Vertical variance analysis of geomagnetic disturbance during solar cycle 23

300-309The geomagnetic field consists of temporal variations induced primarily by the variations in the solar wind and embedded interplanetary magnetic field. 34 stations across the Earth have been categorized in this paper on the basis of their geomagnetic disturbance during solar cycle 23 (1997-2008). The Vertical Variance (VV) disturbance quantifier has been used to develop such profile. The latitude profile of geomagnetic disturbance has been found to exhibit a typical ‘Knee’ behaviour, with the fluctuation content seen to rise sharply beyond this critical latitude determined near 52° latitude. The increasing trend in geomagnetic fluctuation content however is seen to end around the auroral oval beyond where abrupt variations has been observed indicating the transition from closed to open magnetic field lines. The physical mechanism behind this trend has also been explored. The VV analysis of geomagnetic disturbance has revealed prominent features of solar wind – magnetosphere coupling

Vertical variance analysis of geomagnetic disturbance during solar cycle 23

The geomagnetic field consists of temporal variations induced primarily by the variations in the solar wind and embedded interplanetary magnetic field. 34 stations across the Earth have been categorized in this paper on the basis of their geomagnetic disturbance during solar cycle 23 (1997-2008). The Vertical Variance (VV) disturbance quantifier has been used to develop such profile. The latitude profile of geomagnetic disturbance has been found to exhibit a typical 'Knee' behaviour, with the fluctuation content seen to rise sharply beyond this critical latitude determined near 52° latitude. The increasing trend in geomagnetic fluctuation content however is seen to end around the auroral oval beyond where abrupt variations has been observed indicating the transition from closed to open magnetic field lines. The physical mechanism behind this trend has also been explored. The VV analysis of geomagnetic disturbance has revealed prominent features of solar wind – magnetosphere coupling

Reorganization of a 2D disordered granular medium due to a small local cyclic perturbation

We measure experimentally the rearrangements due to a small localized cyclic displacement applied to a packing of rigid grains under gravity in a 2D geometry. We analyze the evolution of the response to this perturbation by considering the individual particle displacement and the coarse grained displacement field, as well as the mean packing fraction and coordination number. We find that the displacement response is rather long ranged, and evolves considerably with the number of cycles. We show that a small difference in the preparation method (induced by tapping the container) leads to a significant modification in the response though the packing fraction changes are minute. Not only the initial response but also its further evolution change with preparation, demonstrating that the system still retains a memory of the initial preparation after many cycles. Nevertheless, after a sufficient number of cycles, the displacement response for both preparation methods converges to a nearly radial field with a 1/r decay from the perturbation source. The observed differences between the preparation methods seem to be related to the changes in the coordination number (which is more sensitive to the evolution of the packing than the packing fraction). Specifically, it may be understood as an effect of the breaking of local arches, which affects the lateral transmission of forces.Comment: 13 pages, revised and resubmitted to J. Stat. Mech.: Theory and Exp. (JSTAT

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin with gemtuzumab ozogamicin improves event-free survival in younger patients with newly diagnosed aml and overall survival in patients with npm1 and flt3 mutations

Purpose To determine the optimal induction chemotherapy regimen for younger adults with newly diagnosed AML without known adverse risk cytogenetics. Patients and Methods One thousand thirty-three patients were randomly assigned to intensified (fludarabine, cytarabine, granulocyte colony-stimulating factor, and idarubicin [FLAG-Ida]) or standard (daunorubicin and Ara-C [DA]) induction chemotherapy, with one or two doses of gemtuzumab ozogamicin (GO). The primary end point was overall survival (OS). Results There was no difference in remission rate after two courses between FLAG-Ida + GO and DA + GO (complete remission [CR] + CR with incomplete hematologic recovery 93% v 91%) or in day 60 mortality (4.3% v 4.6%). There was no difference in OS (66% v 63%; P = .41); however, the risk of relapse was lower with FLAG-Ida + GO (24% v 41%; P < .001) and 3-year event-free survival was higher (57% v 45%; P < .001). In patients with an NPM1 mutation (30%), 3-year OS was significantly higher with FLAG-Ida + GO (82% v 64%; P = .005). NPM1 measurable residual disease (MRD) clearance was also greater, with 88% versus 77% becoming MRD-negative in peripheral blood after cycle 2 (P = .02). Three-year OS was also higher in patients with a FLT3 mutation (64% v 54%; P = .047). Fewer transplants were performed in patients receiving FLAG-Ida + GO (238 v 278; P = .02). There was no difference in outcome according to the number of GO doses, although NPM1 MRD clearance was higher with two doses in the DA arm. Patients with core binding factor AML treated with DA and one dose of GO had a 3-year OS of 96% with no survival benefit from FLAG-Ida + GO. Conclusion Overall, FLAG-Ida + GO significantly reduced relapse without improving OS. However, exploratory analyses show that patients with NPM1 and FLT3 mutations had substantial improvements in OS. By contrast, in patients with core binding factor AML, outcomes were excellent with DA + GO with no FLAG-Ida benefit

Fat-Specific Protein 27/CIDEC Promotes Development of Alcoholic Steatohepatitis in Mice and Humans

BACKGROUND &amp; AIMS: Alcoholic steatohepatitis (ASH) is the progressive form of alcoholic liver disease and may lead to cirrhosis and hepatocellular carcinoma. We studied mouse models and human tissues to identify molecules associated with ASH progression and focused on the mouse fat-specific protein 27 (FSP-27)/human cell death-inducing DFF45-like effector C (CIDEC) protein, which is expressed in white adipose tissues and promotes formation of fat droplets. METHODS: C57BL/6N mice or mice with hepatocyte-specific disruption of Fsp27 (Fsp27(Hep-/-) mice) were fed the Lieber-Decarli ethanol liquid diet (5% ethanol) for 10 days to 12 weeks, followed by 1 or multiple binges of ethanol (5 or 6 g/kg) during the chronic feeding. Some mice were given an inhibitor (GW9662) of peroxisome proliferator-activated receptor gamma (PPARG). Adenoviral vectors were used to express transgenes or small hairpin (sh) RNAs in cultured hepatocytes and in mice. Liver tissue samples were collected from ethanolfed mice or from 31 patients with alcoholic hepatitis (AH) with biopsy-proved ASH and analyzed histologically and immunohistochemically and by transcriptome, immunoblotting, and real-time PCR analyses. RESULTS: Chronic-plus-binge ethanol feeding of mice, which mimics the drinking pattern of patients with AH, produced severe ASH and mild fibrosis. Microarray analyses revealed similar alterations in expression of many hepatic genes in ethanol-fed mice and humans with ASH, including up-regulation of mouse Fsp27 (also called Cidec) and human CIDEC. Fsp27(Hep-/-) mice and mice given injections of adenovirus-Fsp27shRNA had markedly reduced ASH following chronic-plus-binge ethanol feeding. Inhibition of PPARG and cyclic AMP-responsive element binding protein H (CREBH) prevented the increases in Fsp27 alpha and FSP27 beta mRNAs, respectively, and reduced liver injury in this chronic-plusbinge ethanol feeding model. Overexpression of FSP27 and ethanol exposure had synergistic effects in inducing production of mitochondrial reactive oxygen species and damage to hepatocytes in mice. Hepatic CIDEC mRNA expression was increased in patients with AH and correlated with the degree of hepatic steatosis and disease severity including mortality. CONCLUSIONS: In mice, chronic-plus-binge ethanol feeding induces ASH that mimics some histological and molecular features observed in patients with AH. Hepatic expression of FSP27/CIDEC is highly up-regulated in mice following chronic-plus-binge ethanol feeding and in patients with AH; this up-regulation contributes to alcohol-induced liver damage.Intramural NIH HHS [Z01 AA000369-06, Z99 AA999999]; NIAAA NIH HHS [1U01AA021908-01, U01 AA020821, U01 AA021908]SCI(E)[email protected]