Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation between Venereal Diseases Research Laboratory titers and CD4 T-lymphocyte count determined by flow cytometry in HIV-infected adults: A 5-year study

Introduction: Venereal Diseases Research Laboratory (VDRL) is one of the key tests for the diagnosis of syphilis; however in HIV-positive individuals, it has been reported to give inappropriate results at times. Thus, this study was conducted to determine if the VDRL test titers vary with the severity of immunosuppression as determined by CD4 cell count. Materials and Methods: A total of 2630 samples from HIV-positive adults were tested by qualitative and quantitative VDRL test and if reactive, by Treponema pallidum hemagglutination (TPHA) test. CD4 cell counts were determined at the same time by flow cytometry (BD FACSCount™ system). Correlation between CD4 T-lymphocyte cell count and VDRL titers was sought for. Results: Nearly 6.7% (176/2631) of individuals were VDRL reactive, males more than females (7.6% vs. 5.1%, P = 0.014). Four of the VDRL-reactive patients were found negative by TPHA test and were excluded from further study. VDRL titers ranged from weakly reactive to being reactive at 1:128 (median = 1:2). The CD4 cell count ranged from 23 cells/μl to 883 cells/μl (median = 276 cells/μl, mean = 323.9 ± 200.9). Pearson's coefficient of correlation (R) between CD4 cell count and VDRL titers was calculated to be 0.0559; coefficient of determination (R2) was 0.0031. Conclusions: Although the correlation coefficient shows a positive correlation, the association was very weak. Therefore, CD4 cell count cannot be expected to influence VDRL titers in HIV-positive adults significantly.
Associations Between State Tobacco Control Policies and Adolescent ENDS Use

Background: Despite an increase in adolescent use of electronic nicotine delivery systems (ENDS), little is known about the role of tobacco control policies on ENDS use. Objective: For aim 1, we examined how trends in adolescent use of cigarettes were affected by the introduction of ENDS; for aim 2, we examined the associations between ENDS age restrictions, cigarette taxes, and smoke-free legislation and adolescent use of ENDS and cigarettes. Design and Setting: Repeated cross-sections of the 1999-2015 Youth Risk Behavior Surveys linked to state-level tobacco control policies. Participants: 938 486 adolescents aged 14 to 18 years from 45 states. Main Outcome Measures: For aim 1, we examined adolescent use of cigarettes. For aim 2, we examined adolescent use of ENDS, only ENDS, and cigarettes. Results: We found there was an overall decreasing trend in adolescent use of cigarettes, but the actual decline was greater than the predicted decline for 17- and 18-year-olds. While we found no associations between ENDS use and ENDS age restrictions or cigarette taxes, ENDS use was 3.8 percentage points higher in those states with smoke-free legislation for combustible tobacco products. Conclusions: Our findings highlight that ENDS age restrictions may not be adequate to curb ENDS use and additional local- and state-level policies governing ENDS are needed.
Fluorescein Leakage within Recent Subretinal Hemorrhage in Pathologic Myopia: Suggestive of CNV?

Purpose To determine whether fluorescein leakage within subretinal hemorrhage is definitely suggestive of choroidal neovascularization (CNV) by multimodal imaging including optical coherence tomography angiography (OCTA). Methods Twenty-five consecutive highly myopic patients (25 eyes) with fluorescein leakage within subretinal hemorrhage detected within 1 month were prospectively included. All patients underwent OCTA and spectral-domain optical coherence tomography (SD-OCT). The OCTA and SD-OCT findings at the site of fluorescein leakage were analyzed. In cases of a doubtful diagnosis, indocyanine green angiography (ICGA) was also performed to differentiate myopic CNV from lacquer crack if necessary; all patients were followed up by SD-OCT and/or OCTA for at least 2 weeks. Results In terms of the site of fluorescein leakage, OCTA revealed an abnormal vascular network in the outer retina and a choriocapillaris slab in 22 out of 25 eyes (88%), which were confirmed to be CNV. However, no high-flow signal was observed in 3 of 25 eyes (12%). In these 3 cases, SD-OCT showed a focal rupture of the retinal pigment epithelium-Bruch's membrane-choriocapillaris (RPE-BM-CC) complex and a columnar hyperreflective signal of blood originating from defects with a volcanic geyser-like appearance, and no exudative signs were detected. Notably, all ruptures of the RPE-BM-CC complex were located exactly at lacquer crack sites. Moreover, with the absorption of subretinal hemorrhage, ruptures of the RPE-BM-CC complex spontaneously resolved without any intervention. Considering the multimodal imaging appearance and follow-up outcomes, these 3 eyes were eventually diagnosed as simple bleeding associated with lacquer cracks. Conclusions Dye leakage within recent subretinal hemorrhage on FA could be caused by new-onset lacquer cracks in pathologic myopia. Multimodal imaging including OCTA is helpful to differentiate lacquer cracks from myopic CNV.
JuncNet: A Deep Neural Network for Road Junction Disambiguation for Autonomous Vehicles

With a great amount of research going on in the field of autonomous vehicles or self-driving cars, there has been considerable progress in road detection and tracking algorithms. Most of these algorithms use GPS to handle road junctions and its subsequent decisions. However, there are places in the urban environment where it becomes difficult to get GPS fixes which render the junction decision handling erroneous or possibly risky. Vision-based junction detection, however, does not have such problems. This paper proposes a novel deep convolutional neural network architecture for disambiguation of junctions from roads with a high degree of accuracy. This network is benchmarked against other well known classifying network architectures like AlexNet and VGGnet. Further, we discuss a potential road navigation methodology which uses the proposed network model. We conclude by performing an experimental validation of the trained network and the navigational method on the roads of the Indian Institute of Science (IISc).
Thapsigargin Increases IL-2 Production in T Cells at Nanomolar Concentrations

Thapsigargin (TGN) is a potent and selective inhibitor of sarco-endoplasmic Ca2+-ATPase, leading to rapid elevation of cytoplasmic Ca2+ concentration. Previous reports have shown that TGN increases the production of various cytokines from macrophages and dendritic cells. Here, we examine the effects of TGN on murine T cells. Nanomolar concentrations of TGN are a significant inducer of IL-2 production with full activity at 50 nM. Micromolar concentrations of TGN, however, are inhibitory to IL-2 production and T cell proliferation. The IL-2 production-inducing activity of TGN is much more prominent when T cells are primed with concanavalin A or anti-CD3 mAb, and is due to the increase of cytoplasmic Ca2+ concentration. TGN at 50 nM does not affect interferon-gamma or IL-4 production from T cells. Thus, the present study shows that low nanomolar concentrations of TGN could be useful in potentiating IL-2 production from antigen-primed T cells.
Crowdsourcing Semantic Label Propagation in Relation Classification

Distant supervision is a popular method for performing relation extraction from text that is known to produce noisy labels. Most progress in relation extraction and classification has been made with crowdsourced corrections to distant-supervised labels, and there is evidence that indicates still more would be better. In this paper, we explore the problem of propagating human annotation signals gathered for open-domain relation classification through the CrowdTruth methodology for crowdsourcing, that captures ambiguity in annotations by measuring inter-annotator disagreement. Our approach propagates annotations to sentences that are similar in a low dimensional embedding space, expanding the number of labels by two orders of magnitude. Our experiments show significant improvement in a sentence-level multi-class relation classifier.
Admission and Congestion Control for 5G Network Slicing

Network Slicing has been widely accepted as essential feature of future 5thGeneration (5G) mobile communication networks. Accounting the potentially dense demand of network slices as a cloud service and the limited resource of mobile network operators (MNOs), an efficient inter-slice management and orchestration plays a key role in 5G networks. This calls advanced solutions for slice admission and congestion control. This paper proposes a novel approach of inter-slice control that well copes with existing pre-standardized 5G architectures.
IoTDots: A Digital Forensics Framework for Smart Environments

IoT devices and sensors have been utilized in a cooperative manner to enable the concept of a smart environment. In these smart settings, abundant data is generated as a result of the interactions between devices and users' day-to-day activities. Such data contain valuable forensic information about events and actions occurring inside the smart environment and, if analyzed, may help hold those violating security policies accountable. In this paper, we introduce IoTDots, a novel digital forensic framework for a smart environment such as smart homes and smart offices. IoTDots has two main components: IoTDots-Modifier and IoTDots-Analyzer. At compile time, IoTDots-Modifier performs the source code analysis of smart apps, detects forensically-relevant information, and automatically insert tracing logs. Then, at runtime, the logs are stored into a IoTDots database. Later, in the event of a forensic investigation, the IoTDots-Analyzer applies data processing and machine learning techniques to extract valuable and usable forensic information from the devices' activity. In order to test the performance of IoTDots, we tested IoTDots in a realistic smart office environment with a total of 22 devices and sensors. The evaluation results show that IoTDots can achieve, on average, over 98% of accuracy on detecting user activities and over 96% accuracy on detecting the behavior of users, devices, and apps in a smart environment. Finally, IoTDots performance yields no overhead to the smart devices and very minimal overhead to the cloud server.
A Comprehensive Look at Irritable Bowel Syndrome and its Associated Factors Considering the Rome IV Criteria: A Penalized Smoothly Clipped Absolute Deviation Regression Approach in the Pars Cohort Study

BACKGROUND After the introduction of the Rome IV criteria for the diagnosis of irritable bowel syndrome (IBS), studies on the clinical significance of the new criteria in the settings of a large study has been scarce. Objective: Herein we used the infrastructures provided by one the largest cohort studies in Iran to evaluate the epidemiological features related to IBS. METHODS A total of 9264 participants, were enrolled in the initial registry. Diagnosis of IBS was done using the Rome IV criteria. Individuals with IBS were compared with a control group. Since the study included a large sample size of patients, we used the penalized smoothly clipped absolute deviation (SCAD) regression analysis to construct a model for the evaluation of factors associated with IBS. RESULTS Overall, data of 9163 participants entered the final analysis. In total, 1067 (11.6%) individuals were diagnosed with IBS, among which 57 (5.3%) were diarrhea dominant (IBS-D), 380 (35.6%) were constipation dominant (IBS-C), and 630 (59%) did not mention having any of the two (IBS-U). In the regression model, back pain/arthralgia (OR: 1.98, 95% CI: 1.65 - 2.40), insomnia (OR: 1.65, 95% CI: 1.40 - 1.93), depression (OR: 1.64, 95% CI: 1.38 - 1.95), female sex (OR: 1.58, 95% CI: 1.27 - 1.96), anxiety (OR: 1.43, 95% CI: 1.21 - 1.69), and being married (OR: 1.23, 95% CI: 1.03 - 1.48), were associated with higher rates of IBS. We found that IBS prevalence displays a peak at the age of 41 years for both men and women. CONCLUSION The present study provides a background for follow-up studies to be conducted in order to evaluate causality between IBS and some major diseases such as liver disease. We also found that opium use, although not statistically significant, in addition to sex, education, back/joint pain, depression, insomnia, anxiety, and marital status might be a contributing factor in IBS.
The Effect of Time Delay on the Average Data Rate and Performance in Networked Control Systems

This article studies the performance of a feedback control loop closed via an error-free digital communication channel with transmission delay. The system comprises a discrete-time noisy linear time-invariant plant, whose single measurement output is mapped into its single control input by a causal, but otherwise arbitrary, coding and control scheme. We consider a single-input multiple-output channel between the encoder–controller and the decoder–controller, which is lossless and imposes random time delay. We derive a lower bound on the minimum average feedback data rate that guarantees achieving a certain level of average quadratic performance over all possible realizations of the random delay. For the special case of a constant channel delay, we obtain an upper bound by proposing linear source-coding schemes that attain desired performance levels with rates that are at most 1.254 b per sample greater than the lower bound. We supplement our results with a numerical experiment demonstrating that the obtained bounds and operational rates are increasing functions of the constant delay.
Eliminating Boundaries in Cloud Storage with Anna

In this paper, we describe how we extended a distributed key-value store called Anna into an elastic, multi-tier service for the cloud. In its extended form, Anna is designed to overcome the narrow cost-performance limitations typical of current cloud storage systems. We describe three key aspects of Anna's new design: multi-master selective replication of hot keys, a vertical tiering of storage layers with different cost-performance tradeoffs, and horizontal elasticity of each tier to add and remove nodes in response to load dynamics. Anna's policy engine uses these mechanisms to balance service-level objectives around cost, latency and fault tolerance. Experimental results explore the behavior of Anna's mechanisms and policy, exhibiting orders of magnitude efficiency improvements over both commodity cloud KVS services and research systems.
NTUA-SLP at IEST 2018: Ensemble of Neural Transfer Methods for Implicit Emotion Classification

In this paper we present our approach to tackle the Implicit Emotion Shared Task (IEST) organized as part of WASSA 2018 at EMNLP 2018. Given a tweet, from which a certain word has been removed, we are asked to predict the emotion of the missing word. In this work, we experiment with neural Transfer Learning (TL) methods. Our models are based on LSTM networks, augmented with a self-attention mechanism. We use the weights of various pretrained models, for initializing specific layers of our networks. We leverage a big collection of unlabeled Twitter messages, for pretraining word2vec word embeddings and a set of diverse language models. Moreover, we utilize a sentiment analysis dataset for pretraining a model, which encodes emotion related information. The submitted model consists of an ensemble of the aforementioned TL models. Our team ranked 3rd out of 30 participants, achieving an F1 score of 0.703.
The Effect of Context on Metaphor Paraphrase Aptness Judgments

We conduct two experiments to study the effect of context on metaphor paraphrase aptness judgments. The first is an AMT crowd source task in which speakers rank metaphor-paraphrase candidate sentence pairs in short document contexts for paraphrase aptness. In the second we train a composite DNN to predict these human judgments, first in binary classifier mode, and then as gradient ratings. We found that for both mean human judgments and our DNN’s predictions, adding document context compresses the aptness scores towards the center of the scale, raising low out-of-context ratings and decreasing high out-of-context scores. We offer a provisional explanation for this compression effect.
A cancer-associated polymorphism in ESCRT-III disrupts the abscission checkpoint and promotes genome instability

Significance The final step of cell division, abscission, is temporally regulated by the Aurora B kinase and charged multivesicular body protein 4C (CHMP4C) in a conserved pathway called the “abscission checkpoint” which arrests abscission in the presence of lingering mitotic problems. Despite extensive study, the physiological importance of this pathway to human health has remained elusive. We now demonstrate that a cancer-predisposing polymorphism in CHMP4C disrupts the abscission checkpoint and results in DNA damage accumulation. Moreover, deficits in this checkpoint synergize with p53 loss and generate aneuploidy under stress conditions that increase the frequency of chromosome missegregation. Therefore, cells expressing the cancer-associated polymorphism in CHMP4C are genetically unstable, thus suggesting an oncogenic mechanism that may involve the dysregulation of abscission. Cytokinetic abscission facilitates the irreversible separation of daughter cells. This process requires the endosomal-sorting complexes required for transport (ESCRT) machinery and is tightly regulated by charged multivesicular body protein 4C (CHMP4C), an ESCRT-III subunit that engages the abscission checkpoint (NoCut) in response to mitotic problems such as persisting chromatin bridges within the midbody. Importantly, a human polymorphism in CHMP4C (rs35094336, CHMP4CT232) increases cancer susceptibility. Here, we explain the structural and functional basis for this cancer association: The CHMP4CT232 allele unwinds the C-terminal helix of CHMP4C, impairs binding to the early-acting ESCRT factor ALIX, and disrupts the abscission checkpoint. Cells expressing CHMP4CT232 exhibit increased levels of DNA damage and are sensitized to several conditions that increase chromosome missegregation, including DNA replication stress, inhibition of the mitotic checkpoint, and loss of p53. Our data demonstrate the biological importance of the abscission checkpoint and suggest that dysregulation of abscission by CHMP4CT232 may synergize with oncogene-induced mitotic stress to promote genomic instability and tumorigenesis.
Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition

Purpose: Poor prognosis in triple-negative breast cancer (TNBC) is due to an aggressive phenotype and lack of biomarker-driven targeted therapies. Overexpression of cyclin E and phosphorylated-CDK2 are correlated with poor survival in patients with TNBC, and the absence of CDK2 desensitizes cells to inhibition of Wee1 kinase, a key cell-cycle regulator. We hypothesize that cyclin E expression can predict response to therapies, which include the Wee1 kinase inhibitor, AZD1775. Experimental Design: Mono- and combination therapies with AZD1775 were evaluated in TNBC cell lines and multiple patient-derived xenograft (PDX) models with different cyclin E expression profiles. The mechanism(s) of cyclin E–mediated replicative stress were investigated following cyclin E induction or CRISPR/Cas9 knockout by a number of assays in multiple cell lines. Results: Cyclin E overexpression (i) is enriched in TNBCs with high recurrence rates, (ii) sensitizes TNBC cell lines and PDX models to AZD1775, (iii) leads to CDK2-dependent activation of DNA replication stress pathways, and (iv) increases Wee1 kinase activity. Moreover, treatment of cells with either CDK2 inhibitors or carboplatin leads to transient transcriptional induction of cyclin E (in cyclin E–low tumors) and result in DNA replicative stress. Such drug-mediated cyclin E induction in TNBC cells and PDX models sensitizes them to AZD1775 in a sequential treatment combination strategy. Conclusions: Cyclin E is a potential biomarker of response (i) for AZD1775 as monotherapy in cyclin E–high TNBC tumors and (ii) for sequential combination therapy with CDK2 inhibitor or carboplatin followed by AZD1775 in cyclin E–low TNBC tumors.
Review of clinical approaches in fluorescence lifetime imaging ophthalmoscopy

Abstract. Autofluorescence-based imaging techniques have become very important in the ophthalmological field. Being noninvasive and very sensitive, they are broadly used in clinical routines. Conventional autofluorescence intensity imaging is largely influenced by the strong fluorescence of lipofuscin, a fluorophore that can be found at the level of the retinal pigment epithelium. However, different endogenous retinal fluorophores can be altered in various diseases. Fluorescence lifetime imaging ophthalmoscopy (FLIO) is an imaging modality to investigate the autofluorescence of the human fundus in vivo. It expands the level of information, as an addition to investigating the fluorescence intensity, and autofluorescence lifetimes are captured. The Heidelberg Engineering Spectralis-based fluorescence lifetime imaging ophthalmoscope is used to investigate a 30-deg retinal field centered at the fovea. It detects FAF decays in short [498 to 560 nm, short spectral channel (SSC) and long (560 to 720 nm, long spectral channel (LSC)] spectral channels, the mean fluorescence lifetimes (τm) are calculated using bi- or triexponential approaches. These are meant to be relatively independent of the fluorophore’s intensity; therefore, fluorophores with less intense fluorescence can be detected. As an example, FLIO detects the fluorescence of macular pigment, retinal carotenoids that help protect the human fundus from light damages. Furthermore, FLIO is able to detect changes related to various retinal diseases, such as age-related macular degeneration, albinism, Alzheimer’s disease, diabetic retinopathy, macular telangiectasia type 2, retinitis pigmentosa, and Stargardt disease. Some of these changes can already be found in healthy eyes and may indicate a risk to developing such diseases. Other changes in already affected eyes seem to indicate disease progression. This review article focuses on providing detailed information on the clinical findings of FLIO. This technique detects not only structural changes at very early stages but also metabolic and disease-related alterations. Therefore, it is a very promising tool that might soon be used for early diagnostics.