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Showing papers by "Temple University published in 2019"


Journal ArticleDOI
TL;DR: Blood eosinophils are recommended as a biomarker to support clinical decisions regarding the use of inhaled corticosteroids in chronic obstructive pulmonary disease patients, based on recent evidence from clinical trials.
Abstract: Precision medicine is a patient-specific approach that integrates all relevant clinical, genetic and biological information in order to optimise the therapeutic benefit relative to the possibility of side-effects for each individual. Recent clinical trials have shown that higher blood eosinophil counts are associated with a greater efficacy of inhaled corticosteroids (ICSs) in chronic obstructive pulmonary disease (COPD) patients. Blood eosinophil counts are a biomarker with potential to be used in clinical practice, to help target ICS treatment with more precision in COPD patients with a history of exacerbations despite appropriate bronchodilator treatment. The Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2017 pharmacological treatment algorithms, based on the ABCD assessment, can be applied relatively easily to treatment-naive individuals at initial presentation. However, their use is more problematic during follow-up in patients who are already on maintenance treatment. There is a need for a different system to guide COPD pharmacological management during follow-up. Recent large randomised controlled trials have provided important new information concerning the therapeutic effects of ICSs and long-acting bronchodilators on exacerbations. The new evidence regarding blood eosinophils and inhaled treatments, and the need to distinguish between initial and follow-up pharmacological management, led to changes in the GOLD pharmacological treatment recommendations. This article explains the evidence and rationale for the GOLD 2019 pharmacological treatment recommendations.

1,122 citations


Proceedings ArticleDOI
15 Jun 2019
TL;DR: LaSOT is presented, a high-quality benchmark for Large-scale Single Object Tracking that consists of 1,400 sequences with more than 3.5M frames in total, and is the largest, to the best of the authors' knowledge, densely annotated tracking benchmark.
Abstract: In this paper, we present LaSOT, a high-quality benchmark for Large-scale Single Object Tracking. LaSOT consists of 1,400 sequences with more than 3.5M frames in total. Each frame in these sequences is carefully and manually annotated with a bounding box, making LaSOT the largest, to the best of our knowledge, densely annotated tracking benchmark. The average video length of LaSOT is more than 2,500 frames, and each sequence comprises various challenges deriving from the wild where target objects may disappear and re-appear again in the view. By releasing LaSOT, we expect to provide the community with a large-scale dedicated benchmark with high quality for both the training of deep trackers and the veritable evaluation of tracking algorithms. Moreover, considering the close connections of visual appearance and natural language, we enrich LaSOT by providing additional language specification, aiming at encouraging the exploration of natural linguistic feature for tracking. A thorough experimental evaluation of 35 tracking algorithms on LaSOT is presented with detailed analysis, and the results demonstrate that there is still a big room for improvements.

653 citations


Book ChapterDOI
Matej Kristan1, Ales Leonardis2, Jiří Matas3, Michael Felsberg4  +155 moreInstitutions (47)
23 Jan 2019
TL;DR: The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative; results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years.
Abstract: The Visual Object Tracking challenge VOT2018 is the sixth annual tracker benchmarking activity organized by the VOT initiative. Results of over eighty trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis and a “real-time” experiment simulating a situation where a tracker processes images as if provided by a continuously running sensor. A long-term tracking subchallenge has been introduced to the set of standard VOT sub-challenges. The new subchallenge focuses on long-term tracking properties, namely coping with target disappearance and reappearance. A new dataset has been compiled and a performance evaluation methodology that focuses on long-term tracking capabilities has been adopted. The VOT toolkit has been updated to support both standard short-term and the new long-term tracking subchallenges. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website (http://votchallenge.net).

639 citations


Journal ArticleDOI
17 Jul 2019
TL;DR: A powerful end-to-end one-stage object detector called M2Det is designed and train by integrating it into the architecture of SSD, and achieve better detection performance than state-of-the-art one- stage detectors.
Abstract: Feature pyramids are widely exploited by both the state-of-the-art one-stage object detectors (e.g., DSSD, RetinaNet, RefineDet) and the two-stage object detectors (e.g., Mask RCNN, DetNet) to alleviate the problem arising from scale variation across object instances. Although these object detectors with feature pyramids achieve encouraging results, they have some limitations due to that they only simply construct the feature pyramid according to the inherent multiscale, pyramidal architecture of the backbones which are originally designed for object classification task. Newly, in this work, we present Multi-Level Feature Pyramid Network (MLFPN) to construct more effective feature pyramids for detecting objects of different scales. First, we fuse multi-level features (i.e. multiple layers) extracted by backbone as the base feature. Second, we feed the base feature into a block of alternating joint Thinned U-shape Modules and Feature Fusion Modules and exploit the decoder layers of each Ushape module as the features for detecting objects. Finally, we gather up the decoder layers with equivalent scales (sizes) to construct a feature pyramid for object detection, in which every feature map consists of the layers (features) from multiple levels. To evaluate the effectiveness of the proposed MLFPN, we design and train a powerful end-to-end one-stage object detector we call M2Det by integrating it into the architecture of SSD, and achieve better detection performance than state-of-the-art one-stage detectors. Specifically, on MSCOCO benchmark, M2Det achieves AP of 41.0 at speed of 11.8 FPS with single-scale inference strategy and AP of 44.2 with multi-scale inference strategy, which are the new stateof-the-art results among one-stage detectors. The code will be made available on https://github.com/qijiezhao/M2Det.

462 citations


Journal ArticleDOI
TL;DR: Key challenges to understand clock mechanisms and biomarker utility are discussed, including dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models.
Abstract: Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.

457 citations


Journal ArticleDOI
TL;DR: A review of the cell signaling pathways involved in cancer development and proliferation, and which are targeted by curcumin, suggests this polyphenol compound, alone or combined with other agents, could represent an effective drug for cancer therapy.
Abstract: Curcumin, a polyphenol extracted from Curcuma longa in 1815, has gained attention from scientists worldwide for its biological activities (e.g., antioxidant, anti-inflammatory, antimicrobial, antiviral), among which its anticancer potential has been the most described and still remains under investigation. The present review focuses on the cell signaling pathways involved in cancer development and proliferation, and which are targeted by curcumin. Curcumin has been reported to modulate growth factors, enzymes, transcription factors, kinase, inflammatory cytokines, and proapoptotic (by upregulation) and antiapoptotic (by downregulation) proteins. This polyphenol compound, alone or combined with other agents, could represent an effective drug for cancer therapy.

442 citations


Proceedings ArticleDOI
Heng Fan1, Haibin Ling1
15 Jun 2019
TL;DR: C-RPN as discussed by the authors proposes a multi-stage tracking framework, which consists of a sequence of RPNs cascaded from deep high-level to shallow low-level layers in a Siamese network.
Abstract: Recently, the region proposal networks (RPN) have been combined with the Siamese network for tracking, and shown excellent accuracy with high efficiency. Nevertheless, previously proposed one-stage Siamese-RPN trackers degenerate in presence of similar distractors and large scale variation. Addressing these issues, we propose a multi-stage tracking framework, Siamese Cascaded RPN (C-RPN), which consists of a sequence of RPNs cascaded from deep high-level to shallow low-level layers in a Siamese network. Compared to previous solutions, C-RPN has several advantages: (1) Each RPN is trained using the outputs of RPN in the previous stage. Such process stimulates hard negative sampling, resulting in more balanced training samples. Consequently, the RPNs are sequentially more discriminative in distinguishing difficult background (i.e.,, similar distractors). (2) Multi-level features are fully leveraged through a novel feature transfer block (FTB) for each RPN, further improving the discriminability of C-RPN using both high-level semantic and low-level spatial information. (3) With multiple steps of regressions, C-RPN progressively refines the location and shape of the target in each RPN with adjusted anchor boxes in the previous stage, which makes localization more accurate. C-RPN is trained end-to-end with the multi-task loss function. In inference, C-RPN is deployed as it is, without any temporal adaption, for real-time tracking. In extensive experiments on OTB-2013, OTB-2015, VOT-2016, VOT-2017, LaSOT and TrackingNet, C-RPN consistently achieves state-of-the-art results and runs in real-time.

380 citations


Journal ArticleDOI
TL;DR: This study develops and empirically tests a theoretical model of artificially intelligent device use acceptance (AIDUA) that aims to explain customers’ willingness to accept AI device use in service encounters, and provides a conceptual AI device acceptance framework that can be used by other researchers to better investigate AI related topics in the service context.

352 citations


Journal ArticleDOI
TL;DR: A multi-dimensional Service Robot Integration Willingness (SRIW) Scale is conceptualize and test that uncovers the key dimensions characterizing consumers’ long-term willingness to integrate artificial intelligence and service robots into regular service transactions.

328 citations


Journal ArticleDOI
09 Apr 2019-Nature
TL;DR: It is shown that expression of human microRNA-199a in infarcted pig hearts can stimulate cardiac repair and achieving cardiac repair through the stimulation of endogenous cardiomyocyte proliferation is attainable in large mammals, however dosage of this therapy needs to be tightly controlled.
Abstract: Prompt coronary catheterization and revascularization have markedly improved the outcomes of myocardial infarction, but have also resulted in a growing number of surviving patients with permanent structural damage of the heart, which frequently leads to heart failure. There is an unmet clinical need for treatments for this condition1, particularly given the inability of cardiomyocytes to replicate and thereby regenerate the lost contractile tissue2. Here we show that expression of human microRNA-199a in infarcted pig hearts can stimulate cardiac repair. One month after myocardial infarction and delivery of this microRNA through an adeno-associated viral vector, treated animals showed marked improvements in both global and regional contractility, increased muscle mass and reduced scar size. These functional and morphological findings correlated with cardiomyocyte de-differentiation and proliferation. However, subsequent persistent and uncontrolled expression of the microRNA resulted in sudden arrhythmic death of most of the treated pigs. Such events were concurrent with myocardial infiltration of proliferating cells displaying a poorly differentiated myoblastic phenotype. These results show that achieving cardiac repair through the stimulation of endogenous cardiomyocyte proliferation is attainable in large mammals, however dosage of this therapy needs to be tightly controlled.

315 citations


Journal ArticleDOI
TL;DR: Chatbot identity disclosure negatively affects customer purchases because customers perceive the disclosed bot as less knowledgeable and less empathetic.
Abstract: Chatbot identity disclosure negatively affects customer purchases because customers perceive the disclosed bot as less knowledgeable and less empathetic.

Journal ArticleDOI
TL;DR: In this paper, student satisfaction is used as one of the key elements to evaluate online courses, while perceived learning is considered as an indicator of learning, and a study aimed to explore how online learni...
Abstract: Student satisfaction is used as one of the key elements to evaluate online courses, while perceived learning is considered as an indicator of learning. This study aimed to explore how online learni...

Journal ArticleDOI
TL;DR: This paper designs secure building blocks, such as secure polynomial multiplication and secure comparison, by employing a homomorphic cryptosystem, Paillier, and constructs a secure SVM training algorithm, which requires only two interactions in a single iteration, with no need for a trusted third-party.
Abstract: Machine learning (ML) techniques have been widely used in many smart city sectors, where a huge amount of data is gathered from various (IoT) devices. As a typical ML model, support vector machine (SVM) enables efficient data classification and thereby finds its applications in real-world scenarios, such as disease diagnosis and anomaly detection. Training an SVM classifier usually requires a collection of labeled IoT data from multiple entities, raising great concerns about data privacy. Most of the existing solutions rely on an implicit assumption that the training data can be reliably collected from multiple data providers, which is often not the case in reality. To bridge the gap between ideal assumptions and realistic constraints, in this paper, we propose secureSVM , which is a privacy-preserving SVM training scheme over blockchain-based encrypted IoT data. We utilize the blockchain techniques to build a secure and reliable data sharing platform among multiple data providers, where IoT data is encrypted and then recorded on a distributed ledger. We design secure building blocks, such as secure polynomial multiplication and secure comparison, by employing a homomorphic cryptosystem, Paillier, and construct a secure SVM training algorithm, which requires only two interactions in a single iteration, with no need for a trusted third-party. Rigorous security analysis prove that the proposed scheme ensures the confidentiality of the sensitive data for each data provider as well as the SVM model parameters for data analysts. Extensive experiments demonstrates the efficiency of the proposed scheme.

Journal ArticleDOI
TL;DR: The cases and synthesis presented here are organized around four key themes (resource access, governance, culture, and knowledge), which are approach from four social science fields (cultural anthropology, archaeology, human geography, and sociology).
Abstract: The varied effects of recent extreme weather events around the world exemplify the uneven impacts of climate change on populations, even within relatively small geographic regions. Differential human vulnerability to environmental hazards results from a range of social, economic, historical, and political factors, all of which operate at multiple scales. While adaptation to climate change has been the dominant focus of policy and research agendas, it is essential to ask as well why some communities and peoples are disproportionately exposed to and affected by climate threats. The cases and synthesis presented here are organized around four key themes (resource access, governance, culture, and knowledge), which we approach from four social science fields (cultural anthropology, archaeology, human geography, and sociology). Social scientific approaches to human vulnerability draw vital attention to the root causes of climate change threats and the reasons that people are forced to adapt to them. Because vulnerability is a multidimensional process rather than an unchanging state, a dynamic social approach to vulnerability is most likely to improve mitigation and adaptation planning efforts. This article is categorized under:Vulnerability and Adaptation to Climate Change > Values-Based Approach to Vulnerability and Adaptation.

Journal ArticleDOI
TL;DR: A neural network that has two branches for attention box prediction (ABP) and aesthetics assessment (AA) that produces high-quality cropping results, even with the limited availability of training data for photo cropping.
Abstract: We study the problem of photo cropping, which aims to find a cropping window of an input image to preserve as much as possible its important parts while being aesthetically pleasant. Seeking a deep learning-based solution, we design a neural network that has two branches for attention box prediction (ABP) and aesthetics assessment (AA), respectively. Given the input image, the ABP network predicts an attention bounding box as an initial minimum cropping window, around which a set of cropping candidates are generated with little loss of important information. Then, the AA network is employed to select the final cropping window with the best aesthetic quality among the candidates. The two sub-networks are designed to share the same full-image convolutional feature map, and thus are computationally efficient. By leveraging attention prediction and aesthetics assessment, the cropping model produces high-quality cropping results, even with the limited availability of training data for photo cropping. The experimental results on benchmark datasets clearly validate the effectiveness of the proposed approach. In addition, our approach runs at 5 fps, outperforming most previous solutions. The code and results are available at: https://github.com/shenjianbing/DeepCropping.

Journal ArticleDOI
12 Feb 2019-JAMA
TL;DR: It is concluded with moderate certainty that providing or referring pregnant or postpartum women at increased risk to counseling interventions has a moderate net benefit in preventing perinatal depression.
Abstract: Importance Perinatal depression, which is the occurrence of a depressive disorder during pregnancy or following childbirth, affects as many as 1 in 7 women and is one of the most common complications of pregnancy and the postpartum period. It is well established that perinatal depression can result in adverse short- and long-term effects on both the woman and child. Objective To issue a new US Preventive Services Task Force (USPSTF) recommendation on interventions to prevent perinatal depression. Evidence Review The USPSTF reviewed the evidence on the benefits and harms of preventive interventions for perinatal depression in pregnant or postpartum women or their children. The USPSTF reviewed contextual information on the accuracy of tools used to identify women at increased risk of perinatal depression and the most effective timing for preventive interventions. Interventions reviewed included counseling, health system interventions, physical activity, education, supportive interventions, and other behavioral interventions, such as infant sleep training and expressive writing. Pharmacological approaches included the use of nortriptyline, sertraline, and omega-3 fatty acids. Findings The USPSTF found convincing evidence that counseling interventions, such as cognitive behavioral therapy and interpersonal therapy, are effective in preventing perinatal depression. Women with a history of depression, current depressive symptoms, or certain socioeconomic risk factors (eg, low income or young or single parenthood) would benefit from counseling interventions and could be considered at increased risk. The USPSTF found adequate evidence to bound the potential harms of counseling interventions as no greater than small, based on the nature of the intervention and the low likelihood of serious harms. The USPSTF found inadequate evidence to assess the benefits and harms of other noncounseling interventions. The USPSTF concludes with moderate certainty that providing or referring pregnant or postpartum women at increased risk to counseling interventions has a moderate net benefit in preventing perinatal depression. Conclusions and Recommendation The USPSTF recommends that clinicians provide or refer pregnant and postpartum persons who are at increased risk of perinatal depression to counseling interventions. (B recommendation)

Posted Content
Fan Yang1, Lei Zhang1, Sijia Yu1, Danil V. Prokhorov2, Xue Mei2, Haibin Ling1 
TL;DR: A novel network architecture, named feature pyramid and hierarchical boosting network (FPHBN), is proposed, Inspired by recent advances of deep learning in computer vision, for pavement crack detection that outperforms the state-of-the-art crack detection, edge detection, and semantic segmentation methods.
Abstract: Pavement crack detection is a critical task for insuring road safety. Manual crack detection is extremely time-consuming. Therefore, an automatic road crack detection method is required to boost this progress. However, it remains a challenging task due to the intensity inhomogeneity of cracks and complexity of the background, e.g., the low contrast with surrounding pavements and possible shadows with similar intensity. Inspired by recent advances of deep learning in computer vision, we propose a novel network architecture, named Feature Pyramid and Hierarchical Boosting Network (FPHBN), for pavement crack detection. The proposed network integrates semantic information to low-level features for crack detection in a feature pyramid way. And, it balances the contribution of both easy and hard samples to loss by nested sample reweighting in a hierarchical way. To demonstrate the superiority and generality of the proposed method, we evaluate the proposed method on five crack datasets and compare it with state-of-the-art crack detection, edge detection, semantic segmentation methods. Extensive experiments show that the proposed method outperforms these state-of-the-art methods in terms of accuracy and generality.

Journal ArticleDOI
TL;DR: It is shown that AAV-mediated delivery of the circRNA circFndc3b prevents cardiomyocyte apoptosis, enhances angiogenesis, and attenuates LV dysfunction post-MI in mice by regulating FUS-VEGF-A signalling.
Abstract: Circular RNAs are generated from many protein-coding genes, but their role in cardiovascular health and disease states remains unknown. Here we report identification of circRNA transcripts that are differentially expressed in post myocardial infarction (MI) mouse hearts including circFndc3b which is significantly down-regulated in the post-MI hearts. Notably, the human circFndc3b ortholog is also significantly down-regulated in cardiac tissues of ischemic cardiomyopathy patients. Overexpression of circFndc3b in cardiac endothelial cells increases vascular endothelial growth factor-A expression and enhances their angiogenic activity and reduces cardiomyocytes and endothelial cell apoptosis. Adeno-associated virus 9 -mediated cardiac overexpression of circFndc3b in post-MI hearts reduces cardiomyocyte apoptosis, enhances neovascularization and improves left ventricular functions. Mechanistically, circFndc3b interacts with the RNA binding protein Fused in Sarcoma to regulate VEGF expression and signaling. These findings highlight a physiological role for circRNAs in cardiac repair and indicate that modulation of circFndc3b expression may represent a potential strategy to promote cardiac function and remodeling after MI.

Journal ArticleDOI
20 Aug 2019-JAMA
TL;DR: It is recommended that primary care clinicians assess women with a personal or family history of breast, ovarian, tubal, or peritoneal cancer or who have an ancestry associated with BRCA1/2 gene mutations with an appropriate brief familial risk assessment tool.
Abstract: Importance Potentially harmful mutations of the breast cancer susceptibility 1 and 2 genes (BRCA1/2) are associated with increased risk for breast, ovarian, fallopian tube, and peritoneal cancer. For women in the United States, breast cancer is the most common cancer after nonmelanoma skin cancer and the second leading cause of cancer death. In the general population,BRCA1/2mutations occur in an estimated 1 in 300 to 500 women and account for 5% to 10% of breast cancer cases and 15% of ovarian cancer cases. Objective To update the 2013 US Preventive Services Task Force (USPSTF) recommendation on risk assessment, genetic counseling, and genetic testing forBRCA-related cancer. Evidence Review The USPSTF reviewed the evidence on risk assessment, genetic counseling, and genetic testing for potentially harmfulBRCA1/2mutations in asymptomatic women who have never been diagnosed withBRCA-related cancer, as well as those with a previous diagnosis of breast, ovarian, tubal, or peritoneal cancer who have completed treatment and are considered cancer free. In addition, the USPSTF reviewed interventions to reduce the risk for breast, ovarian, tubal, or peritoneal cancer in women with potentially harmfulBRCA1/2mutations, including intensive cancer screening, medications, and risk-reducing surgery. Findings For women whose family or personal history is associated with an increased risk for harmful mutations in theBRCA1/2genes, or who have an ancestry associated withBRCA1/2gene mutations, there is adequate evidence that the benefits of risk assessment, genetic counseling, genetic testing, and interventions are moderate. For women whose personal or family history or ancestry is not associated with an increased risk for harmful mutations in theBRCA1/2genes, there is adequate evidence that the benefits of risk assessment, genetic counseling, genetic testing, and interventions are small to none. Regardless of family or personal history, the USPSTF found adequate evidence that the overall harms of risk assessment, genetic counseling, genetic testing, and interventions are small to moderate. Conclusions and Recommendation The USPSTF recommends that primary care clinicians assess women with a personal or family history of breast, ovarian, tubal, or peritoneal cancer or who have an ancestry associated withBRCA1/2gene mutations with an appropriate brief familial risk assessment tool. Women with a positive result on the risk assessment tool should receive genetic counseling and, if indicated after counseling, genetic testing. (B recommendation) The USPSTF recommends against routine risk assessment, genetic counseling, or genetic testing for women whose personal or family history or ancestry is not associated with potentially harmfulBRCA1/2gene mutations. (D recommendation)

Journal ArticleDOI
TL;DR: Although further studies are needed to elucidate detailed mechanisms and the functional roles in liver diseases, DR can be a therapeutic target to inhibit liver fibrosis and to promote liver regeneration.

Journal ArticleDOI
TL;DR: A novel paradigm in which specific strains of a gut commensal may contribute to the immune pathogenesis of lupus nephritis is suggested.
Abstract: Background/Purpose To search for a transmissible agent involved in lupus pathogenesis, we investigated the faecal microbiota of patients with systemic lupus erythematosus (SLE) for candidate pathobiont(s) and evaluated them for special relationships with host immunity. Methods In a cross-sectional discovery cohort, matched blood and faecal samples from 61 female patients with SLE were obtained. Faecal 16 S rRNA analyses were performed, and sera profiled for antibacterial and autoantibody responses, with findings validated in two independent lupus cohorts. Results Compared with controls, the microbiome in patients with SLE showed decreased species richness diversity, with reductions in taxonomic complexity most pronounced in those with high SLE disease activity index (SLEDAI). Notably, patients with SLE had an overall 5-fold greater representation of Ruminococcus gnavus (RG) of the Lachnospiraceae family, and individual communities also displayed reciprocal contractions of a species with putative protective properties. Gut RG abundance correlated with serum antibodies to only 1/8 RG strains tested. Anti-RG antibodies correlated directly with SLEDAI score and antinative DNA levels, but inversely with C3 and C4. These antibodies were primarily against antigen(s) in an RG strain-restricted pool of cell wall lipoglycans. Novel structural features of these purified lipoglycans were characterised by mass spectrometry and NMR. Highest levels of serum anti-RG strain-restricted antibodies were detected in those with active nephritis (including Class III and IV) in the discovery cohort, with findings validated in two independent cohorts. Conclusion These findings suggest a novel paradigm in which specific strains of a gut commensal may contribute to the immune pathogenesis of lupus nephritis.

Journal ArticleDOI
Naihui Zhou1, Yuxiang Jiang2, Timothy Bergquist3, Alexandra J. Lee4  +185 moreInstitutions (71)
TL;DR: The third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed, concluded that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not.
Abstract: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.

Proceedings ArticleDOI
15 Jun 2019
TL;DR: This paper quantitatively verified the high consistency of visual attention behavior among human observers, and found strong correlation between human attention and explicit primary object judgements during dynamic, task-driven viewing.
Abstract: This paper conducts a systematic study on the role of visual attention in Unsupervised Video Object Segmentation (UVOS) tasks. By elaborately annotating three popular video segmentation datasets (DAVIS, Youtube-Objects and SegTrack V2) with dynamic eye-tracking data in the UVOS setting, for the first time, we quantitatively verified the high consistency of visual attention behavior among human observers, and found strong correlation between human attention and explicit primary object judgements during dynamic, task-driven viewing. Such novel observations provide an in-depth insight into the underlying rationale behind UVOS. Inspired by these findings, we decouple UVOS into two sub-tasks: UVOS-driven Dynamic Visual Attention Prediction (DVAP) in spatiotemporal domain, and Attention-Guided Object Segmentation (AGOS) in spatial domain. Our UVOS solution enjoys three major merits: 1) modular training without using expensive video segmentation annotations, instead, using more affordable dynamic fixation data to train the initial video attention module and using existing fixation-segmentation paired static/image data to train the subsequent segmentation module; 2) comprehensive foreground understanding through multi-source learning; and 3) additional interpretability from the biologically-inspired and assessable attention. Experiments on popular benchmarks show that, even without using expensive video object mask annotations, our model achieves compelling performance in comparison with state-of-the-arts.

Proceedings ArticleDOI
01 Sep 2019
TL;DR: This paper presents LEDNet, which employs an asymmetric encoder-decoder architecture for the task of real-time semantic segmentation, which adopts a ResNet as backbone network to greatly reduce computation cost while maintaining higher segmentation accuracy.
Abstract: The extensive computational burden limits the usage of CNNs in mobile devices for dense estimation tasks. In this paper, we present a lightweight network to address this problem, namely LEDNet, which employs an asymmetric encoder-decoder architecture for the task of real-time semantic segmentation. More specifically, the encoder adopts a ResNet as backbone network, where two new operations, channel split and shuffle, are utilized in each residual block to greatly reduce computation cost while maintaining higher segmentation accuracy. On the other hand, an attention pyramid network (APN) is employed in the decoder to further lighten the entire network complexity. Our model has less than 1M parameters, and is able to run at over 71 FPS in a single GTX 1080Ti GPU. The comprehensive experiments demonstrate that our approach achieves state-of-the-art results in terms of speed and accuracy trade-off on CityScapes dataset.

Journal ArticleDOI
11 Jun 2019-JAMA
TL;DR: The USPSTF concludes with high certainty that the magnitude of benefit of PrEP with oral tenofovir disoproxil fumarate-based therapy to reduce the risk of acquisition of HIV infection in persons at high risk is substantial.
Abstract: Importance An estimated 1.1 million individuals in the United States are currently living with HIV, and more than 700 000 persons have died of AIDS since the first cases were reported in 1981. In 2017, there were 38 281 new diagnoses of HIV infection reported in the United States; 81% of these new diagnoses were among males and 19% were among females. Although treatable, HIV infection has no cure and has significant health consequences. Objective To issue a new US Preventive Services Task Force (USPSTF) recommendation on preexposure prophylaxis (PrEP) for the prevention of HIV infection. Evidence Review The USPSTF reviewed the evidence on the benefits of PrEP for the prevention of HIV infection with oral tenofovir disoproxil fumarate monotherapy or combined tenofovir disoproxil fumarate and emtricitabine and whether the benefits vary by risk group, population subgroup, or regimen or dosing strategy; the diagnostic accuracy of risk assessment tools to identify persons at high risk of HIV acquisition; the rates of adherence to PrEP in primary care settings; the association between adherence and effectiveness of PrEP; and the harms of PrEP when used for HIV prevention. Findings The USPSTF found convincing evidence that PrEP is of substantial benefit in decreasing the risk of HIV infection in persons at high risk of HIV acquisition. The USPSTF also found convincing evidence that adherence to PrEP is highly associated with its efficacy in preventing the acquisition of HIV infection; thus, adherence to PrEP is central to realizing its benefit. The USPSTF found adequate evidence that PrEP is associated with small harms, including kidney and gastrointestinal adverse effects. The USPSTF concludes with high certainty that the magnitude of benefit of PrEP with oral tenofovir disoproxil fumarate–based therapy to reduce the risk of acquisition of HIV infection in persons at high risk is substantial. Conclusions and Recommendation The USPSTF recommends offering PrEP with effective antiretroviral therapy to persons at high risk of HIV acquisition. (A recommendation)

Journal ArticleDOI
TL;DR: It is believed that CNS delivery of NF (CRISPR/Cas9-gRNA-MENPs) across the BBB certainly will have clinical utility as future personalized nanomedicine to manage neuroHIV/AIDS.
Abstract: CRISPR-Cas9/gRNA exhibits therapeutic efficacy against latent human immunodeficiency virus (HIV) genome but the delivery of this therapeutic cargo to the brain remains as a challenge. In this research, for the first time, we demonstrated magnetically guided non-invasive delivery of a nano-formulation (NF), composed of Cas9/gRNA bound with magneto-electric nanoparticles (MENPs), across the blood-brain barrier (BBB) to inhibit latent HIV-1 infection in microglial (hμglia)/HIV (HC69) cells. An optimized ac-magnetic field of 60 Oe was applied on NF to release Cas9/gRNA from MENPs surface and to facilitate NF cell uptake resulting in intracellular release and inhibition of HIV. The outcomes suggested that developed NF reduced HIV-LTR expression significantly in comparison to unbound Cas9/gRNA in HIV latent hμglia/HIV (HC69) cells. These findings were also validated qualitatively using fluorescence microscopy to assess NF efficacy against latent HIV in the microglia cells. We believe that CNS delivery of NF (CRISPR/Cas9-gRNA-MENPs) across the BBB certainly will have clinical utility as future personalized nanomedicine to manage neuroHIV/AIDS.

Journal ArticleDOI
06 Aug 2019-JAMA
TL;DR: The USPSTF reaffirms its previous conclusion that the potential benefits of screening for pancreatic cancer in asymptomatic adults do not outweigh the potential harms.
Abstract: Importance Pancreatic cancer is an uncommon cancer with an age-adjusted annual incidence of 12.9 cases per 100 000 person-years. However, the death rate is 11.0 deaths per 100 000 person-years because the prognosis of pancreatic cancer is poor. Although its incidence is low, pancreatic cancer is the third most common cause of cancer death in the United States. Because of the increasing incidence of pancreatic cancer, along with improvements in early detection and treatment of other types of cancer, it is estimated that pancreatic cancer may soon become the second-leading cause of cancer death in the United States. Objective To update the 2004 US Preventive Services Task Force (USPSTF) recommendation on screening for pancreatic cancer. Evidence Review The USPSTF reviewed the evidence on the benefits and harms of screening for pancreatic cancer, the diagnostic accuracy of screening tests for pancreatic cancer, and the benefits and harms of treatment of screen-detected or asymptomatic pancreatic cancer. Findings The USPSTF found no evidence that screening for pancreatic cancer or treatment of screen-detected pancreatic cancer improves disease-specific morbidity or mortality, or all-cause mortality. The USPSTF found adequate evidence that the magnitude of the benefits of screening for pancreatic cancer in asymptomatic adults can be bounded as no greater than small. The USPSTF found adequate evidence that the magnitude of the harms of screening for pancreatic cancer and treatment of screen-detected pancreatic cancer can be bounded as at least moderate. The USPSTF reaffirms its previous conclusion that the potential benefits of screening for pancreatic cancer in asymptomatic adults do not outweigh the potential harms. Conclusions and Recommendation The USPSTF recommends against screening for pancreatic cancer in asymptomatic adults. (D recommendation)

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TL;DR: This proof-of-concept study suggests that HIV-1 elimination is possible, and shows that sequential treatment with long-acting slow-effective release antiviral therapy and AAV9- based delivery of CRISPR-Cas9 results in undetectable levels of virus and integrated DNA in a subset of humanized HIV- 1 infected mice.
Abstract: Elimination of HIV-1 requires clearance and removal of integrated proviral DNA from infected cells and tissues. Here, sequential long-acting slow-effective release antiviral therapy (LASER ART) and CRISPR-Cas9 demonstrate viral clearance in latent infectious reservoirs in HIV-1 infected humanized mice. HIV-1 subgenomic DNA fragments, spanning the long terminal repeats and the Gag gene, are excised in vivo, resulting in elimination of integrated proviral DNA; virus is not detected in blood, lymphoid tissue, bone marrow and brain by nested and digital-droplet PCR as well as RNAscope tests. No CRISPR-Cas9 mediated off-target effects are detected. Adoptive transfer of human immunocytes from dual treated, virus-free animals to uninfected humanized mice fails to produce infectious progeny virus. In contrast, HIV-1 is readily detected following sole LASER ART or CRISPR-Cas9 treatment. These data provide proof-of-concept that permanent viral elimination is possible.

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TL;DR: In this paper, the authors focus on a pervasive trend among Millennial consumers: the experience of benign envy toward others' positive travel experience sharing on social networking sites, and reveal why and under what conditions others positive experience sharing may trigger Millennials' destination visit intention.
Abstract: The sharing of travel experiences has become ubiquitous in today’s era. This study focuses on a pervasive trend among Millennial consumers: the experience of benign envy toward others’ positive travel experience sharing on social networking sites. Drawing on social comparison theory, the current study reveals why and under what conditions others’ positive experience sharing may trigger Millennial consumers’ destination visit intention. Using a mixed experimental design, this study finds that, among consumers with low trait self-esteem, luxury travel experiences shared by similar others stimulate focal consumers’ own intentions to visit the same destination. In addition, destination visit intention is triggered by benign envy toward the experience sharer. Important theoretical insights are provided regarding peer influence mechanism on social networking sites and travel consumption. Finally, managerial implications for destination marketers are presented with a focus on how to improve the effectiveness of social media marketing in targeting Millennials.

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TL;DR: Scholars in urban political ecology, urban geography, and planning have suggested that urban greening interventions can create elite enclaves of environmental privilege and green gentrification, an idea that has been explored in this article.
Abstract: Scholars in urban political ecology, urban geography, and planning have suggested that urban greening interventions can create elite enclaves of environmental privilege and green gentrification, an...