‐defining adverse events. Normalization of this ratio with antiretroviral therapy (ART) is suboptimal in adults, despite viral suppression, and is less well described in paediatric populations. We investigated rates of CD4:CD8 ratio recovery in children with perinatally acquired HIV infection (PaHIV) on ART.