Modeling Turbidity Currents Using the Multiple-state Discrete-time Markov Chain Approach

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

The Influence of Dopamine Receptor D4 Polymorphism on Resting EEG in Healthy Young Females

The polymorphism of variable number of tandem repeat (VNTR) in dopamine receptor D4 (DRD4) gene exon III has been linked to various neuro-psychiatric conditions with disinhibition/impulsivity as one of the core features. This study examined the modulatory effects of long-allele variant of DRD4 VNTR on the regional neural activity as well as inter-regional neural interactions in a young female population. Blood sample and resting state eyes-closed EEG signals were collected in 233 healthy females, stratified into two groups by polymerase chain reaction: long-allele carriers (>4- repeat) and non-carriers (<=4-repeat/<=4-repeat). The values of mean power of 18 electrodes and mutual information of 38 channel pairs across theta, alpha, and beta frequencies were analyzed. Our connectivity analysis was based on information theory, which combined Morlet wavelet transform and mutual information calculation. Between-group differences of regional power and connectivity strength were quantified by independent t-test, while between-group differences in global trends were examined by non-parametric analyses. We noticed that DRD4 VNTR long-allele was associated with decreased global connectivity strength (from non-parametric analysis), especially over bi-frontal, biparietal and right fronto-parietal and right fronto-temporal connections (from independent t-tests). The between-group differences in regional power were not robust. Our findings fit with the networks of response inhibition, providing evidence bridging DRD4 long-allele and disinhibition/impulsivity in neuropsychiatric disorders. We suggest future DRD4 studies of imaging genetics incorporate connectivity analysis to unveil its impact on cerebral network

Pulmonary IL- 33 orchestrates innate immune cells to mediate respiratory syncytial virus- evoked airway hyperreactivity and eosinophilia

BackgroundRespiratory syncytial virus (RSV) infection is epidemiologically linked to asthma. During RSV infection, IL- 33 is elevated and promotes immune cell activation, leading to the development of asthma. However, which immune cells are responsible for triggering airway hyperreactivity (AHR), inflammation and eosinophilia remained to be clarified. We aimed to elucidate the individual roles of IL- 33- activated innate immune cells, including ILC2s and ST2+ myeloid cells, in RSV infection- triggered pathophysiology.MethodsThe role of IL- 33/ILC2 axis in RSV- induced AHR inflammation and eosinophilia were evaluated in the IL- 33- deficient and YetCre- 13 Rosa- DTA mice. Myeloid- specific, IL- 33- deficient or ST2- deficient mice were employed to examine the role of IL- 33 and ST2 signaling in myeloid cells.ResultsWe found that IL- 33- activated ILC2s were crucial for the development of AHR and airway inflammation, during RSV infection. ILC2- derived IL- 13 was sufficient for RSV- driven AHR, since reconstitution of wild- type ILC2 rescued RSV- driven AHR in IL- 13- deficient mice. Meanwhile, myeloid cell- derived IL- 33 was required for airway inflammation, ST2+ myeloid cells contributed to exacerbation of airway inflammation, suggesting the importance of IL- 33 signaling in these cells. Local and peripheral eosinophilia is linked to both ILC2 and myeloid IL- 33 signaling.ConclusionsThis study highlights the importance of IL- 33- activated ILC2s in mediating RSV- triggered AHR and eosinophilia. In addition, IL- 33 signaling in myeloid cells is crucial for airway inflammation.Respiratory syncytial virus induces ILC2 to produce IL- 5 and IL- 13 through IL- 33, which is crucial for the development of airway hyperreactivity and airway inflammation. Myeloid cell- derived IL- 33 and suppression of tumorigenicity 2- positive myeloid cells contribute to cytokine production and cellular inflammation in airway. Both ILC2 and myeloid cell IL- 33 signaling contribute to local and peripheral eosinophilia.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/154896/1/all14091.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154896/2/all14091-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/154896/3/all14091_am.pd

Seismologically determined bedload flux during the typhoon season

Continuous seismic records near river channels can be used to quantify the energy induced by river sediment transport. During the 2011 typhoon season, we deployed a seismic array along the Chishan River in the mountain area of southern Taiwan, where there is strong variability in water discharge and high sedimentation rates. We observe hysteresis in the high-frequency (5-15 Hz) seismic noise level relative to the associated hydrological parameters. In addition, our seismic noise analysis reveals an asymmetry and a high coherence in noise cross-correlation functions for several station pairs during the typhoon passage, which corresponds to sediment particles and turbulent flows impacting along the riverbed where the river bends sharply. Based on spectral characteristics of the seismic records, we also detected 20 landslide/debris flow events, which we use to estimate the sediment supply. Comparison of sediment flux between seismologically determined bedload and derived suspended load indicates temporal changes in the sediment flux ratio, which imply a complex transition process from the bedload regime to the suspension regime between typhoon passage and off-typhoon periods. Our study demonstrates the possibility of seismologically monitoring river bedload transport, thus providing valuable additional information for studying fluvial bedrock erosion and mountain landscape evolution. S ediment transport and bedrock incision are critical parameters in the study of landscape evolution 1-5 and are needed for diverse applications including sedimentation engineering, river restoration, and flood hazard mitigation. However, their assessment with traditional geomorphic methods is rarely possible. For example, most measurement techniques (e.g., sediment traps) are in situ and cannot be used in extreme flow conditions. Thus, no information is available during typhoon events when sediment is most mobile and erosion processes are strongest. A potential solution to this data gap is to use remote monitoring by geophones or seismometers that capture the ground vibration caused by surface processes. In the last decade, seismic observations have been widely used to study earth surface processes such as landslides 6-8 , rockslides 9 , rock falls 10 and debris flows 11 , which we collectively term &apos;landquakes&apos; in this study. Recently, a seismological study has found a correlation between observations of short-period (#1 sec) seismic noise near rivers and hydrological data, and observed a significant increase in highfrequency seismic energy during the summer monsoon season 12 . Based on seasonal variability in seismic noise levels for a given discharge, termed hysteresis, they suggested that a large portion of this seismic noise is likely due to bedload transport. Other studies similarly observed that the amplitudes of high-frequency seismic noise nearby gravel-rich mountain streams in Taiwan are higher on the rising limb than on the falling limb of each storm event (for the same discharge) Results Characteristics of the river seismic noise. To study the characteristics (e.g., frequency range and spatial distribution) of river-generated seismic noise, especially during the passage of Typhoon Nanmadol on 28-2

Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

<p>Abstract</p> <p>Background</p> <p>Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of a predicate (verb) and several arguments (noun phrases, adverbial phrases, etc.) with different semantic roles, including main arguments (agent or patient) as well as adjunct arguments (time, manner, or location). PropBank is the most widely used PAS corpus and annotation format in the newswire domain. In the biomedical field, however, more detailed and restrictive PAS annotation formats such as PASBio are popular. Unfortunately, due to the lack of an annotated PASBio corpus, no publicly available machine-learning (ML) based SRL systems based on PASBio have been developed. In previous work, we constructed a biomedical corpus based on the PropBank standard called BioProp, on which we developed an ML-based SRL system, BIOSMILE. In this paper, we aim to build a system to convert BIOSMILE's BioProp annotation output to PASBio annotation. Our system consists of BIOSMILE in combination with a BioProp-PASBio rule-based converter, and an additional semi-automatic rule generator.</p> <p>Results</p> <p>Our first experiment evaluated our rule-based converter's performance independently from BIOSMILE performance. The converter achieved an F-score of 85.29%. The second experiment evaluated combined system (BIOSMILE + rule-based converter). The system achieved an F-score of 69.08% for PASBio's 29 verbs.</p> <p>Conclusion</p> <p>Our approach allows PAS conversion between BioProp and PASBio annotation using BIOSMILE alongside our newly developed semi-automatic rule generator and rule-based converter. Our system can match the performance of other state-of-the-art domain-specific ML-based SRL systems and can be easily customized for PASBio application development.</p

Multiple Lineages of Human Breast Cancer Stem/Progenitor Cells Identified by Profiling with Stem Cell Markers

Heterogeneity of cancer stem/progenitor cells that give rise to different forms of cancer has been well demonstrated for leukemia. However, this fundamental concept has yet to be established for solid tumors including breast cancer. In this communication, we analyzed solid tumor cancer stem cell markers in human breast cancer cell lines and primary specimens using flow cytometry. The stem/progenitor cell properties of different marker expressing-cell populations were further assessed by in vitro soft agar colony formation assay and the ability to form tumors in NOD/SCID mice. We found that the expression of stem cell markers varied greatly among breast cancer cell lines. In MDA-MB-231 cells, PROCR and ESA, instead of the widely used breast cancer stem cell markers CD44+/CD24-/low and ALDH, could be used to highly enrich cancer stem/progenitor cell populations which exhibited the ability to self renew and divide asymmetrically. Furthermore, the PROCR+/ESA+ cells expressed epithelial-mesenchymal transition markers. PROCR could also be used to enrich cells with colony forming ability from MB-361 cells. Moreover, consistent with the marker profiling using cell lines, the expression of stem cell markers differed greatly among primary tumors. There was an association between metastasis status and a high prevalence of certain markers including CD44+/CD24−/low, ESA+, CD133+, CXCR4+ and PROCR+ in primary tumor cells. Taken together, these results suggest that similar to leukemia, several stem/progenitor cell-like subpopulations can exist in breast cancer

HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features

<p>Abstract</p> <p>Background</p> <p>The genetic factors leading to hypertension have been extensively studied, and large numbers of research papers have been published on the subject. One of hypertension researchers' primary research tasks is to locate key hypertension-related genes in abstracts. However, gathering such information with existing tools is not easy: (1) Searching for articles often returns far too many hits to browse through. (2) The search results do not highlight the hypertension-related genes discovered in the abstract. (3) Even though some text mining services mark up gene names in the abstract, the key genes investigated in a paper are still not distinguished from other genes. To facilitate the information gathering process for hypertension researchers, one solution would be to extract the key hypertension-related genes in each abstract. Three major tasks are involved in the construction of this system: (1) gene and hypertension named entity recognition, (2) section categorization, and (3) gene-hypertension relation extraction.</p> <p>Results</p> <p>We first compare the retrieval performance achieved by individually adding template features and position features to the baseline system. Then, the combination of both is examined. We found that using position features can almost double the original AUC score (0.8140vs.0.4936) of the baseline system. However, adding template features only results in marginal improvement (0.0197). Including both improves AUC to 0.8184, indicating that these two sets of features are complementary, and do not have overlapping effects. We then examine the performance in a different domain--diabetes, and the result shows a satisfactory AUC of 0.83.</p> <p>Conclusion</p> <p>Our approach successfully exploits template features to recognize true hypertension-related gene mentions and position features to distinguish key genes from other related genes. Templates are automatically generated and checked by biologists to minimize labor costs. Our approach integrates the advantages of machine learning models and pattern matching. To the best of our knowledge, this the first systematic study of extracting hypertension-related genes and the first attempt to create a hypertension-gene relation corpus based on the GAD database. Furthermore, our paper proposes and tests novel features for extracting key hypertension genes, such as relative position, section, and template features, which could also be applied to key-gene extraction for other diseases.</p

High wintertime particulate matter pollution over an offshore island (Kinmen) off southeastern China: an overview

Both the Yangtze River Delta (YRD) and the Pearl River Delta (PRD), the two most rapidly developing areas in eastern China, have suffered from serious air pollution, and thus, numerous investigations were devoted to studying these problems. Other areas in eastern China have received less attention despite similar rapid development in their industries and economy. In this study, we analyzed air‐quality data from Kinmen Island (24°27′26′′N, 118°19′36′′E) located off Fujian Province and between the two above‐mentioned deltas. Our results clearly show that the study area is experiencing serious air quality deterioration. Particularly, high levels of suspended particulate matter (PM) were observed during winter, when the northeasterly monsoon prevails. For example, concentrations of wintertime PM10 (particles ≤ 10 mm in diameter) frequently exceeded 100 mg/m3 in the last three years. In addition to the air‐quality data analysis, aerosol samples were collected between 22 November 2007 and 6 March 2008 and subjected to chemical analyses of various species. Our findings show that the three principal PM components include organic, mineral, and sulfate species with moderate to minor fractions of nitrate, sea salt, elemental carbon, and trace metal oxides. The high PM levels observed over the island may be partly attributed to the transport from a mixed‐type industrial area located ∼40 km northeast of Kinmen. Our study could partially fill the air quality data gap between the YRD and PRD regions, and highlight the alarming fact that air pollution has gradually expanded along eastern China’s coastal zone