Supervised learning for suicidal ideation detection in online user content

Copyright © 2018 Shaoxiong Ji et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Early detection and treatment are regarded as the most effective ways to prevent suicidal ideation and potential suicide attempts-two critical risk factors resulting in successful suicides. Online communication channels are becoming a new way for people to express their suicidal tendencies. This paper presents an approach to understand suicidal ideation through online user-generated content with the goal of early detection via supervised learning. Analysing users' language preferences and topic descriptions reveals rich knowledge that can be used as an early warning system for detecting suicidal tendencies. Suicidal individuals express strong negative feelings, anxiety, and hopelessness. Suicidal thoughts may involve family and friends. And topics they discuss cover both personal and social issues. To detect suicidal ideation, we extract several informative sets of features, including statistical, syntactic, linguistic, word embedding, and topic features, and we compare six classifiers, including four traditional supervised classifiers and two neural network models. An experimental study demonstrates the feasibility and practicability of the approach and provides benchmarks for the suicidal ideation detection on the active online platforms: Reddit SuicideWatch and Twitter

Resampling methods to reduce the selection bias in genetic effect estimation in genome-wide scans

Using the simulated data of Problem 2 for Genetic Analysis Workshop 14 (GAW14), we investigated the ability of three bootstrap-based resampling estimators (a shrinkage, an out-of-sample, and a weighted estimator) to reduce the selection bias for genetic effect estimation in genome-wide linkage scans. For the given marker density in the preliminary genome scans (7 cM for microsatellite and 3 cM for SNP), we found that the two sets of markers produce comparable results in terms of power to detect linkage, localization accuracy, and magnitude of test statistic at the peak location. At the locations detected in the scan, application of the three bootstrap-based estimators substantially reduced the upward selection bias in genetic effect estimation for both true and false positives. The relative effectiveness of the estimators depended on the true genetic effect size and the inherent power to detect it. The shrinkage estimator is recommended when the power to detect the disease locus is low. Otherwise, the weighted estimator is recommended

阿爾泰哈巴河群的沉積時代及其構造背景

Habahe Group mainly consists of elastic sediments, which widely distribute in the Chinese Altai and can provide important constraints on the tectonic evolution of the Central Asian Orogenic Belt (CAOB). However, there are different opinions about its deposition time and tectonic background. Previous studies suggested that the Habahe Group formed in Sinian to Mid-Ordovician or Mid- to Late Ordovician in a passive continental margin. On the other hand, recent geological investigations reveal a long lasting subduction-related setting in the Chinese Altai at least since Cambrian. The current geochronological study for detrital zircons from the Habahe Group reveals that the detrital zircons of individual samples, irrespective of their lithological and metamorphic differences, all show similar age patterns, with the early Paleozoic ( 206Pb/ 238U age = 463 ± 542Ma) grains predominating. The youngest detrital zircons from different samples display similar ages (ca. 470Ma), which may reflect the maximum deposition time of the Habahe Group. Dating of growth rim of detrital zircons from migmatite yielded a Mid-Devonian age (384 ± 6Ma), which was coeval with intrusion of Early to Mid-Devonian granitic plutons in the area and clearly indicates the minimum deposition time of the Hababe Group. Therefore, the deposition time of the Habahe Group can be constrained to be Mid-Ordovician to Early Devonian. Zircon U Pb dating results indicate that the detrital zircons of the Habahe Group are dominated by early Paleozoic grains, with small proportion formed in Precambrian. The early Paleozoic detrital zircons are mostly magmatic in origin, and their less rounded shapes indicate a limited transportation. The age and morphological characteristics of the detrital zircons are consistent with those of detrital zircons in active tectonic settings and indicate that the Chinese Altai was under an active continental margin environment during the Early Paleozoic. 北疆阿爾泰造山帶的哈巴河群變質碎屑巖分布廣泛,其沉積時代和構造環境對于認識中亞造山帶的演化歷史有重要意義。早期研究認為哈巴河群沉積于震旦紀—中奧陶世時期,形成于被動大陸邊緣構造環境。而最近有學者根據中亞造山帶的地質演化背景提出,阿爾泰形成于活動陸緣構造環境。對哈巴河群中碎屑鋯石的年代學研究表明,不同巖性或變質程度不同的樣品碎屑鋯石主要類群具有相似的年齡分布特征,其206Pb/238U 年齡主要介于463～542Ma 之間。在這些樣品中, 最年輕的碎屑鋯石年齡均集中于470Ma 左右,代表了碎屑沉積的時代下限。而哈巴河群混合巖樣品中碎屑鋯石增生邊形成于中泥盆世晚期（384±6Ma）,與侵入該群的早古生代花崗巖的年齡十分接近,大致反映了哈巴河群碎屑巖沉積時代的上限,因此哈巴河群的沉積時代應在早泥盆世—中奧陶世之間。鋯石的形態和內部結構特征顯示哈巴河群的年輕碎屑鋯石類群（463～542Ma）主要為巖漿鋯石,其磨圓度較差,而且在比例上遠高于前寒武紀碎屑鋯石。上述特點與活動大陸邊緣碎屑鋯石類群分布特征完全一致,反映阿爾泰在中奧陶世至早泥盆世可能處于活動大陸邊緣構造環境。postprin

Comparison of family-based association tests in chromosome regions selected by linkage-based confidence intervals

We use the Genetic Analysis Workshop 14 simulated data to explore the effectiveness of a two-stage strategy for mapping complex disease loci consisting of an initial genome scan with confidence interval construction for gene location, followed by fine mapping with family-based tests of association on a dense set of single-nucleotide polymorphisms. We considered four types of intervals: the 1-LOD interval, a basic percentile bootstrap confidence interval based on the position of the maximum Zlr score, and asymptotic and bootstrap confidence intervals based on a generalized estimating equations method. For fine mapping we considered two family-based tests of association: a test based on a likelihood ratio statistic and a transmission-disequilibrium-type test implemented in the software FBAT. In two of the simulation replicates, we found that the bootstrap confidence intervals based on the peak Zlr and the 1-LOD support interval always contained the true disease loci and that the likelihood ratio test provided further strong confirmatory evidence of the presence of disease loci in these regions

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

MicroRNAs targeting oncogenes are down-regulated in pancreatic malignant transformation from benign tumors

BACKGROUND MicroRNA (miRNA) expression profiles have been described in pancreatic ductal adenocarcinoma (PDAC), but these have not been compared with pre-malignant pancreatic tumors. We wished to compare the miRNA expression signatures in pancreatic benign cystic tumors (BCT) of low and high malignant potential with PDAC, in order to identify miRNAs deregulated during PDAC development. The mechanistic consequences of miRNA dysregulation were further evaluated. METHODS Tissue samples were obtained at a tertiary pancreatic unit from individuals with BCT and PDAC. MiRNA profiling was performed using a custom microarray and results were validated using RT-qPCR prior to evaluation of miRNA targets. RESULTS Widespread miRNA down-regulation was observed in PDAC compared to low malignant potential BCT. We show that amongst those miRNAs down-regulated, miR-16, miR-126 and let-7d regulate known PDAC oncogenes (targeting BCL2, CRK and KRAS respectively). Notably, miR-126 also directly targets the KRAS transcript at a "seedless" binding site within its 3'UTR. In clinical specimens, miR-126 was strongly down-regulated in PDAC tissues, with an associated elevation in KRAS and CRK proteins. Furthermore, miR-21, a known oncogenic miRNA in pancreatic and other cancers, was not elevated in PDAC compared to serous microcystic adenoma (SMCA), but in both groups it was up-regulated compared to normal pancreas, implicating early up-regulation during malignant change. CONCLUSIONS Expression profiling revealed 21 miRNAs down-regulated in PDAC compared to SMCA, the most benign lesion that rarely progresses to invasive carcinoma. It appears that miR-21 up-regulation is an early event in the transformation from normal pancreatic tissue. MiRNA expression has the potential to distinguish PDAC from normal pancreas and BCT. Mechanistically the down-regulation of miR-16, miR-126 and let-7d promotes PDAC transformation by post-transcriptional up-regulation of crucial PDAC oncogenes. We show that miR-126 is able to directly target KRAS; re-expression has the potential as a therapeutic strategy against PDAC and other KRAS-driven cancers

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response

How defense genes originated with the evolution of their specific pathogen-responsive traits remains an important problem. It is generally known that a form of duplication can generate new genes, suggesting that a new gene usually evolves from an ancestral gene. However, we show that a new defense gene in plants may evolve by de novo origination, resulting in sophisticated disease-resistant functions in rice. Analyses of gene evolution showed that this new gene, OsDR10, had homologs only in the closest relative, Leersia genus, but not other subfamilies of the grass family; therefore, it is a rice tribe-specific gene that may have originated de novo in the tribe. We further show that this gene may evolve a highly conservative rice-specific function that contributes to the regulation difference between rice and other plant species in response to pathogen infections. Biologic analyses including gene silencing, pathologic analysis, and mutant characterization by transformation showed that the OsDR10-suppressed plants enhanced resistance to a broad spectrum of Xanthomonas oryzae pv. oryzae strains, which cause bacterial blight disease. This enhanced disease resistance was accompanied by increased accumulation of endogenous salicylic acid (SA) and suppressed accumulation of endogenous jasmonic acid (JA) as well as modified expression of a subset of defense-responsive genes functioning both upstream and downstream of SA and JA. These data and analyses provide fresh insights into the new biologic and evolutionary processes of a de novo gene recruited rapidly

A Measurement of Rb using a Double Tagging Method

The fraction of Z to bbbar events in hadronic Z decays has been measured by the OPAL experiment using the data collected at LEP between 1992 and 1995. The Z to bbbar decays were tagged using displaced secondary vertices, and high momentum electrons and muons. Systematic uncertainties were reduced by measuring the b-tagging efficiency using a double tagging technique. Efficiency correlations between opposite hemispheres of an event are small, and are well understood through comparisons between real and simulated data samples. A value of Rb = 0.2178 +- 0.0011 +- 0.0013 was obtained, where the first error is statistical and the second systematic. The uncertainty on Rc, the fraction of Z to ccbar events in hadronic Z decays, is not included in the errors. The dependence on Rc is Delta(Rb)/Rb = -0.056*Delta(Rc)/Rc where Delta(Rc) is the deviation of Rc from the value 0.172 predicted by the Standard Model. The result for Rb agrees with the value of 0.2155 +- 0.0003 predicted by the Standard Model.Comment: 42 pages, LaTeX, 14 eps figures included, submitted to European Physical Journal

Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4  fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation