AdaSampling for positive-unlabeled and label noise learning with bioinformatics applications

© 2018 IEEE. Class labels are required for supervised learning but may be corrupted or missing in various applications. In binary classification, for example, when only a subset of positive instances is labeled whereas the remaining are unlabeled, positive-unlabeled (PU) learning is required to model from both positive and unlabeled data. Similarly, when class labels are corrupted by mislabeled instances, methods are needed for learning in the presence of class label noise (LN). Here we propose adaptive sampling (AdaSampling), a framework for both PU learning and learning with class LN. By iteratively estimating the class mislabeling probability with an adaptive sampling procedure, the proposed method progressively reduces the risk of selecting mislabeled instances for model training and subsequently constructs highly generalizable models even when a large proportion of mislabeled instances is present in the data. We demonstrate the utilities of proposed methods using simulation and benchmark data, and compare them to alternative approaches that are commonly used for PU learning and/or learning with LN. We then introduce two novel bioinformatics applications where AdaSampling is used to: 1) identify kinase-substrates from mass spectrometry-based phosphoproteomics data and 2) predict transcription factor target genes by integrating various next-generation sequencing data

Hmong Adults Self-Rated Oral Health: A Pilot Study

Since 1975, the Hmong refugee population in the U.S. has increased over 200%. However, little is known about their dental needs or self-rated oral health (SROH). The study aims were to: (1) describe the SROH, self-rated general health (SRGH), and use of dental/physician services; and (2) identify the factors associated with SROH among Hmong adults. A cross-sectional study design with locating sampling methodology was used. Oral health questionnaire was administered to assess SROH and SRGH, past dental and physician visits, and language preference. One hundred twenty adults aged 18–50+ were recruited and 118 had useable information. Of these, 49% rated their oral health as poor/fair and 30% rated their general health as poor/fair. Thirty-nine percent reported that they did not have a regular source of dental care, 46% rated their access to dental care as poor/fair, 43% visited a dentist and 66% visited a physician within the past 12 months. Bivariate analyses demonstrated that access to dental care, past dental visits, age and SRGH were significantly associated with SROH (P \u3c 0.05). Multivariate analyses demonstrated a strong association between access to dental care and good/excellent SROH. About half of Hmong adults rated their oral health and access to dental care as poor. Dental insurance, access to dental care, past preventive dental/physician visits and SRGH were associated with SROH

Redistribution of multi-phase particulate organic carbon in a marine shelf and canyon system during an exceptional river flood: Effects of Typhoon Morakot on the Gaoping River-Canyon system

This is the final published version of the article. It was originally published in Marine Geology (Sparkes RB, Lin I-T, Hovius N, Galy A, Liu JT, Xu X, Yang R, Marine Geology 2015, 363, 191–201, doi:10.1016/j.margeo.2015.02.013) http://dx.doi.org/10.1016/j.margeo.2015.02.013Volumetrically, turbidity currents are the prime suppliers of sediment to the deep sea, and conveyors of organic carbon from the terrestrial biosphere and submarine shelf into marine depositional basins. They result from complex processes of erosion, transport and deposition that can be difficult to study in detail. Here we present data from the Gaoping submarine canyon system, off SW Taiwan, which was perturbed in 2009 by the addition of flood deposits following Typhoon Morakot and sampled by gravity coring less than 2 months after the event. We use the different origins of organic carbon, distinguished by their carbon and nitrogen concentrations and δ13C and δ15N isotopic composition, to compare and contrast standard and extreme sedimentological conditions. Using well-constrained end-members, the results were de-convolved into inputs of metamorphic and sedimentary fossil organic carbon eroded within the Gaoping River basin, terrestrial non-fossil carbon and marine organic matter. In the upper Gaoping Canyon, sedimentation is dominated by the highly-localised hyperpycnal input of river washload and submarine sediment slumps, each associated with extensive flooding following Typhoon Morakot, whilst the shelf experienced deposition and reworking of hemi-pelagic marine sediments. A terrestrial signal is also found in the core-top of a fine-grained shelf sample over 20 km from the Gaoping Canyon, in a region normally dominated by marine carbon deposition, showing that Morakot was an unusually large flood event. Conversely, sediment from just above the canyon thalweg contains 0.23 wt.% depth-averaged marine organic carbon (37% of the TOC content) implying that terrestrial OC-dominated turbidites are tightly constrained within the canyon. Hyperpycnal processes can lead to the rapid and efficient transport of both terrestrial and submarine sediments to more permanent burial locations.RS was supported by an Engineering and Physical Sciences Research Council (EP/P502365/1 and EP/P504120/1) studentship. JTL was supported by grant number NSC95-2745-M-110-001 for the Fate of Terrestrial–Nonterrestrial Sediments in High Yield Particle–Export River–Sea Systems Program, which provided the cores in this study. We thank Peter Talling for his insightful and constructive comments on the manuscript and a further, anonymous reviewer for generous endorsement

Clinical relevance of integrin alpha 4 in gastrointestinal stromal tumours

The molecular mechanisms for the dissemination and metastasis of gastrointestinal stromal tumours (GIST) are incompletely understood. The purpose of the study was to investigate the clinical relevance of integrin alpha 4 (ITGA4) expression in GIST. GIST transcriptomes were first compared with transcriptomes of other types of cancer and histologically normal gastrointestinal tract tissue in the MediSapiens in silico database. ITGA4 was identified as an unusually highly expressed gene in GIST. Therefore, the effects of ITGA4 knock-down and selective integrin alpha 4 beta 1 (VLA-4) inhibitors on tumour cell proliferation and invasion were investigated in three GIST cell lines. In addition, the prognostic role of ITGA4 expression in cancer cells was investigated in a series of 147 GIST patients with immunohistochemistry. Inhibition of ITGA4-related signalling decreased GIST cell invasion in all investigated GIST cell lines. ITGA4 protein was expressed in 62 (42.2%) of the 147 GISTs examined, and expression was significantly associated with distant metastases during the course of the disease and several adverse prognostic features. Patients whose GIST expressed strongly ITGA4 had unfavourable GIST-specific survival and overall survival compared to patients with low or no ITGA4 expression. Taken together, ITGA4 is an important integrin in the molecular pathogenesis of GIST and may influence their clinical behaviour.Peer reviewe

Asymptomatic members with SOD1 mutation in a large kindred with familial amyotrophic lateral sclerosis have abnormal water diffusion characterisitcs

DTI was carried out in FALS/SALS patients and familial members with SOD1 mutation (AFALS) who may be in a pre-symptomatic phase of ALS. The changes in FA and TT were investigated in CBT/CST and in whole brain. In FALS/SALS, diffusion pattern changes were found in cerebral peduncle, internal capsule, sub-cortical white matter, cerebellum and frontal lobe while in AFALS, abnormal pattern could also be detected in the cerebral peduncle, cerebellum and frontal lobe but with a smaller extent. Our study indicates that DTI can show early diffusion changes in members with SOD1 mutation in FALS prior to symptom-onset.published_or_final_versio

Experimental demonstration of a hyper-entangled ten-qubit Schr\"odinger cat state

Coherent manipulation of an increasing number of qubits for the generation of entangled states has been an important goal and benchmark in the emerging field of quantum information science. The multiparticle entangled states serve as physical resources for measurement-based quantum computing and high-precision quantum metrology. However, their experimental preparation has proved extremely challenging. To date, entangled states up to six, eight atoms, or six photonic qubits have been demonstrated. Here, by exploiting both the photons' polarization and momentum degrees of freedom, we report the creation of hyper-entangled six-, eight-, and ten-qubit Schr\"odinger cat states. We characterize the cat states by evaluating their fidelities and detecting the presence of genuine multi-partite entanglement. Small modifications of the experimental setup will allow the generation of various graph states up to ten qubits. Our method provides a shortcut to expand the effective Hilbert space, opening up interesting applications such as quantum-enhanced super-resolving phase measurement, graph-state generation for anyonic simulation and topological error correction, and novel tests of nonlocality with hyper-entanglement.Comment: 11 pages, 5 figures, comments welcom

Intelligent Financial Fraud Detection Practices: An Investigation

Financial fraud is an issue with far reaching consequences in the finance industry, government, corporate sectors, and for ordinary consumers. Increasing dependence on new technologies such as cloud and mobile computing in recent years has compounded the problem. Traditional methods of detection involve extensive use of auditing, where a trained individual manually observes reports or transactions in an attempt to discover fraudulent behaviour. This method is not only time consuming, expensive and inaccurate, but in the age of big data it is also impractical. Not surprisingly, financial institutions have turned to automated processes using statistical and computational methods. This paper presents a comprehensive investigation on financial fraud detection practices using such data mining methods, with a particular focus on computational intelligence-based techniques. Classification of the practices based on key aspects such as detection algorithm used, fraud type investigated, and success rate have been covered. Issues and challenges associated with the current practices and potential future direction of research have also been identified.Comment: Proceedings of the 10th International Conference on Security and Privacy in Communication Networks (SecureComm 2014

Lentiviral Vector Delivery of Human Interleukin-7 (hIL-7) to Human Immune System (HIS) Mice Expands T Lymphocyte Populations

Genetically modified mice carrying engrafted human tissues provide useful models to study human cell biology in physiologically relevant contexts. However, there remain several obstacles limiting the compatibility of human cells within their mouse hosts. Among these is inadequate cross-reactvitiy between certain mouse cytokines and human cellular receptors, depriving the graft of important survival and growth signals. To circumvent this problem, we utilized a lentivirus-based delivery system to express physiologically relevant levels of human interleukin-7 (hIL-7) in Rag2-/-γc-/- mice following a single intravenous injection. hIL-7 promoted homeostatic proliferation of both adoptively transferred and endogenously generated T-cells in Rag2-/-γc-/- Human Immune System (HIS) mice. Interestingly, we found that hIL-7 increased T lymphocyte numbers in the spleens of HIV infected HIS mice without affecting viral load. Taken together, our study unveils a versatile approach to deliver human cytokines to HIS mice, to both improve engraftment and determine the impact of cytokines on human diseases

Upregulated sirtuin 1 by miRNA-34a is required for smooth muscle cell differentiation from pluripotent stem cells

© 2015 Macmillan Publishers Limited. All rights reserved. microRNA-34a (miR-34a) and sirtuin 1 (SirT1) have been extensively studied in tumour biology and longevityaging, but little is known about their functional roles in smooth muscle cell (SMC) differentiation from pluripotent stem cells. Using well-established SMC differentiation models, we have demonstrated that miR-34a has an important role in SMC differentiation from murine and human embryonic stem cells. Surprisingly, deacetylase sirtuin 1 (SirT1), one of the top predicted targets, was positively regulated by miR-34a during SMC differentiation. Mechanistically, we demonstrated that miR-34a promoted differentiating stem cells' arrest at G0G1 phase and observed a significantly decreased incorporation of miR-34a and SirT1 RNA into Ago2-RISC complex upon SMC differentiation. Importantly, we have identified SirT1 as a transcriptional activator in the regulation of SMC gene programme. Finally, our data showed that SirT1 modulated the enrichment of H3K9 tri-methylation around the SMC gene-promoter regions. Taken together, our data reveal a specific regulatory pathway that miR-34a positively regulates its target gene SirT1 in a cellular context-dependent and sequence-specific manner and suggest a functional role for this pathway in SMC differentiation from stem cells in vitro and in vivo