Miracle-dz/UniFAR-FTUs huggingface dataset:
Visual Function in Older Eyes in Normal Macular Health: Association with Incident Early Age-Related Macular Degeneration 3 Years Later

Purpose In older eyes in normal macular health, we examined associations between impaired photopic acuity, mesopic acuity, spatial contrast sensitivity, light sensitivity, and the presence of low luminance deficit (difference between photopic and mesopic acuity) at baseline and incident AMD 3 years later. Associations were compared with an association between delayed rod-mediated dark adaptation and incident AMD, previously reported for this cohort. Methods Enrollees were 60 years or older. Eyes at step 1 in the AREDS nine-step classification system based on masked grading of color fundus photographs were included. Photopic and mesopic acuity, contrast sensitivity, and light sensitivity, and the presence of low luminance deficit, were measured at baseline. Demographic, lifestyle, general health, and blood markers were assessed at baseline as potential confounders. Three years later fundus grading was repeated to determine AMD presence. Results For the analysis, 827 eyes of 467 persons were eligible. Impaired mesopic acuity at baseline was associated with incident AMD, age-adjusted rate ratio (RR) 1.57 (95% confidence interval [CI] 1.04–2.35), whereas impaired photopic acuity, contrast sensitivity and macular light sensitivity, and the presence of a low luminance deficit were not. The mesopic acuity association was slightly weaker than the association between abnormal dark adaptation and incident AMD (RR 1.85, 95% CI 1.07–3.20). Conclusions Impaired mesopic acuity in eyes in normal macular health is a risk factor for incident early AMD 3 years later, however, photopic acuity, contrast sensitivity, and light sensitivity, and the presence of a low luminance deficit are not risk factors.
An On-Chip Learning Neuromorphic Autoencoder With Current-Mode Transposable Memory Read and Virtual Lookup Table

This paper presents an IC implementation of on-chip learning neuromorphic autoencoder unit in a form of rate-based spiking neural network. With a current-mode signaling scheme embedded in a 500 × 500 6b SRAM-based memory, the proposed architecture achieves simultaneous processing of multiplications and accumulations. In addition, a transposable memory read for both forward and backward propagations and a virtual lookup table are also proposed to perform an unsupervised learning of restricted Boltzmann machine. The IC is fabricated using 28-nm CMOS process and is verified in a three-layer network of encoder–decoder pair for training and recovery of images with two-dimensional ${\text{16}}\times {\text{16}}$ pixels. With a dataset of 50 digits, the IC shows a normalized root mean square error of 0.078. Measured energy efficiencies are 4.46 pJ per synaptic operation for inference and 19.26 pJ per synaptic weight update for learning, respectively. The learning performance is also estimated by simulations if the proposed hardware architecture is extended to apply to a batch training of 60 000 MNIST datasets.
Serological Prevalence of Schistosoma japonicum in Mobile Populations in Previously Endemic but Now Non-Endemic Regions of China: A Systematic Review and Meta-Analysis

Background Schistosomiasis japonica has been resurging in certain areas of China where its transmission was previously well controlled or interrupted. Several factors may be contributing to this, including mobile populations, which if infected, may spread the disease. A wide range of estimates have been published for S. japonicum infections in mobile populations, and a synthesis of these data will elucidate the relative risk presented from these groups. Methods A literature search for publications up to Oct 31, 2014 on S. japonicum infection in mobile populations in previously endemic but now non-endemic regions was conducted using four bibliographic databases: China National Knowledge Infrastructure, WanFang, VIP Chinese Journal Databases, and PubMed. A meta-analysis was conducted by pooling one arm binary data with MetaAnalyst Beta 3.13. The protocol is available on PROSPERO (No. CRD42013005967). Results A total of 41 studies in Chinese met the inclusion criteria, covering seven provinces of China. The time of post-interruption surveillance ranged from the first year to the 31st year. After employing a random-effects model, from 1992 to 2013 the pooled seroprevalence ranged from 0.9% (95% CI: 0.5-1.6%) in 2003 to 2.3% (95% CI: 1.5-3.4) in 1995; from the first year after the disease had been interrupted to the 31st year, the pooled seroprevalence ranged from 0.6% (95% CI: 0.2-2.1%) in the 27th year to 4.0% (95%CI: 1.3-11.3%) in the second year. The pooled seroprevalence in mobile populations each year was significantly lower than among the residents of endemic regions, whilst four papers reported a lower level of infection in the mobile populations than in the local residents out of only 13 papers which included this data. Conclusions The re-emergence of S. japonicum in areas which had previously interrupted transmission might be due to other factors, although risk from re-introduction from mobile populations could not be excluded.
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia

The transcription factor Hypoxia-inducible factor 1 (HIF-1) plays a central role in the transcriptional response to oxygen flux. To gain insight into the molecular pathways regulated by HIF-1, it is essential to identify the downstream-target genes. We report here a strategy to identify HIF-1-target genes based on an integrative genomic approach combining computational strategies and experimental validation. To identify HIF-1-target genes microarrays data sets were used to rank genes based on their differential response to hypoxia. The proximal promoters of these genes were then analyzed for the presence of conserved HIF-1-binding sites. Genes were scored and ranked based on their response to hypoxia and their HIF-binding site score. Using this strategy we recovered 41% of the previously confirmed HIF-1-target genes that responded to hypoxia in the microarrays and provide a catalogue of predicted HIF-1 targets. We present experimental validation for ANKRD37 as a novel HIF-1-target gene. Together these analyses demonstrate the potential to recover novel HIF-1-target genes and the discovery of mammalian-regulatory elements operative in the context of microarray data sets.
RRAD Promotes EGFR-Mediated STAT3 Activation and Induces Temozolomide Resistance of Malignant Glioblastoma

Glioblastoma multiforme (GBM) is an extremely aggressive brain cancer with a median survival of less than 2 years. GBM is characterized by abnormal activation of receptor tyrosine kinase and constitutively activated STAT3. Although EGFR phosphorylation and STAT3 activation are essential for the maintenance of GBM cancer stem cells, the molecular mechanism underlying endosome-mediated STAT3 activation is not fully understood. In the current study, we showed that GTP-binding protein RRAD (RAS associated with diabetes, RAD) physically associates with EGFR, and EEA1, enhancing the stability and endosome-associated nuclear translocation of EGFR. Functionally, RRAD contributes to the activation of STAT3 and expression of the stem cell factors OCT4, NANOG, and SOX2, thereby enhancing self-renewing ability, tumor sphere formation, EMT, and in vivo tumorigenesis. Most importantly, RRAD contributes to poor survival in patients with GBM. RRAD expression is correlated with temozolomide resistance, and, conversely, depletion of RRAD leads to sensitization of highly temozolomide-resistant GBM cells. Our data collectively support a novel function of RRAD in STAT3 activation and provide evidence that RRAD acts as a positive regulator in the EGFR signaling pathway. These results demonstrate a critical role for RRAD in GBM tumorigenesis and provide a rationale for the development of pharmacologic inhibitors of RRAD in GBM. Mol Cancer Ther; 13(12); 3049–61. ©2014 AACR.
Dietary Intakes and Risk of Lymphoid and Myeloid Leukemia in the European Prospective Investigation into Cancer and Nutrition (EPIC)

The etiology of leukemias cannot entirely be explained by known risk factors, including ionizing radiation, benzene exposure, and infection with human T cell leukemia virus. A number of studies suggested that diet influences the risk of adult leukemias. However, results have been largely inconsistent. We examined the potential association between dietary factors and risk of leukemias among participants of the European Prospective Investigation into Cancer and Nutrition study. Among the 477,325 participants with mean follow-up of 11.34 yr (SD = 2.47), 773 leukemias (373 and 342 cases of lymphoid and myeloid leukemia, respectively) were identified. Diet over the previous 12 mo was assessed at baseline using a validated country-specific dietary questionnaire. Cox proportional hazards regression was used to explore the association between dietary factors that have previously been associated with leukemia risk, including red and processed meat, poultry, offal, fish, dairy products, vegetables, fruits, and seeds/nuts, and risk of both lymphoid and myeloid leukemias. No significant associations were observed between dietary measures and total, lymphoid, and myeloid leukemias. Additional subtype analyses showed no dietary association with risk of major subtypes of leukemias. In summary, this study did not support a possible link between selected dietary factors and risk of leukemias.
Economic constrained transfer capability assessment

Following the deregulation of electric power utilities around the globe, it has been widely acknowledged that quantifying power system transfer capability is of increasingly importance in today's large-scale and interconnected power system operation and planning procedures. This paper introduces a novel framework to evaluate transfer capability incorporating electricity market dispatching considerations, which we termed it as economic constrained transfer capability (ETC) problem. A mathematical model of a multi-objective optimization (MOOP) approach is presented to solve this ETC problem. The proposed methodology has been tested on a classical 3-machine 9-bus system and the IEEE 30-bus system. Preliminary simulation results from several case studies are presented with relevant analyses and discussions.
Quantifying audience experience in the wild: Heuristics for developing and deploying a biosensor infrastructure in theaters

Measuring the experience of audience of arts events is essential in the “experience economy” of this day and age, but it is a difficult task. The value of such information goes beyond evaluating the impact of the arts, as it can provide insights and feedback to enhance the work of artists and the experiences of other audience members. Through in-depth understanding of the needs of the providers and consumers of the arts, we progressively developed a biosensor infrastructure that was deployed in theaters. Over the years, we identified the challenges and issues related to developing and deploying a biosensor infrastructure in theaters. These collective experiences and identified issues were categorized into three main areas: processes, data, and system. A total of seven heuristics are developed across the three main areas. Processes place the stakeholders and audiences at the core of the research; data provides guidelines for data validity, collecting a variety of data, and supporting real-time data gathering; and systems covers the concurrency, scalability, deployment and feedback of the infrastructure. We believe that this set of heuristics forms the foundation for an adequate infrastructure to measure audience experience in the wild and it is a valuable source of guideline for future work.
Summarized Network Behavior Prediction

This work studies the entity-wise topical behavior from massive network logs. Both the temporal and the spatial relationships of the behavior are explored with the learning architectures combing the recurrent neural network (RNN) and the convolutional neural network (CNN). To make the behavioral data appropriate for the spatial learning in CNN, several reduction steps are taken to form the topical metrics and place them homogeneously like pixels in the images. The experimental result shows both the temporal- and the spatial- gains when compared to a multilayer perceptron (MLP) network. A new learning framework called spatially connected convolutional networks (SCCN) is introduced to more efficiently predict the behavior.
Pentraxin 3 Is a Predictor for Fibrosis and Arterial Stiffness in Patients with Nonalcoholic Fatty Liver Disease

Objective. The aim of the present study was to investigate whether pentraxin 3 (PTX3) can be a new noninvasive marker for prediction of liver fibrosis in patients with NAFLD. We also aimed to evaluate the relationship between PTX3 and atherosclerosis in patients with NAFLD. Method. Fifty-four male patients with biopsy-proven NAFLD and 20 apparently healthy male volunteers were included. PTX3 levels were determined, using an ELISA method (R&D Sysytems, Quantikine ELISA, USA). To detect the presence of subclinical atherosclerosis in NAFLD, measurements of CIMT, FMD, and cf-PWV levels were performed. Results. PTX3 levels in NAFLD patients with fibrosis were higher than both NAFLD patients without fibrosis and controls (P = 0.032 and P = 0.028, respectively), but there was no difference between controls and NAFLD patients without fibrosis in terms of PTX3 levels (P = 0.903). PTX3 levels were strongly correlated with cf-PWV (r = 0.359, P = 0.003), whereas no significant correlation was found with other atherosclerosis markers, CIMT and FMD. Conclusion. Elevated plasma PTX3 levels are associated with the presence of fibrosis in patients with NAFLD, independently of metabolic syndrome components. This study demonstrated that for the first time there is a close association between elevated PTX3 levels and increased arterial stiffness in patients with NAFLD.
In-Network Computation in Random Wireless Networks: A PAC Approach to Constant Refresh Rates with Lower Energy Costs

We propose a method to compute a probably approximately correct (PAC) normalized histogram of observations with a refresh rate of Θ(1) time units per histogram sample on a random geometric graph with noise-free links. The delay in computation is Θ(√n) time units. We further extend our approach to a network with noisy links. While the refresh rate remains Θ(1) time units per sample, the delay increases to Θ(√n log n). The number of transmissions in both cases is Θ(n) per histogram sample. The achieved Θ(1) refresh rate for PAC histogram computation is a significant improvement over the refresh rate of Θ(1/log n) for histogram computation in noiseless networks. We achieve this by operating in the supercritical thermodynamic regime where large pathways for communication build up, but the network may have more than one component. The largest component however will have an arbitrarily large fraction of nodes in order to enable approximate computation of the histogram to the desired level of accuracy. Operation in the supercritical thermodynamic regime also reduces energy consumption. A key step in the proof of our achievability result is the construction of a connected component having bounded degree and any desired fraction of nodes. This construction may also prove useful in other communication settings on the random geometric graph.
Secure Data Deletion for Linux File Systems

Security conscious users of file systems require that deleted information and its associated meta-data are no longer accessible on the underlying physical disk. Existing file system implementations only reset the file system data structures to reflect the removal of data, leaving both the actual data and its associated meta-data on the physical disk. Even when this information has been overwritten, it may remain visible to advanced probing techniques such as magnetic force microscopy or magnetic force scanning tunneling microscopy. Our project addresses this problem by adding support to the Linux kernel for asynchronous secure deletion of file data and meta-data. We provide an implementation for the Ext2 file system; other file systems can be accommodated easily. An asynchronous overwriting process sacrifices immediate security but ultimately provides a far more usable and complete secure deletion facility. We justify our design by arguing that user-level secure deletion tools are inadequate in many respects and that synchronous deletion facilities are too time consuming to be acceptable to users. Further, we contend that encrypting file information, either using manual tools or a encrypted file system, is not a sufficient solution to alleviate the need for secure data deletion.
ResearchActivated networking of platelet activating factor receptor and FAK / STAT 1 induces malignant potential in BRCA 1-mutant at-risk ovarian epithelium

Objectives: It is essential to understand the molecular basis of ovarian cancer etiology and tumor development to provide more effective preventive and therapeutic approaches to reduce mortality. Particularly, the molecular targets and pathways involved in early malignant transformation are still not clear. Pro-inflammatory lipids and pathways have been reported to play significant roles in ovarian cancer progression and metastasis. The major objective of this study was to explore and determine whether platelet activating factor (PAF) and receptor associated networking pathways might significantly induce malignant potential in BRCA1-mutant at-risk epithelial cells. Methods: BRCA1-mutant ovarian epithelial cell lines including (HOSE-636, HOSE-642), BRCA1-mutant ovarian cancer cell (UWB1.289), wild type normal ovarian epithelial cell (HOSE-E6E7) and cancerous cell line (OVCA429), and the nonmalignant BRCA1-mutant distal fallopian tube (fimbria) tissue specimens were used in this study. Mutation analysis, kinase microarray, western blot, immune staining, co-immune precipitation, cell cycle, apoptosis, proliferation and bioinformatic pathway analysis were applied. Results: We found that PAF, as a potent pro-inflammatory mediator, induced significant anti-apoptotic effect in BRCA1mutant ovarian surface epithelial cells, but not in wild type HOSE cells. With kinase microarray technology and the specific immune approaches, we found that phosphor-STAT1 was activated by 100 nM PAF treatment only in BRCA1mutant associated at-risk ovarian epithelial cells and ovarian cancer cells, but not in BRCA1-wild type normal (HOSEE6E7) or malignant (OVCA429) ovarian epithelial cells. Co-immune precipitation revealed that elevated PAFR expression is associated with protein-protein interactions of PAFR-FAK and FAK-STAT1 in BRCA1-mutant ovarian epithelial cells, but not in the wild-type control cells. Conclusion: Previous studies showed that potent inflammatory lipid mediators such as PAF and its receptor (PAFR) significantly contribute to cancer progression and metastasis. Our findings suggest that these potent inflammatory lipids and receptor pathways are significantly involved in the early malignant transformation through PAFR-FAK-STAT1 networking and to block apoptosis pathway in BRCA1 dysfunctional at-risk ovarian epithelium. * Correspondence: wjianliu@netease.com, bye@partners.org 1 Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA 3 Obstetrics and Gynecology Department, Peking University People's Hospital,
The MTHFR C677T Variant is Associated with Responsiveness to Disulfiram Treatment for Cocaine Dependency

Objective: Disulfiram is a one of the few pharmacotherapies for cocaine addiction that shows promise. Since disulfiram and cocaine both affect levels of global methylation we hypothesized the MTHFR gene, whose product is involved in supplying methyl groups for DNA and protein methylation, may be associated with responsiveness to disulfiram in cocaine-dependent individuals. Methods: Sixty-seven cocaine-dependent patients were stabilized on methadone for 2 weeks and then randomized into disulfiram (250 mg/day, N = 32) and placebo groups (N = 35) for 10 weeks. Patients were genotyped for the MTHFR (rs1801133, also known as C677T) polymorphism and the data was evaluated for association with cocaine-free urines in the disulfiram or placebo groups. Data from patients that completed all 10 weeks of the study (N = 56) were analyzed using repeated measures analysis of variance (ANOVA), corrected for population structure. Results: The CT or TT MTHFR genotype group (N = 32) dropped from 73 to 52% cocaine-positive urines on disulfiram (p = 0.0001), while the placebo group showed no treatment effect. The CC MTHFR genotype group (N = 24) showed a smaller, but still significant, reduction in cocaine-positive urines on disulfiram compared to placebo; 81–69% (p = 0.007). Conclusion: This study indicates that a patient’s MTHFR genotype may be used to identify individuals who might show improved response to disulfiram treatment for cocaine dependence. Clinical Trial: Pharmacogenetics of Disulfiram for Cocaine, clinicaltrials.gov/ct2/show/NCT00149630, NIDA-18197-2, NCT00149630.
Morphologically controlled synthesis of colloidal upconversion nanophosphors and their shape-directed self-assembly

We report a one-pot chemical approach for the synthesis of highly monodisperse colloidal nanophosphors displaying bright upconversion luminescence under 980 nm excitation. This general method optimizes the synthesis with initial heating rates up to 100 °C/minute generating a rich family of nanoscale building blocks with distinct morphologies (spheres, rods, hexagonal prisms, and plates) and upconversion emission tunable through the choice of rare earth dopants. Furthermore, we employ an interfacial assembly strategy to organize these nanocrystals (NCs) into superlattices over multiple length scales facilitating the NC characterization and enabling systematic studies of shape-directed assembly. The global and local ordering of these superstructures is programmed by the precise engineering of individual NC’s size and shape. This dramatically improved nanophosphor synthesis together with insights from shape-directed assembly will advance the investigation of an array of emerging biological and energy-related nanophosphor applications.
Multigrid waveform relaxation on spatial finite element meshes

The waveform relaxation method and its multigrid acceleration are studied as solution procedures for the system of ordinary differential equations obtained by finite element discretisation of a linear parabolic initial boundary value problem. The convergence properties of the continuous-time algorithm are theoretically investigated on finite-length and infinite-length time-intervals. In addition, quantitative convergence estimates and numerical results are presented for one-dimensional and two-dimensional model problems.