A text-mining system for extracting metabolic reactions from full-text articles

Background: Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway—metabolic pathways—has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction information from free text that scores different permutations of assigned entities (enzymes and metabolites) within a given sentence based on the presence and location of stemmed keywords. This method extends an approach that has proved effective in the context of the extraction of protein–protein interactions. Results: When evaluated on a set of manually-curated metabolic pathways using standard performance criteria, our method performs surprisingly well. Precision and recall rates are comparable to those previously achieved for the well-known protein-protein interaction extraction task. Conclusions: We conclude that automated metabolic pathway construction is more tractable than has often been assumed, and that (as in the case of protein–protein interaction extraction) relatively simple text-mining approaches can prove surprisingly effective. It is hoped that these results will provide an impetus to further research and act as a useful benchmark for judging the performance of more sophisticated methods that are yet to be developed

A Side-channel Analysis of Sensor Multiplexing for Covert Channels and Application Fingerprinting on Mobile Devices

Mobile devices often distribute measurements from a single physical sensor to multiple applications using software-based multiplexing. On Android devices, the highest requested sampling frequency is returned to all applications even if other applications request measurements at lower frequencies. In this paper, we comprehensively demonstrate that this design choice exposes practically exploitable side-channels based on frequency-key shifting. By carefully modulating sensor sampling frequencies in software, we show that unprivileged malicious applications can construct reliable spectral covert channels that bypass existing security mechanisms. Moreover, we present a novel variant that allows an unprivileged malicious observer app to fingerprint other victim applications at a coarse-grained level. Both techniques do not impose any special assumptions beyond accessing standard mobile services from unprivileged applications. As such, our work reports side-channel vulnerabilities that exploit subtle yet insecure design choices in mobile sensor stacks

ZKP Enabled Identity and Reputation Verification in P2P Marketplaces

In the realm of Distributed Ledger Technology, privacy and regulatory challenges loom large for marketplaces. Regulation requires to conduct Know Your Customer (KYC) procedures to verify the identity of participants, while privacy concerns necessitate the protection of personal data. Current approaches to KYC are inefficient and are potentially even harmful to privacy due to centralization and data exposure.This paper proposes a zero-knowledge proof enabled KYC scheme, utilizing Soulbound Tokens (SBT) to create a discreet, compliant, and secure KYC process. We present a privacy-preserving mechanism that shares only essential information while adhering to Self-Sovereign Identity (SSI) principles, placing users in the full control of their data. The proposed scheme further introduces the usage of SBTs for reputation to incentivize good conduct and build trust within marketplaces

Ecologically significant invasive species, a monitoring framework for natural resource management groups in Western Australia

This publication is the result of the project titled \u27Resource Condition Monitoring for Ecologically Significant Species. The project identified and addressed key weaknesses in the State\u27s capacity to monitor threat posed by ecologically significant species. The invasive species monitoring framework for Western Australia developed through this project, along with the rationales underpinning the deign, are presented in this report.https://researchlibrary.agric.wa.gov.au/bulletins/1164/thumbnail.jp

Birth weight and stuttering:Evidence from three birth cohorts

Purpose Previous studies have produced conflicting results with regard to the association between birth weight and developmental stuttering. This study sought to determine whether birth weight was associated with childhood and/or adolescent stuttering in three British birth cohort samples. Methods Logistic regression analyses were carried out on data from the Millenium Cohort Study (MCS), British Cohort Study (BCS70) and National Child Development Study (NCDS), whose initial cohorts comprised over 56,000 individuals. The outcome variables were parent-reported stuttering in childhood or in adolescence; the predictors, based on prior research, were birth weight, sex, multiple birth status, vocabulary score and mother's level of education. Birth weight was analysed both as a categorical variable (low birth weight, <2500 g; normal range; high birth weight, ≥ 4000 g) and as a continuous variable. Separate analyses were carried out to determine the impact of birth weight and the other predictors on stuttering during childhood (age 3, 5 and 7 and MCS, BCS70 and NCDS, respectively) or at age 16, when developmental stuttering is likely to be persistent. Results None of the multivariate analyses revealed an association between birth weight and parent-reported stuttering. Sex was a significant predictor of stuttering in all the analyses, with males 1.6 to 3.6 times more likely than females to stutter. Conclusion Our results suggest that birth weight is not a clinically useful predictor of childhood or persistent stuttering

Confronting 3 Dimensional Time-dependent Jet Simulations with HST Observations

We perform state-of-the-art, 3D, time-dependent simulations of magnetized disk winds, carried out to simulation scales of 60 Astronomical Units, in order to confront optical HST observations of protostellar jets. We ``observe'' the optical forbidden line emission produced by shocks within our simulated jets and compare these with actual observations. Our simulations reproduce the rich structure of time varying jets, including jet rotation far from the source, an inner (up to 400 km/s) and outer (less than 100 km/s) component of the jet, and jet widths of up to 20 Astronomical Units in agreement with observed jets. These simulations when compared with the data are able to constrain disk wind models. In particular, models featuring a disk magnetic field with a modest radial spatial variation across the disk are favored.Comment: Accepted for publication in Ap

Creating and Using Learning Objects in Qualitative Research Education

Based upon the lessons learned and the educational materials generated from a doctoral course on qualitative data analysis, a group of doctoral students, their professor, and a linguistics consultant launched an on- going project to create a series of reusable learning objects designed to help other groups of students and professors learn how to analyze qualitative data. The results of the first six months of this project are shared, as the team describes how they have begun to use instructional design and software applications to create a digital learning environment in the form of a series of activities engineered to help analysts learn how to master grounded theory open codin

Increased ice flow in Western Palmer Land linked to ocean melting

A decrease in the mass and volume of Western Palmer Land has raised the prospect that ice speed has increased in this marine-based sector of Antarctica. To assess this possibility, we measure ice velocity over 25 years using satellite imagery and an optimized modeling approach. More than 30 unnamed outlet glaciers drain the 800 km coastline of Western Palmer Land at speeds ranging from 0.5 to 2.5 m/d, interspersed with near-stagnant ice. Between 1992 and 2015, most of the outlet glaciers sped up by 0.2 to 0.3 m/d, leading to a 13% increase in ice flow and a 15 km3/yr increase in ice discharge across the sector as a whole. Speedup is greatest where glaciers are grounded more than 300 m below sea level, consistent with a loss of buttressing caused by ice shelf thinning in a region of shoaling warm circumpolar water

The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase

Protoporphyrinogen IX oxidase (PPO), the last enzyme that is common to both chlorophyll and heme biosynthesis pathways, catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX. PPO has several isoforms, including the oxygen-dependent HemY and an oxygen-independent enzyme, HemG. However, most cyanobacteria encode HemJ, the least characterized PPO form. We have characterized HemJ from the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803) as a bona fide PPO; HemJ down-regulation resulted in accumulation of tetrapyrrole precursors and in the depletion of chlorophyll precursors. The expression of FLAG-tagged Synechocystis 6803 HemJ protein (HemJ.f) and affinity isolation of HemJ.f under native conditions revealed that it binds heme b. The most stable HemJ.f form was a dimer, and higher oligomeric forms were also observed. Using both oxygen and artificial electron acceptors, we detected no enzymatic activity with the purified HemJ.f, consistent with the hypothesis that the enzymatic mechanism for HemJ is distinct from those of other PPO isoforms. The heme absorption spectra and distant HemJ homology to several membrane oxidases indicated that the heme in HemJ is redox-active and involved in electron transfer. HemJ was conditionally complemented by another PPO, HemG from Escherichia coli. If grown photoautotrophically, the complemented strain accumulated tripropionic tetrapyrrole harderoporphyrin, suggesting a defect in enzymatic conversion of coproporphyrinogen III to protoporphyrinogen IX, catalyzed by coproporphyrinogen III oxidase (CPO). This observation supports the hypothesis that HemJ is functionally coupled with CPO and that this coupling is disrupted after replacement of HemJ by HemG