Using the Gene Ontology to Annotate Biomedical Journal Articles

We are creating a gold-standard corpus of manually annotated full-text biomedical journal articles toward natural-language-processing applications. Central to this is our use of entire ontologies of the Open Biomedical Ontologies initiative as well as other terminologies as term sources, in contrast to most other such annotation projects, which have used small, ad hoc schemas. In addition to the standard difficulties in such annotation projects, each of the terminologies we have used has idiosyncrasies and ambiguities that present further challenges to consistent, high-quality annotation of these articles. In this paper we present and discuss the most salient of these with regard to the Gene Ontology that we have encountered and addressed in our annotation guidelines and training. The utility of these guidelines can be seen in the high and still-increasing interannotator-agreement statistics that we continually monitor.
&#xa

Cross-Product Extensions of the Gene Ontology

The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries

Preparation and evaluation of nanocomposite sodalite/-Al2O3 tubular membranes for H2/CO2 separation

Nanocomposite sodalite/ceramic membranes supported on -Al2O3 tubular support were prepared via the pore-plugging hydrothermal (PPH) synthesis protocol using one interruption and two interruption steps. In parallel, thin-film membranes were prepared via the direct hydrothermal synthesis technique. The as-synthesized membranes were evaluated for H2/CO2 separation in the context of pre-combustion CO2 capture. Scanning electron microscopy (SEM) was used to check the surface morphology while x-ray diffraction (XRD) was used to check the crystallinity of the sodalite crystals and as-synthesized membranes. Single gas permeation of H2, CO2, N2 and mixture gas H2/CO2 was used to probe the quality of the membranes. Gas permeation results revealed nanocomposite membrane prepared via the PPH synthesis protocols using two interruption steps displayed the best performance. This was attributed to the enhanced pore-plugging effect of sodalite crystals in the pores of the support after the second interruption step. The nanocomposite membrane displayed H2 permeance of 7.97 107 mols1m2Pa1 at 100 C and 0.48 MPa feed pressure with an ideal selectivity of 8.76. Regarding H2/CO2 mixture, the H2 permeance reduced from 8.03 107 mols1m2Pa1 to 1.06 107 mols1m2Pa1 at 25 C and feed pressure of 0.18 MPa. In the presence of CO2, selectivity of the nanocomposite membrane reduced to 4.24.The Department of Science and Innovation Research Foundation (DSI-NRF) South Africa’s SARChI Clean Coal Technology.http://www.mdpi.com/journal/membranesam2021Chemical Engineerin

Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH4), hydrogen sulfide (H2S), ammonia (NH3), and carbon dioxide (CO2). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H2S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery

Extraterrestrial Amino Acids in the Almahata Sitta Meteorite

Amino acid analysis of a meteorite fragment of asteroid 2008 TC3 called Almahata Sitta was carried out using reverse-phase liquid chromatography coupled with UV fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS) as part of a sample analysis consortium. LC-FD/ToF-MS analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to seven-carbon aliphatic amino acids and one- to three-carbon amines with abundances ranging from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, R-amino-n-butyric acid (beta-ABA), 2-amino-2-methylbutanoic acid (isovaline), and 2-aminopentanoic acid (norvaline) in the meteorite were racemic (D/L approximately 1), indicating that these amino acids are indigenous to the meteorite and not terrestrial contaminants. Several other non-protein amino acids were also identified in the meteorite above background levels including alpha-aminoisobutyric acid (alpha-AIB), 4-amino-2- methylbutanoic acid, 4-amino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. The total abundances of isovaline and alpha-AIB in Almahata Sitta are 1000 times lower than the abundances of these amino acids found in the CM carbonaceous chondrite Murchison. The extremely low abundances and unusual distribution of five carbon amino acids in Almahata Sitta compared to Cl, CM, and CR carbonaceous chondrites may reflect extensive thermal alteration of amino acids on the parent asteroid by partial melting during formation or subsequent impact shock heating. It is also possible that amino acids were synthesized by catalytic reactions on the parent body after asteroid 2008 TC3 cooled to lower temperatures

Mars Sample Handling and Requirements Panel (MSHARP)

In anticipation of the return of samples from Mars toward the end of the first decade of the next century, NASA's Office of Space Sciences chartered a panel to examine how Mars samples should be handled. The panel was to make recommendations in three areas: (1) sample collection and transport back to Earth; (2) certification of the samples as nonhazardous; and (3) sample receiving, curation, and distribution. This report summarizes the findings of that panel. The samples should be treated as hazardous until proven otherwise. They are to be sealed within a canister on Mars, and the canister is not to be opened until within a Biosafety Hazard Level 4 (BSL-4) containment facility here on Earth. This facility must also meet or exceed the cleanliness requirements of the Johnson Space Center (JSC) facility for curation of extraterrestrial materials. A containment facility meeting both these requirements does not yet exist. Hazard assessment and life detection experiments are to be done at the containment facility, while geochemical characterization is being performed on a sterilized subset of the samples released to the science community. When and if the samples are proven harmless, they are to be transferred to a curation facility, such as that at JSC

Proceedings of the 5th Workshop on BioNLP Open Shared Tasks

As part of the BioNLP Open Shared Tasks 2019, the CRAFT Shared Tasks 2019 provides a platform to gauge the state of the art for three fundamental language processing tasks - dependency parse construction, coreference resolution, and ontology concept identification - over full-text biomedical articles.The structural annotation task requires the automatic generation of dependency parses for each sentence of an article given only the article text. The coreference resolution task focuses on linking coreferring base noun phrase mentions into chains using the symmetrical and transitive identity relation. The ontology concept annotation task involves the identification of concept mentions within text using the classes of ten distinct ontologies in the biomedical domain, both unmodified and augmented with extension classes. This paper provides an overview of each task, including descriptions of the data provided to participants and the evaluation metrics used, and discusses participant results relative to baseline performances for each of the three tasks.</p

An Assessment of the Security and Transparency Procedural Components of the Estonian Internet Voting System

The I-Voting system designed and implemented in Estonia is one of the first nationwide Internet voting systems. Since its creation, it has been met with praise but also with close scrutiny. Concerns regarding security breaches have focused on in-person election observations, code reviews and adversarial testing on system components. These concerns have led many to conclude that there are various ways in which insider threats and sophisticated external attacks may compromise the integrity of the system and thus the voting process. In this paper, we examine the procedural components of the I-Voting system, with an emphasis on the controls related to procedural security mechanisms, and on system-transparency measures. Through an approach grounded in primary and secondary data sources, including interviews with key Estonian election personnel, we conduct an initial investigation into the extent to which the present controls mitigate the real security risks faced by the system. The experience and insight we present in this paper will be useful both in the context of the I-Voting system, and potentially more broadly in other voting systems

An Independent Assessment of the Procedural Components of the Estonian Internet Voting System

The I-Voting system that was designed and implemented in Estonia in 2005 is the first Internet voting system to have been adopted anywhere in the world. Since its inception, it has been met with both praise and scrutiny. Concerns include in-person election observations, code reviews, and adversarial testing on system components. As a result of these concerns, some parties have concluded that there are various ways in which insider threats and sophisticated external attacks could compromise the system’s integrity and thus the voting process. This paper examines the procedural components of the I-Voting system, with an emphasis on the controls related to procedural security mechanisms, high-level operational security aspects, and system transparency measures. The methodological approach is based on both primary and secondary data sources, including interviews with key Estonian election personnel, in order to determine the extent to which the present controls mitigate the security risks faced by the system. This study makes three main arguments. First, we found procedural controls to be fundamentally important to the design of the I-Voting system. While these mechanisms go a long way toward preventing cyberattacks, problems in the system still exist. For instance, some security situations appear to be addressed in informal ways which rely heavily on the knowledge, experience, and professional relationships between officials. Second, in terms of operational controls, we were generally impressed by the state of the controls adopted, particularly the incident handling processes during elections, as well as checks and investigations during and after elections. Our main concern regarding resilience is the increasing potential for more highly sophisticated attacks. As time progresses, attackers will naturally become stronger, and the system will have to adapt in order to accommodate this evolution. Third, the system’s transparency measures have had a noteworthy impact on building confidence and trust in the I-Voting system, both locally and internationally. Challenges still exist, however, especially pertaining to the difficulty in running voter awareness campaigns, as well as increasing voter usage of transparency measures

Global crustal stress pattern based on the world stress map database release 2008

The World Stress Map (WSM) project is a global compilation of information on the contemporary crustal stress field from a wide range of stress indicators. The WSM database release 2008 contains 21,750 stress data records that are quality-ranked using an updated and refined quality-ranking scheme. Almost 17,000 of these data records have A–C quality and are considered to record the orientation of maximum horizontal compressional stress SH to within ±25°. As this is almost a triplication of data records compared with the first WSM database release in 1992, we reinvestigate the spatial wave-length of the stress patterns with a statistical analysis on a global 0.5° grid. The resulting smoothed global stress map displays both; the mean SH orientation that follows from the maximum smoothing radius for which the standard deviation is 2000 km) exist for example in North America and NE Asia. These have been used in earlier analyses to conclude that the global stress pattern is primarily controlled by plate boundary forces that are transmitted into the intraplate region. However, our analysis reveals that rather short wave-length of the stress pattern <200 km are quite frequent too, particularly in western Europe, Alaska and the Aleutians, the southern Rocky Mountains, Basin and Range province, Scandinavia, Caucasus, most of the Himalayas and Indonesia. This implies that local stress sources such as density contrasts and active fault systems in some areas have high impact in comparison to plate boundary forces and control the regional stress pattern