Enabling Quality Control for Entity Resolution: A Human and Machine Cooperation Framework

Even though many machine algorithms have been proposed for entity resolution, it remains very challenging to find a solution with quality guarantees. In this paper, we propose a novel HUman and Machine cOoperation (HUMO) framework for entity resolution (ER), which divides an ER workload between the machine and the human. HUMO enables a mechanism for quality control that can flexibly enforce both precision and recall levels. We introduce the optimization problem of HUMO, minimizing human cost given a quality requirement, and then present three optimization approaches: a conservative baseline one purely based on the monotonicity assumption of precision, a more aggressive one based on sampling and a hybrid one that can take advantage of the strengths of both previous approaches. Finally, we demonstrate by extensive experiments on real and synthetic datasets that HUMO can achieve high-quality results with reasonable return on investment (ROI) in terms of human cost, and it performs considerably better than the state-of-the-art alternatives in quality control.Comment: 12 pages, 11 figures. Camera-ready version of the paper submitted to ICDE 2018, In Proceedings of the 34th IEEE International Conference on Data Engineering (ICDE 2018

Gene expression profile based classification models of psoriasis

AbstractPsoriasis is an autoimmune disease, which symptoms can significantly impair the patient's life quality. It is mainly diagnosed through the visual inspection of the lesion skin by experienced dermatologists. Currently no cure for psoriasis is available due to limited knowledge about its pathogenesis and development mechanisms. Previous studies have profiled hundreds of differentially expressed genes related to psoriasis, however with no robust psoriasis prediction model available. This study integrated the knowledge of three feature selection algorithms that revealed 21 features belonging to 18 genes as candidate markers. The final psoriasis classification model was established using the novel Incremental Feature Selection algorithm that utilizes only 3 features from 2 unique genes, IGFL1 and C10orf99. This model has demonstrated highly stable prediction accuracy (averaged at 99.81%) over three independent validation strategies. The two marker genes, IGFL1 and C10orf99, were revealed as the upstream components of growth signal transduction pathway of psoriatic pathogenesis

Comprehensive evolutionary analysis of growth-regulating factor gene family revealing the potential molecular basis under multiple hormonal stress in Gramineae crops

Growth-regulating factors (GRFs) are plant-specific transcription factors that contain two highly conserved QLQ and WRC domains, which control a range of biological functions, including leaf growth, floral organ development, and phytohormone signaling. However, knowledge of the evolutionary patterns and driving forces of GRFs in Gramineae crops is limited and poorly characterized. In this study, a total of 96 GRFs were identified from eight crops of Brachypodium distachyon, Hordeum vulgare, Oryza sativa L. ssp. indica, Oryza rufipogon, Oryza sativa L. ssp. japonica, Setaria italic, Sorghum bicolor and Zea mays. Based on their protein sequences, the GRFs were classified into three groups. Evolutionary analysis indicated that the whole-genome or segmental duplication plays an essential role in the GRFs expansion, and the GRFs were negatively selected during the evolution of Gramineae crops. The GRFs protein function as transcriptional activators with distinctive structural motifs in different groups. In addition, the expression of GRFs was induced under multiple hormonal stress, including IAA, BR, GA3, 6BA, ABA, and MeJ treatments. Specifically, OjGRF11 was significantly induced by IAA at 6 h after phytohormone treatment. Transgenic experiments showed that roots overexpressing OjGRF11 were more sensitive to IAA and affect root elongation. This study will broaden our insights into the origin and evolution of the GRF family in Gramineae crops and will facilitate further research on GRF function

Development of Elite BPH-Resistant Wide-Spectrum Restorer Lines for Three and Two Line Hybrid Rice

Hybrid rice has contributed significantly to the world food security. Breeding of elite high-yield, strong-resistant broad-spectrum restorer line is an important strategy for hybrid rice in commercial breeding programs. Here, we developed three elite brown planthopper (BPH)-resistant wide-spectrum restorer lines by pyramiding big-panicle gene Gn8.1, BPH-resistant genes Bph6 and Bph9, fertility restorer genes Rf3, Rf4, Rf5, and Rf6 through molecular marker assisted selection. Resistance analysis revealed that the newly developed restorer lines showed stronger BPH-resistance than any of the single-gene donor parent Luoyang-6 and Luoyang-9. Moreover, the three new restorer lines had broad spectrum recovery capabilities for Honglian CMS, Wild abortive CMS and two-line GMS sterile lines, and higher grain yields than that of the recurrent parent 9,311 under nature field conditions. Importantly, the hybrid crosses also showed good performance for grain yield and BPH-resistance. Thus, the development of elite BPH-resistant wide-spectrum restorer lines has a promising future for breeding of broad spectrum BPH-resistant high-yield varieties

Biomarker records of D5-6 columns in the eastern Antarctic Peninsula waters: responses of planktonic communities and bio-pump structures to sea ice global warming in the past centenary

Molecular biomarkers (e.g., isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) and proxies, such as di-unsaturated to tri-unsaturated highly branched isoprenoids (D/T) ratio, total organic carbon, δ13C and ice-rafted debris (IRD)) were used to reconstruct the dominant phytoplankton (diatoms, dinoflagellates and coccolithophores), phytoplankton and zooplankton productivity, biological pump structure, and archaea assemblage (Euryarchaeota and Crenarchaeota) from a marine sediment core (D5-6) dated with 210Pb (1922–2012). We characterized the environmental response to sea ice variations/global warming off the eastern Antarctic Peninsula. The results showed that (1) the biomarkers brassicasterol (average = 519.79 ng·g−1), dinosterol (average = 129.68 ng·g−1) and C37 alkenones (average = 40.53 ng·g−1) reconstructed phytoplankton (average = 690.00 ng·g−1) and zooplankton (cholesterol average = 669.25 ng·g−1) productivity. The relative contribution to productivity by different phytoplankton groups was diatoms > dinoflagellates > coccolithophores. This is consistent with field surveys showing that diatoms dominate the phytoplankton in waters adjacent to the Antarctic Peninsula. (2) The relative abundances of different highly branched isoprenoids reflected the contributions of sea ice algae and open water phytoplankton (D/T = 1.2–30.15). Phytoplankton productivity and sea ice showed a good linear relationship with a negative correlation, indicating that more open water during periods of warming and reduced sea ice cover led to an enhanced biological pump. (3) Over the past 100 years, phytoplankton productivity and zooplankton biomass increased. This trend was particularly evident in the last 50 years, corresponding to increased global warming, and showed a negative correlation with IRD and D/T. This suggests that with decreasing sea ice coverage in a warming climate, diatom biomass greatly increased. Coccolithophore/diatom values and the ratio of C37 alkenones to total phytoplankton productivity decreased, indicating the proportion of coccolithophores in the phytoplankton community decreased. The reduction in coccolithophores changes the phytoplankton assemblage and affects the overall efficiency of the biological pump and carbon storage. (4) The results also showed that the abundance of iGDGTs and archaea phyla (Euryarchaeota and Crenarchaeota) showed consistent changes over the past 100 years in response to global warming. Since 1972, trends in archaea, phytoplankton and zooplankton showed variations but a consistent decline. Whether their response to the changing climate off the Antarctic Peninsula involves interactions and influence among different marine biological groups remains an open question. As a result of global warming and reductions in Antarctic sea ice, the relative effectiveness of the Antarctic biological pump can significantly affect global ocean carbon storage

Lentivirus-Mediated ERK2 siRNA Reduces Joint Capsule Fibrosis in a Rat Model of Post-Traumatic Joint Contracture

Extracellular signal-regulated kinase (ERK)-2 is presumed to play an important role in the development of post-traumatic joint contractures. Using a rat injury model, we investigated whether treatment with ERK2 small interfering RNA (siRNA) could reduce the extent of joint capsule fibrosis after an induced injury. Rats were separated into three groups (n = 32 each): non-operated control group, operated contracture group and contracture-treatment group. Stable post-traumatic joint contracture was created through surgical intra-articular joint injury followed by eight weeks of immobilization. In the contracture-treatment group, the rats were treated with lentivirus (LV)-mediated ERK2 siRNA at days 3 and 7 post-surgery. The posterior joint capsule was assessed by western blotting, immunohistochemistry and biochemical analysis for changes in ERK2, phosphorylated (p)-ERK2, myofibroblast, total collagen and relative collagen Type III expression level. Biomechanical testing was used to assess the development of flexion contractures. Statistical analysis was performed using an analysis of variance. In the operated contracture group, rats that developed flexion contractures also showed elevated phosphorylated p-ERK2 expression. In the contracture-treatment group, ERK2 siRNA significantly reduced p-ERK2 expression levels, as well as the severity of flexion contracture development (p < 0.01). Myofibroblast numbers and measurements of total collagen content were also significantly reduced following ERK2 siRNA (p < 0.01). Relative collagen type III expression as a proportion of total of Types I and III collagen, however, was significantly increased in response to ERK2 siRNA (p < 0.01). Our findings demonstrate a role for ERK2 in the induction of joint capsule fibrosis after injury. Furthermore, we show that development of flexion contractures and the resultant increase of joint capsule fibrosis can be reduced by LV-mediated ERK2 siRNA treatment

Prevention of Tendon Adhesions by ERK2 Small Interfering RNAs

Tendon adhesions are one of the most concerning complications after surgical repair of flexor tendon injury. Extracellular signal-regulated kinase (ERK) 2 plays crucial roles in fibroblast proliferation and collagen expression which contributes to the formation of tendon adhesions after flexor tendon surgery. Using a chicken model, we have examined the effects of a small interfering RNA (siRNA) targeting ERK2 delivered by a lentiviral system on tendon adhesion formation with an adhesion scoring system, histological assessment, and biomechanical evaluation. It was found that ERK2 siRNA effectively suppressed the increase of fibroblasts and the formation of tendon adhesions (p < 0.05 compared with the control group). Moreover, no statistically significant reduction in breaking force was detected between the ERK2 siRNA group and the control group. These results show that the lentiviral-mediated siRNA system is effective in preventing tendon adhesion formation but not to tendon healing, and may be used for tendon repair after confirmation and improvement by future detailed studies

Fabrication of Hypericin Imprinted Polymer Nanospheres via Thiol-Yne Click Reaction

To fabricate molecularly imprinted polymer nanospheres via click reaction, five different clickable compounds were synthesized and two types of click reactions (azide-alkyne and thiol-yne) were explored. It was found that molecularly imprinted polymer nanospheres could be successfully synthesized via thiol-yne click reaction using 3,5-diethynyl-pyridine (1) as the monomer, tris(3-mercaptopropionate) (tri-thiol, 5) as the crosslinker, and hypericin as the template (MIP–NSHs). The click polymerization completed in merely 4 h to produce the desired MIP–NSHs, which were characterized by FTIR, SEM, DLS, and BET, respectively. The reaction conditions for adsorption capacity and selectivity towards hypericin were optimized, and the MIP–NSHs synthesized under the optimized conditions showed a high adsorption capacity (Q = 6.03 μmol•g−1) towards hypericin. The imprinting factors of MIP–NSHs towards hypericin, protohypericin, and emodin were 2.44, 2.88, and 2.10, respectively