Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)

Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.
The Privacy Policy Landscape After the GDPR

Abstract The EU General Data Protection Regulation (GDPR) is one of the most demanding and comprehensive privacy regulations of all time. A year after it went into effect, we study its impact on the landscape of privacy policies online. We conduct the first longitudinal, in-depth, and at-scale assessment of privacy policies before and after the GDPR. We gauge the complete consumption cycle of these policies, from the first user impressions until the compliance assessment. We create a diverse corpus of two sets of 6,278 unique English-language privacy policies from inside and outside the EU, covering their pre-GDPR and the post-GDPR versions. The results of our tests and analyses suggest that the GDPR has been a catalyst for a major overhaul of the privacy policies inside and outside the EU. This overhaul of the policies, manifesting in extensive textual changes, especially for the EU-based websites, comes at mixed benefits to the users. While the privacy policies have become considerably longer, our user study with 470 participants on Amazon MTurk indicates a significant improvement in the visual representation of privacy policies from the users’ perspective for the EU websites. We further develop a new workflow for the automated assessment of requirements in privacy policies. Using this workflow, we show that privacy policies cover more data practices and are more consistent with seven compliance requirements post the GDPR. We also assess how transparent the organizations are with their privacy practices by performing specificity analysis. In this analysis, we find evidence for positive changes triggered by the GDPR, with the specificity level improving on average. Still, we find the landscape of privacy policies to be in a transitional phase; many policies still do not meet several key GDPR requirements or their improved coverage comes with reduced specificity.
Collaborative symptoms interpretation for cardiac patients as diagnostic agents

Home monitoring of cardiac patients with an implantable cardioverter-defibrillator (ICD) holds promising benefits such as improved mortality rates, but HCI research shows that patients dislike the passive role imposed by current home monitoring technology. In this paper, we report from a study on how cardiac patients reacted to taking on a more active role of being a diagnostic agent. We developed and implemented a technology probe for reporting symptoms and other health metrics to health providers daily and studied ten ICD patients interacting with the probe for eight weeks. Our analysis resulted in three themes; patient reflection and obsession, patient roles and responsibility towards healthcare staff, and opportunities for nurses to use reports at the hospital. We contribute to HCI research on home monitoring by discussing the role of the diagnostic agent and the potential for implanted chronic patients to engage in collaborative interpretation with health providers.
The role of gene sculptor microRNAs in human precancerous lesions

MicroRNAs (miRNAs) are small noncoding RNAs. These noncoding RNAs regulate the expression of target genes and inhibit the translation of target proteins at the post-transcriptional level. miRNAs also play an important role in human health, from the development and differentiation of cells to the occurrence and progression of disorders such as cancer, cardiovascular diseases, and neurodegenerative diseases. Precancerous lesions are lesions prior to invasive carcinomas, and carcinogenesis is a very complicated process, which is multistage and the result of multigene synergy. miRNAs exert effects as both oncogenes and tumor suppressor genes by regulating target genes involved in signaling pathways. Hence, precancerous lesions are accompanied by relevant miRNA changes. Based on the morphology of miRNAs in vivo and the specificity of miRNA, various novel miRNA analysis methods have been developed, including reverse transcription quantitative PCR, enzyme analysis, molecular beacons, and deep sequencing. For example, in the laryngeal epithelial precancerous lesions, the data demonstrate that the expression of miR-10a-5p is downregulated and miR-484 is the most abundant miRNA in hepatic precancerous lesions. In this review, we discuss the functional roles of miRNAs in human precancerous lesions.
Comparison of stroke- and bleed-related healthcare resource utilization and costs among patients with newly diagnosed non-valvular atrial fibrillation and newly treated with dabigatran, rivaroxaban, or warfarin

ABSTRACT Background: This is one of the first head-to-head real-world evidence studies comparing stroke-related and bleed-related healthcare and resource utilization (HCRU) and costs among non-valvular atrial fibrillation (NVAF) patients initiating oral anticoagulants. Methods: Adult NVAF patients newly diagnosed and treated with dabigatran, rivaroxaban, or warfarin between 10/01/2010 and 12/31/2014 were identified using MarketScan Commercial and Medicare Supplemental databases. Per-patient-per-month stroke and bleed-related HCRU and costs were reported. Results: Dabigatran patients were matched 1:1 to 26,592 rivaroxaban and 33,024 warfarin patients (mean age=68 years). Compared to rivaroxaban, dabigatran patients had lower bleed-related inpatient and outpatient HCRU (0.004 vs. 0.005; 0.099 vs. 0.145) and significantly lower adjusted bleed-related costs ($116 vs. $172), all p <0.05. Compared to warfarin, dabigatran patients had significantly lower stroke-related outpatient visits (0.034 vs. 0.048, p<0.001) and higher bleed-related outpatient visits (0.101 vs. 0.091, p=0.045). Multivariate adjusted bleed-related costs were significantly lower for dabigatran patients than warfarin patients ($94 vs. $138, p<0.001). Conclusions: The results suggest that dabigatran patients had lower bleed-related HCRU and costs than rivaroxaban patients, and lower outpatient stroke-related HCRU, higher bleed-related outpatient HCRU, and lower bleed-related costs than warfarin patients. It provides valuable stroke-related and bleed-related HCRU and costs information among commercially insured and Medicare patients.
The Impact of Uremic Toxicity Induced Inflammatory Response on the Cardiovascular Burden in Chronic Kidney Disease

Uremic toxin (UT) retention in chronic kidney disease (CKD) affects biological systems. We aimed to identify the associations between UT, inflammatory biomarkers and biomarkers of the uremic cardiovascular response (BUCVR) and their impact on cardiovascular status as well as their roles as predictors of outcome in CKD patients. CKD patients stages 3, 4 and 5 (n = 67) were recruited and UT (indoxyl sulfate/IS, p-cresil sulfate/pCS and indole-3-acetic acid/IAA); inflammatory biomarkers [Interleukin-6 (IL-6), high sensitivity C reactive protein (hsCRP), monocyte chemoattractant protein-1 (MCP-1), soluble vascular adhesion molecule-1 (sVCAM-1), soluble intercellular adhesion molecule-1 (sICAM-1) and soluble Fas (sFas)] and BUCVRs [soluble CD36 (sCD36), soluble receptor for advanced glycation end products (sRAGE), fractalkine] was measured. Patients were followed for 5.2 years and all causes of death was used as the primary outcome. Artery segments collected at the moment of transplantation were used for the immunohistochemistry analysis in a separate cohort. Estimated glomerular filtration rate (eGFR), circulating UT, plasma biomarkers of systemic and vascular inflammation and BUCVR were strongly interrelated. Patients with plaque presented higher signs of UT-induced inflammation and arteries from CKD patients presented higher fractalkine receptor (CX3CR1) tissue expression. Circulating IS (p = 0.03), pCS (p = 0.007), IL-6 (p = 0.026), sFas (p = 0.001), sCD36 (p = 0.01) and fractalkine (p = 0.02) were independent predictors of total mortality risk in CKD patients. Our results reinforce the important role of uremic toxicity in the pathogenesis of cardiovascular disease (CVD) in CKD patients through an inflammatory pathway.
Nonlinear Moment-Tensor Inversion of Repetitive Long-Periods Events Recorded at Pacaya Volcano, Guatemala

Detailed models of low-frequency seismicity at volcanoes provide insights into conduit structure and dynamics of magmatic systems. We examine explosion-related long-period (LP) events from Pacaya volcano, Guatemala, that were recorded during a temporary installation of four broadband seismic stations from October 2013 to November 2013. The repetitive LP events are identified with the aid of infrasound measurements using a matched filter due to the high level of background tremor and the small magnitude of the recorded events. We derive a representative seismic signal from the phase-weighted stack of 8,587 of these similar events, and invert for a source moment tensor. To address the limitations posed by the limited number of stations of the local network, we employ a non-linear waveform inversion that uses a grid search for source type to obtain a quantitative measure of the source mechanism reliability. With only four stations, Pacaya represents a case of limited observational data, where a quantitative description of moment tensor uncertainty is needed before any interpretation is to be attempted. Results point to a shallow source mechanism somewhat like a tension crack, dipping ~ 40° to the east, consistent with the dominant E-W motion in the seismic records from stations west, north, and east of the source. The uncertainties determined from the non-linear inversion are not insignificant, but clearly constrain the mechanism to be a source dominated by isotropic components
Comparison of Antioxidant Activities of Different Grape Varieties

Grapes are widely consumed in the world, and different grape varieties could exhibit distinctly different antioxidant activities. In this study, the free radical-scavenging and antioxidant activities of lipophilic, hydrophilic, and insoluble-bound fractions from 30 grape varieties were evaluated by ferric-reducing antioxidant powers (FRAP), Trolox equivalent antioxidant capacities (TEAC), total phenolic contents (TPC), and total flavonoid contents (TFC). The results indicated that the 30 grape varieties exhibited diverse FRAP values (1.289–11.767 μmol Fe(II)/g FW), TEAC values (0.339–4.839 μmol Trolox/g FW), TPC values (0.294–1.407 mg GAE/g FW) and TFC values (0.082–0.132 mg QE/g FW). Several grapes, such as Pearl Black Grape (Xinjiang), Summer Black Grape (Shaanxi), Pearl Green Grape (Xinjiang), Seedless Green Grape (Xinjiang), and Seedless Red Grape (Yunnan), exhibited strong free radical-scavenging and antioxidant activities, which could be consumed as good sources of natural antioxidants to prevent several diseases induced by oxidative stress, such as cardiovascular disease and cancer. Furthermore, several antioxidants were identified and quantified, including caffeic acid, catechin gallate, epicatechin, gallic acid, protocatechuic acid and rutin, which could contribute to the antioxidant activities of grapes.
Social Well-Being in Adolescent and Young Adult Cancer Survivors.

PURPOSE Adolescents and young adults (AYAs) diagnosed with cancer between ages 15-39 years are a unique and vulnerable population, encountering many typical developmental challenges while also dealing with the demands of illness and its aftermath. Overwhelming evidence demonstrates the importance of social well-being in survivorship quality of life. For AYAs, social connections may be of heightened importance as they assert independence from their parents and create their own personal lives. Few studies have characterized AYA survivors' social well-being and its determinants over time, particularly how psychological adjustment might promote improved social well-being. METHODS We assessed 83 AYA survivors at two time points across 1 year to characterize their social well-being, identify common social connection concerns, describe how social well-being changes over time, examine how psychological adjustment relates to social well-being at a given time point, and determine whether psychological adjustment predicts changes in social well-being over time. RESULTS Our sample rated their quality of life as lower than population mean scores, and despite relatively high levels of social support and satisfaction, more than half of participants also reported concerns in specific social well-being domains. On average, social well-being increased across the year. Psychological adjustment was strongly positively related to various aspects of social well-being, and it predicted improved social well-being over time. CONCLUSION These results suggest that improving psychological adjustment may be important for strengthening social support networks and improving AYAs' lives in survivorship.
Publishing musicology using multimedia digital libraries: creating interactive articles through a framework for linked data and MEI

Modern web publishing enables sophisticated presentation of academic arguments, deploying evidence in different formats, using multiple media types, and through interactive user experiences. However, these developments have had little significant effect on the communication of musicology, which largely continues to be published in static and linear forms, and rarely with user interfaces that connect the different forms of supporting material. Our Music Encoding and Linked Data (MELD) framework uses RDF to associate music-related materials via structures afforded by the Music Encoding Initiative (MEI). Here we describe the use of MELD for publishing multimedia musicology articles as web applications in which musically-meaningful relationships are mapped to the interactions a user experiences when moving between digital resources such as text, audio, video, and notation. We motivate our work with an enhanced interactive article studying the performance of works by Frederick Delius, and demonstrate our framework's suitability for this situation by implementing a MELD application integrating TEI text, IIIF-served images, MEI notation and recordings of audio and video. We describe the semantic annotations which underpin this realisation, and how they relate the user experience of moving between this content to the musicological argument being marshalled. Through this example we illustrate how connecting diverse media types using musically-meaningful semantics can support a richer form of publication, beyond the current state of the art.
Feature extraction of ECG signal

Abstract This paper deals with new approaches to analyse electrocardiogram (ECG) signals for extracting useful diagnostic features. Initially, elimination of different types of noise is carried out using maximal overlap discrete wavelet transform (MODWT) and universal thresholding. Next, R-peak fiducial points are detected from these noise free ECG signals using discrete wavelet transform along with thresholding. Then, extraction of other features, viz., Q waves, S waves, P waves, T waves, P wave onset and offset points, T wave onset and offset points, QRS onset and offset points are identified using some rule based algorithms. Eventually, other important features are computed using the above extracted features. The software developed for this purpose has been validated by extensive testing of ECG signals acquired from the MIT-BIH database. The resulting signals and tabular results illustrate the performance of the proposed method. The sensitivity, predictivity and error of beat detection are 99.98%, 99.97% and 0.05%, respectively. The performance of the proposed beat detection method is compared to other existing techniques, which shows that the proposed method is superior to other methods.
IEKF based object pose estimation for Augmented Reality

In this paper, we propose a novel model-free IEKF based object pose estimation approach for Augmented Reality (AR) applications. In contrast to other IEKF methods which set pose as system states, we set both object 6DoF pose and structure as states. We explore state perturbation scheme and develop the IEKF implementation on SE(3). The experiments validate that our method is able to estimate different objects under different complicated trajectories accurately and effectively. The comparison with state-of-art model-based method indicates that our model-free method performs comparably with model-based method which can be used for AR applications.
Some correlates of cranial and cervical morphology with predatory modes in snakes

Dissection of the cervical and basicranial regions in three species of snakes indicates that compared to Crotalus viridis and Lichanura roseofusca, Masticophis flagellum possesses relatively high numbers of compound axial muscle insertions on the atlas‐axis and vertebrae numbers 3‐5. It is suggested that the condition in Masticophis facilitates its vertical‐neck‐horizontal‐head foraging posture and has allowed axial muscles inserting on the dorsocaudal braincase in this snake to generate vertical and lateral head movements more effectively.
Deformable Stacked Structure for Named Entity Recognition

Neural architecture for named entity recognition has achieved great success in the field of natural language processing. Currently, the dominating architecture consists of a bi-directional recurrent neural network (RNN) as the encoder and a conditional random field (CRF) as the decoder. In this paper, we propose a deformable stacked structure for named entity recognition, in which the connections between two adjacent layers are dynamically established. We evaluate the deformable stacked structure by adapting it to different layers. Our model achieves the state-of-the-art performances on the OntoNotes dataset.
A Novel Data-Driven Boolean Model for Genetic Regulatory Networks

A Boolean model is a simple, discrete and dynamic model without the need to consider the effects at the intermediate levels. However, little effort has been made into constructing activation, inhibition, and protein decay networks, which could indicate the direct roles of a gene (or its synthesized protein) as an activator or inhibitor of a target gene. Therefore, we propose to focus on the general Boolean functions at the subfunction level taking into account the effectiveness of protein decay, and further split the subfunctions into the activation and inhibition domains. As a consequence, we developed a novel data-driven Boolean model; namely, the Fundamental Boolean Model (FBM), to draw insights into gene activation, inhibition, and protein decay. This novel Boolean model provides an intuitive definition of activation and inhibition pathways and includes mechanisms to handle protein decay issues. To prove the concept of the novel model, we implemented a platform using R language, called FBNNet. Our experimental results show that the proposed FBM could explicitly display the internal connections of the mammalian cell cycle between genes separated into the connection types of activation, inhibition and protein decay. Moreover, the method we proposed to infer the gene regulatory networks for the novel Boolean model can be run in parallel and; hence, the computation cost is affordable. Finally, the novel Boolean model and related Fundamental Boolean Networks (FBNs) could show significant trajectories in genes to reveal how genes regulated each other over a given period. This new feature could facilitate further research on drug interventions to detect the side effects of a newly-proposed drug.
Adolescent Alcohol Use: The Effects of Parental Knowledge, Peer Substance Use, and Peer Tolerance of Use

Objective: Parents and peers exert significant influence on a young person’s decision to consume alcohol. This study examines the relationship between parental monitoring and adolescent alcohol consumption and tests whether peer substance use and tolerance of use mediates the relationship between monitoring and drinking. Method: Participants included 116 adolescents (53.5% female; Mage = 15.6). All participants reported drinking alcohol in the past 6 months, and 96 participants had been previously admitted to a hospital emergency department for an alcohol-related event. Mediation analyses were used to test the study hypotheses. Results: The total effect of baseline parental monitoring on 6-month alcohol use was −1.15 (p < .01), with higher monitoring related to less use. Controlling for peer use and tolerance of use, the effect of parental monitoring was reduced to . 46, leaving an indirect effect of . 69 (p < .01). Peer use and tolerance of use had no effect on participant alcohol use when controlling for parental monitoring. Conclusions: Study findings extend current knowledge about the interactive effects of parental supervision and peer influence on the drinking patterns of adolescents. Results underscore the importance of addressing both parental monitoring and peer influence in interventions that target adolescent alcohol use, recognizing peer factors as a potential mechanism of the effect that parental monitoring has on adolescent drinking.