scholarly journals The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data

2004 ◽  
Vol 5 (6-7) ◽  
pp. 521-527 ◽  
Author(s):  
Helen Parkinson ◽  
Stuart Aitken ◽  
Richard A. Baldock ◽  
Jonathan B. L. Bard ◽  
Albert Burger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Functional Genomics ◽  
Large Scale ◽  
Controlled Vocabulary ◽  
First Pass ◽  
Relevant Term ◽  
High Level ◽  
Supporting Functional ◽  
Selection Of

A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scalein situgene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies.

scholarly journals Transplantation of the Mediterranean seagrass Posidonia oceanica through naturalistic engineering techniques: value, weakness and further improvements

2015 ◽  
Author(s):  
Stefano Acunto ◽  
Luigi Piazzi ◽  
Francesco L. Cinelli ◽  
Anna Maria De Biasi ◽  
Lorenzo Pacciardi ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Large Scale ◽  
Focal Point ◽  
Posidonia Oceanica ◽  
Hydrodynamic Conditions ◽  
Coastal System ◽  
Pros And Cons ◽  
The Mediterranean ◽  
Selection Of

Transplantation of seagrasses is considered a useful method to favour the recovery of degraded meadows. Hence, many projects have been carried out worldwide and a manifold of techniques have been applied. However, the choice of transplantation procedures remains a main problem to be assessed. In order to optimize efforts and to minimize risks of plants loss, the applied methodologies should take into account typology of hosting substratum, hydrodynamic conditions, depth and seagrass species. Due to their fundamental ecological role in the Mediterranean coastal system, many restoration projects aiming to preserve Posidonia oceanica meadows took place in the last decades. Several transplantation techniques have produced different results. In fact the same transplanting methodology may originate diverse results under different environmental conditions. Recently, naturalistic engineering techniques developed on land, have been used for transplantations of P. oceanica. Pilot projects concerning small surfaces were carried out between 2006 and 2010. More recently, a large-scale program (0.1 km2) was realized in 2012 at Civitavecchia (Roma, Thyrrenian Sea). The applied technique consists basically of mattresses filled with sand coupled with a net covering able to hold steady in situ the plant rhizomes. These structures have been variously modified in time to be adapted to the different type of substratum and various hydrodynamic conditions of the transplanting sites. Following the results of these transplantation experiences, we analyzed pros and cons of the techniques in order to improve the methodology. Firstly, these techniques may be considered suitable to large-scale projects allowing to minimize transplantation times. Secondly, the rhizomes may be successfully fixed to the structures; the majority of the transplanted shoots was not damaged showing a very good vegetative vitality with the production of new rhizomes, leaves and roots few months after transplanting. Finally, this procedure is flexible, as the basic technique can be modified and tailored to the various environmental conditions of the different receiving site. However, the results obtained in different areas are highly heterogeneous suggesting that a careful selection of the hosting site is a focal point. To this aim, a pilot study before the beginning of large-scale project seems mandatory, providing a fundamental support to guarantee successful results.

scholarly journals Effect of Advancing Direction of Working Face on Mining Stress Distribution in Deep Coal Mine

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Yuesong Tang ◽  
Wenchao Sun ◽  
Xin Zhang ◽  
Pengju Liu
Keyword(s):  
Stress Distribution ◽  
Large Scale ◽  
In Situ Stress ◽  
Deep Mining ◽  
Deep Coal Mine ◽  
Working Face ◽  
Geological Conditions ◽  
Original Rock ◽  
High Level

Deep mining has become the normal state of coal mining; compared with the mine with shallow buried depth, the consequent high level of in situ stress and complex distribution have brought severe threats to the stability of the stope and the surrounding rock of the roadway. In this research, taking the 121304 working face of Kouzidong Mine as the engineering background, the characteristics of mining-induced stress distribution under complex in situ stress environment in deep mining are analyzed by using on-site measurement of the original rock stress and mining stress, establishing a theoretical model centered on the middle section of the working face, and establishing large-scale numerical calculation models for different advancing directions. It was found that under deep mining conditions, the maximum stress of the original rock is 25.12 MPa, and the direction is vertical. The advanced influence range of mining stress is about 150 m, and the abutment pressure presents a three-peak distribution characteristic in front of the working face. The research results provide important theoretical guiding value for guiding the mining of coal mines with similar geological conditions.

scholarly journals Application properties of methods for fault detection and isolation in the diagnosis of complex large-scale processes

2014 ◽  
Vol 62 (3) ◽  
pp. 571-582 ◽  
Author(s):  
J.M. Kościelny ◽  
M. Syfert
Keyword(s):  
Fault Detection ◽  
Large Scale ◽  
Fault Detection And Isolation ◽  
Industrial Processes ◽  
Industrial Practice ◽  
Potential Applicability ◽  
Diagnostic Approaches ◽  
Level Of Knowledge ◽  
High Level ◽  
Selection Of

Abstract The survey presents a selection of the methods of the fault detection and isolation suitable to be useful for the diagnostics of the complex, large scale industrial processes. The paper focuses on these methods that have appropriately high level of potential applicability in industrial practice. The novelty of the paper relies on the discussion of the dependency of the level of knowledge about diagnosed process and recommended diagnostic approaches. Appropriate recommendations were given in the convenient form of the table

scholarly journals M3S: a comprehensive model selection for multi-modal single-cell RNA sequencing data

2019 ◽  
Vol 20 (S24) ◽  
Author(s):  
Yu Zhang ◽  
Changlin Wan ◽  
Pengcheng Wang ◽  
Wennan Chang ◽  
Yan Huo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Model Selection ◽  
Statistical Model ◽  
Single Cell ◽  
Differential Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Sequencing Data ◽  
Differential Gene ◽  
Selection Of

Abstract Background Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data generated by different experimental design and platforms, there is currently lack of capability to determine the most proper statistical model. Results We developed an R package, namely Multi-Modal Model Selection (M3S), for gene-wise selection of the most proper multi-modality statistical model and downstream analysis, useful in a single-cell or large scale bulk tissue transcriptomic data. M3S is featured with (1) gene-wise selection of the most parsimonious model among 11 most commonly utilized ones, that can best fit the expression distribution of the gene, (2) parameter estimation of a selected model, and (3) differential gene expression test based on the selected model. Conclusion A comprehensive evaluation suggested that M3S can accurately capture the multimodality on simulated and real single cell data. An open source package and is available through GitHub at https://github.com/zy26/M3S.

scholarly journals Ovarian steroids regulate 24p3 expression in mouse uterus during the natural estrous cycle and the preimplantation period

1999 ◽  
Vol 162 (1) ◽  
pp. 11-19 ◽  
Author(s):  
HL Huang ◽  
ST Chu ◽  
YH Chen
Keyword(s):  
Gene Expression ◽  
Estrous Cycle ◽  
Immunohistochemical Localization ◽  
The Other ◽  
Undetectable Level ◽  
Mouse Uterus ◽  
Ovarian Steroids ◽  
Vaginal Plug ◽  
High Level

We examined 24p3 expression in the mouse uterus at various stages of the natural estrous cycle and during the preimplantation period. The level of 24p3 mRNA appeared intensively in proestrus and estrus, then declined sharply from metestrus to diestrus. Consistent with this observation, 24p3 protein was abundant in proestrus, decreased from estrus to metestrus and declined to a very low level in diestrus. The uterine 24p3 expression closely overlapped with the estradiol (E2) surge in proestrus and estrus but it was suppressed when progesterone (P4) rose to a high level during the reproductive cycle. Neither the protein nor its message was detected in the uteri of immature mice or ovariectomized adult animals. While an injection of P4 to these animals was unable to initiate uterine 24p3 expression, administration of estrogenic steroids to these animals markedly stimulated the gene expression. Treatment of these animals with E2 together with P4, on the other hand, did not stimulate the gene expression. In pregnant animals (day 1 (D1)=day of vaginal plug), 24p3 mRNA remained at a high level on D1 and D2 but dropped to an almost undetectable level on D3 and D4. This was accompanied by a decrease in 24p3 protein from D1 to D2 and a decline in the protein to undetectable levels from D3 to D4. The staining patterns of both the immunohistochemical localization of 24p3 protein and in situ hybridization for the detection of 24p3 mRNA in the uterine sections showed that 24p3 expression took place mainly in the luminal and glandular epithelial cells of the endometrium. This together with our previous observation that 24p3 protein is found in uterine luminal fluid indicates that the protein is secreted primarily from these cells to their respective luminal surfaces during proestrus and estrus.

Proteinase-activated receptors in ovine cervical function

2005 ◽  
Vol 17 (7) ◽  
pp. 693 ◽  
Author(s):  
Sharon E. Mitchell ◽  
John J. Robinson ◽  
Margaret E. King ◽  
Lynda M. Williams
Keyword(s):  
Gene Expression ◽  
In Situ Hybridisation ◽  
Prostaglandin F2α ◽  
Cervical Dilation ◽  
Proteinase Activated Receptors ◽  
Pregnant Ewe ◽  
High Level ◽  
And Function

In sheep, inflammation not only functions in cervical dilation at parturition, but also plays an important part in the non-pregnant ewe cervix, as demonstrated by the high level of expression of interleukin (IL)-8 at oestrus. Ewes artificially induced to ovulate have significantly lower levels of IL-8 gene expression at oestrus compared with natural oestrus, indicating an inhibition of inflammation and function, offering an explanation for the low rates of conception in vaginally inseminated synchronised ewes. To identify potential pro-inflammatory agents to combat the anti-inflammatory effects of hormonal synchronisation of oestrus, we have investigated the role of proteinase-activated receptor (PAR)-1 and PAR-2. To localise and measure the level of expression of these receptors, ovine-specific probes were derived for PAR-1 and PAR-2 and used for quantitative in situ hybridisation in the ovine cervix. Both PAR-1 and PAR-2 were expressed in the luminal epithelium of the cervix throughout the oestrous cycle, with expression being highest at oestrus. The gene expression of PAR-2 at oestrus was approximately 30% higher than that of PAR-1. Artificial synchronisation of oestrus by either an intravaginal progesterone sponge or prostaglandin F2α injections did not inhibit PAR-1 or PAR-2 expression at oestrus; rather, in the case of PAR-2, progesterone synchronisation increased it. Both synchronising procedures increased the expression of PAR-1 and PAR-2 during the luteal phase of the cycle. Therefore, agonists of PAR-1 and PAR-2 may be potentially useful pro-inflammatory agents countering the inhibition of inflammation by hormonal synchronisation.

Production and fish identification of wheat- Aegilops biuncialis addition lines and their use for the selection of U and M genome-specific molecular (SSR) markers

2010 ◽  
Vol 58 (2) ◽  
pp. 151-158 ◽  
Author(s):  
A. Schneider ◽  
I. Molnár ◽  
M. Molnár-Láng
Keyword(s):  
Ssr Markers ◽  
Addition Lines ◽  
Wheat Genotype ◽  
Exact Identification ◽  
Translocation Lines ◽  
The Individual ◽  
High Level ◽  
M Genome ◽  
Selection Of

One way of incorporating useful traits from Aegilops biuncialis (2n=4x=28, U b U b M b M b ) into wheat ( Triticum aestivum L. 2n=6x=42, AABBDD) is to develop first addition then translocation lines. The 2M b , 3M b , 7M b , 3U b , 5U b and 5U b /6U b wheat- Ae. biuncialis addition lines were produced in Martonvásár. To facilitate the exact identification of the addition lines, it was necessary to analyse the fluorescence in situ hybridisation patterns of the parental wheat genotype, Ae. biuncialis and its diploid progenitors ( Ae. umbellulata 2n=2x=14, UU and Ae. comosa 2n=2x=14, MM). The great genetic variability of the Aegilops species causes polymorphism in the fluorescence in situ hybridisation (FISH) patterns of the individual chromosomes. Due to the high level of FISH polymorphism, it is advisable to confirm the identification of the Ae. biuncialis chromosomes with the help of molecular (microsatellite, SSR) markers, so 119 wheat SSR markers were tested on Aegilops biuncialis , on Ae. geniculata (2n=4x=28, U g U g M g M g ), on five wheat- Ae. biuncialis addition lines (2M b , 3M b , 7M b , 3U b , 5U b ) and on an addition series of wheat- Ae. geniculata in order to select SSR markers specific to the U and M genomes of Ae. biuncialis and Ae. geniculata .

scholarly journals Transplantation of the Mediterranean seagrass Posidonia oceanica through naturalistic engineering techniques: value, weakness and further improvements

2015 ◽  
Author(s):  
Stefano Acunto ◽  
Luigi Piazzi ◽  
Francesco L. Cinelli ◽  
Anna Maria De Biasi ◽  
Lorenzo Pacciardi ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Large Scale ◽  
Focal Point ◽  
Posidonia Oceanica ◽  
Hydrodynamic Conditions ◽  
Coastal System ◽  
Pros And Cons ◽  
The Mediterranean ◽  
Selection Of

Transplantation of seagrasses is considered a useful method to favour the recovery of degraded meadows. Hence, many projects have been carried out worldwide and a manifold of techniques have been applied. However, the choice of transplantation procedures remains a main problem to be assessed. In order to optimize efforts and to minimize risks of plants loss, the applied methodologies should take into account typology of hosting substratum, hydrodynamic conditions, depth and seagrass species. Due to their fundamental ecological role in the Mediterranean coastal system, many restoration projects aiming to preserve Posidonia oceanica meadows took place in the last decades. Several transplantation techniques have produced different results. In fact the same transplanting methodology may originate diverse results under different environmental conditions. Recently, naturalistic engineering techniques developed on land, have been used for transplantations of P. oceanica. Pilot projects concerning small surfaces were carried out between 2006 and 2010. More recently, a large-scale program (0.1 km2) was realized in 2012 at Civitavecchia (Roma, Thyrrenian Sea). The applied technique consists basically of mattresses filled with sand coupled with a net covering able to hold steady in situ the plant rhizomes. These structures have been variously modified in time to be adapted to the different type of substratum and various hydrodynamic conditions of the transplanting sites. Following the results of these transplantation experiences, we analyzed pros and cons of the techniques in order to improve the methodology. Firstly, these techniques may be considered suitable to large-scale projects allowing to minimize transplantation times. Secondly, the rhizomes may be successfully fixed to the structures; the majority of the transplanted shoots was not damaged showing a very good vegetative vitality with the production of new rhizomes, leaves and roots few months after transplanting. Finally, this procedure is flexible, as the basic technique can be modified and tailored to the various environmental conditions of the different receiving site. However, the results obtained in different areas are highly heterogeneous suggesting that a careful selection of the hosting site is a focal point. To this aim, a pilot study before the beginning of large-scale project seems mandatory, providing a fundamental support to guarantee successful results.

scholarly journals Thermal–hydraulic–mechanical (THM) behaviour of a large-scale in situ heating experiment during cooling and dismantling

2012 ◽  
Vol 49 (10) ◽  
pp. 1169-1195 ◽  
Author(s):  
M. Sánchez ◽  
A. Gens ◽  
L. Guimarães
Keyword(s):  
Large Scale ◽  
Element Formulation ◽  
Model Predictions ◽  
Engineered Barriers ◽  
Heating Test ◽  
High Level ◽  
Fully Coupled ◽  
Clay Barrier

A geological disposal facility for high-level radioactive waste (HLW) encompasses both natural (host rock) and (generally clay-based) engineered barriers. Many processes can influence, either positively or negatively, the effectiveness of the safety functions of isolation and retardation. This paper focuses on the analysis of a large-scale heating test when subjected to cooling and subsequent partial dismantling. The experiment reproduces the conditions of an HLW repository at full scale under realistic conditions. Key thermal, hydraulic, and mechanical (THM) variables, such as temperature, relative humidity, stresses, and fluid pressures, were measured in the clay barrier and surrounding rock. The experimental observations recorded during the cooling down and clay barrier excavation are analyzed in light of a fully coupled THM finite element formulation. This analysis has provided the opportunity to explore the behaviour of the clay and natural barriers under conditions very relevant for the repository performance but not analyzed previously. Overall, the model predictions are quite satisfactory when compared against experimental observations. Furthermore, model predictions for a period of 20 years, including the transient phase induced by the partial dismantling, are also presented. This additional analysis has allowed a better understanding of the effect of thermal gradient on long-term clay hydration.

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