Automatic Assignment of EC Numbers

A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology. When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function, the EC number introduced by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) is used. However, each and every one of these applications is critically dependent upon the consistency and reliability of the underlying data for success. We have developed tools for the validation of the EC number classification scheme. In this paper, we present validated data of 3788 enzymatic reactions including 229 sub-subclasses of the EC classification system. Over 80% agreement was found between our assignment and the EC classification. For 61 (i.e., only 2.5%) reactions we found that their assignment was inconsistent with the rules of the nomenclature committee; they have to be transferred to other sub-subclasses. We demonstrate that our validation results can be used to initiate corrections and improvements to the EC number classification scheme

Turbulence modelling and role of compressibility on oil spilling from a damaged double hull tank

The viscosity plays an important role, and a multiphase solver is necessary to numerically simulate the oil spilling from a damaged double hull tank (DHT). However, it is uncertain whether turbulence modelling is necessary, which turbulence model is suitable; and what the role of compressibility of the fluids is. This paper presents experimental and numerical investigations to address these issues for various cases representing different scenarios of the oil spilling, including grounding and collision. In the numerical investigations, various approaches to model the turbulence, including the large eddy simulation (LES), direct numerical simulation and the Reynolds average Navier-Stokes equation (RANS) with different turbulence models, are employed. Based on the investigations, it is suggested that the effective Reynolds numbers corresponding to both oil outflow and water inflow shall be considered when classifying the significance of the turbulence and selecting the appropriate turbulence models. This is confirmed by new lab tests considering the axial offset between the internal and the external holes on two hulls of the DHT. The investigations conclude for numerically simulating oil spilling from a damaged DHT that when the effective Re is smaller the RANS approaches should not be used and LES modelling should be employed; while when the effective Reynolds numbers is large, the RANS models may be used as they can give similar results to LES in terms of the height of the mixture in the ballast tank and discharge but costing much less CPU time. The investigation on the role of the compressibility of the fluid reveals that the compressibility of the fluid may be considerable in a small temporal-spatial scale but plays an insignificant role on macroscopic process of the oil spilling

Galaxy And Mass Assembly (GAMA): galaxy close pairs, mergers and the future fate of stellar mass

We use a highly complete subset of the Galaxy And Mass Assembly II (GAMA-II) redshift sample to fully describe the stellar mass dependence of close pairs and mergers between 10(8) and 10(12)M(circle dot). Using the analytic form of this fit we investigate the total stellar mass accreting on to more massive galaxies across all mass ratios. Depending on how conservatively we select our robust merging systems, the fraction of mass merging on to more massive companions is 2.0-5.6 per cent. Using the GAMA-II data we see no significant evidence for a change in the close pair fraction between redshift z = 0.05 and 0.2. However, we find a systematically higher fraction of galaxies in similar mass close pairs compared to published results over a similar redshift baseline. Using a compendium of data and the function gamma(M) = A(1 + z)(m) to predict the major close pair fraction, we find fitting parameters of A = 0.021 +/- 0.001 and m = 1.53 +/- 0.08, which represents a higher low-redshift normalization and shallower power-law slope than recent literature values. We find that the relative importance of in situ star formation versus galaxy merging is inversely correlated, with star formation dominating the addition of stellar material below M* and merger accretion events dominating beyond M*. We find mergers have a measurable impact on the whole extent of the galaxy stellar mass function (GSMF), manifest as a deepening of the &#39;dip&#39; in the GSMF over the next similar to Gyr and an increase in M* by as much as 0.01-0.05 dex.</p

Galaxy And Mass Assembly (GAMA): galaxy close pairs, mergers and the future fate of stellar mass

We use a highly complete subset of the GAMA-II redshift sample to fully describe the stellar mass dependence of close-pairs and mergers between 108M_ and 1012M_. Using the analytic form of this fit we investigate the total stellar mass accreting onto more massive galaxies across all mass ratios. Depending on how conservatively we select our robust merging systems, the fraction of mass merging onto more massive companions is 2:0%{5:6%. Using the GAMA-II data we see no significant evidence for a change in the close-pair fraction between redshift z = 0:05{0:2. However, we find a systematically higher fraction of galaxies in similar mass close-pairs compared to published results over a similar redshift baseline. Using a compendium of data and the function M = A(1+z)m to predict the major close-pair fraction, we find fitting parameters of A = 0:021 _ 0:001 and m = 1:53 _ 0:08, which represents a higher low-redshift normalisation and shallower power-law slope than recent literature values.We find that the relative importance of in-situ star-formation versus galaxy merging is inversely correlated, with star-formation dominating the addition of stellar material below M_ and merger accretion events dominating beyond M_. We find mergers have a measurable impact on the whole extent of the GSMF, manifest as a deepening of the `dip' in the GSMF over the next _Gyr and an increase in M_ by as much as 0.01{0.05 dex

Galaxy And Mass Assembly (GAMA): galaxy close pairs, mergers and the future fate of stellar mass

We use a highly complete subset of the GAMA-II redshift sample to fully describe the stellar mass dependence of close-pairs and mergers between 108M_ and 1012M_. Using the analytic form of this fit we investigate the total stellar mass accreting onto more massive galaxies across all mass ratios. Depending on how conservatively we select our robust merging systems, the fraction of mass merging onto more massive companions is 2:0%{5:6%. Using the GAMA-II data we see no significant evidence for a change in the close-pair fraction between redshift z = 0:05{0:2. However, we find a systematically higher fraction of galaxies in similar mass close-pairs compared to published results over a similar redshift baseline. Using a compendium of data and the function M = A(1+z)m to predict the major close-pair fraction, we find fitting parameters of A = 0:021 _ 0:001 and m = 1:53 _ 0:08, which represents a higher low-redshift normalisation and shallower power-law slope than recent literature values.We find that the relative importance of in-situ star-formation versus galaxy merging is inversely correlated, with star-formation dominating the addition of stellar material below M_ and merger accretion events dominating beyond M_. We find mergers have a measurable impact on the whole extent of the GSMF, manifest as a deepening of the `dip' in the GSMF over the next _Gyr and an increase in M_ by as much as 0.01{0.05 dex

Text Mining the History of Medicine

Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform

Intelligent Monitoring and Controlling of Public Policies Using Social Media and Cloud Computing

Part 3: Government and InfrastructureInternational audienceLack of public participation in various policy making decision has always been a major cause of concern for government all around the world while formulating as well as evaluating such policies. With availability of latest IT infrastructure and the migration of government think-tank towards realizing more efficient cloud based e-government, this problem has been partially answered, but this predicament still persists. However, the exponential rise in usage of social media platforms by general public has given the government a wider insight to overcome this long pending dilemma. This paper presents a pragmatic approach that combines the capabilities of cloud computing and social media analytics towards efficient monitoring and controlling of public policies. The proposed arrangement has provided us some encouraging results, when tested for the policy of the century i.e. GST implementation by Indian government and established that proposed system can be successfully implemented for efficient policy making and implementation

Protein quality control: the who’s who, the where’s and therapeutic escapes

In cells the quality of newly synthesized proteins is monitored in regard to proper folding and correct assembly in the early secretory pathway, the cytosol and the nucleoplasm. Proteins recognized as non-native in the ER will be removed and degraded by a process termed ERAD. ERAD of aberrant proteins is accompanied by various changes of cellular organelles and results in protein folding diseases. This review focuses on how the immunocytochemical labeling and electron microscopic analyses have helped to disclose the in situ subcellular distribution pattern of some of the key machinery proteins of the cellular protein quality control, the organelle changes due to the presence of misfolded proteins, and the efficiency of synthetic chaperones to rescue disease-causing trafficking defects of aberrant proteins

"It's what midwifery is all about": Western Australian midwives' experiences of being 'with woman' during labour and birth in the known midwife model

Background: The phenomenon of being 'with woman' is fundamental to midwifery as it underpins its philosophy, relationships and practices. There is an identified gap in knowledge around the 'with woman' phenomenon from the perspective of midwives providing care in a variety of contexts. As such, the aim of this study was to explore the experiences of being 'with woman' during labour and birth from the perspective of midwives' working in a model where care is provided by a known midwife. Methods: A descriptive phenomenological design was employed with ten midwives working in a 'known midwife' model who described their experiences of being 'with woman' during labour and birth. The method was informed by Husserlian philosophy which seeks to explore the same phenomenon through rich descriptions by individuals revealing commonalities of the experience. Results: Five themes emerged 1) Building relationships; 2) Woman centred care; 3) Impact on the midwife; 4) Impact on the woman; and 5) Challenges in the Known Midwife model. Midwives emphasised the importance of trusting relationships while being 'with woman', confirming that this relationship extends beyond the woman - midwife relationship to include the woman's support people and family. Being 'with woman' during labour and birth in the context of the relationship facilitates woman-centred care. Being 'with woman' influences midwives, and, it is noted, the women that midwives are working with. Finally, challenges that impact being 'with woman' in the known midwife model are shared by midwives. Conclusions: Findings offer valuable insight into midwives' experiences of being 'with woman' in the context of models that provide care by a known midwife. In this model, the trusting relationship is the conduit for being 'with woman' which influences the midwife, the profession of midwifery, as well as women and their families. Descriptions of challenges to being 'with woman' provide opportunities for professional development and service review. Rich descriptions from the unique voice of midwives, provided insight into the applied practices of being 'with woman' in a known midwife model which adds important knowledge concerning a phenomenon so deeply embedded in the philosophy and practices of the profession of midwifery

Temporal-spatial profiling of pedunculopontine galanin-cholinergic neurons in the lactacystin rat model of Parkinson’s disease

Parkinson’s disease (PD) is conventionally seen as resulting from single-system neurodegeneration affecting nigrostriatal dopaminergic neurons. However, accumulating evidence indicates a multi-system degeneration and neurotransmitter deficiencies, including cholinergic neurons which degenerate in a brainstem nucleus, the pedunculopontine nucleus (PPN), resulting in motor- and cognitive impairments. The neuropeptide galanin can inhibit cholinergic transmission, whilst being upregulated in degenerating brain regions associated with cognitive decline. Here we determined the temporal-spatial profile of progressive expression of endogenous galanin within degenerating cholinergic neurons, across the rostro-caudal axis of the PPN, by utilising the lactacystin-induced rat model of PD. First, we show progressive neuronal death affecting nigral dopaminergic and PPN cholinergic neurons, reflecting that seen in PD patients, to facilitate use of this model for assessing the therapeutic potential of bioactive peptides. Next, stereological analyses of the lesioned brain hemisphere found that the number of PPN cholinergic neurons expressing galanin increased by 11%, compared to sham-lesioned controls, increasing by a further 5% as the neurodegenerative process evolved. Galanin upregulation within cholinergic PPN neurons was most prevalent closest to the intra-nigral lesion site, suggesting that galanin upregulation in such neurons adapt intrinsically to neurodegeneration, to possibly neuroprotect. This is the first report on the extent and pattern of galanin expression in cholinergic neurons across distinct PPN subregions in both the intact rat CNS and lactacystin lesioned rats. The findings pave the way for future work to target galanin signaling in the PPN, to determine the extent to which upregulated galanin expression could offer a viable treatment strategy for ameliorating PD symptoms associated with cholinergic degeneration