scholarly journals Rosemary: a flexible programming framework to build Science Gateways

2017 ◽  
Author(s):  
Shayan Shahand ◽  
Sílvia Olabarriaga
Keyword(s):  
Data Model ◽  
Lessons Learned ◽  
Design Development ◽  
Sequencing Data ◽  
High Throughput Analysis ◽  
Vitro Fertilization ◽  
Neuroimaging Data ◽  
Generic Data Model ◽  
Flexible Programming

The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions, namely related to data, computing, and collaboration management, are integrated together. Our earlier studies showed that complete integration between these functions is a feature that is usually overlooked in the existing SG platforms. Rosemary provides a generic data model, RESTful API, and responsive UI that can be customized through programming to build customized SGs. Moreover, Rosemary is designed and implemented to be flexible to changes in e-Infrastructures and user community requirements. The software frameworks, tools and libraries employed in the realization of Rosemary streamline the development, deployment and operation of customized SGs for the users needs. The code of Rosemary is open source, available at https://github.com/AMCeScience/Rosemary-Vanilla. So far the platform has been used to implement prototypes of three SGs for high-throughput analysis and management of neuroimaging data, sharing of data in in-vitro fertilization research, and provenance tracking of DNA sequencing data. This paper presents the design considerations, data model, and system architecture of Rosemary and highlights some of the features that are intrinsic to its design and implementation with examples from the three prototypes.

scholarly journals Rosemary: a flexible programming framework to build Science Gateways

2016 ◽  
Author(s):  
Shayan Shahand ◽  
Sílvia Olabarriaga
Keyword(s):  
Data Model ◽  
Lessons Learned ◽  
Design Development ◽  
Sequencing Data ◽  
High Throughput Analysis ◽  
Vitro Fertilization ◽  
Neuroimaging Data ◽  
Generic Data Model ◽  
Flexible Programming

The lessons learned during six years of experience in design, development, and operation of four Science Gateway (SG) generations motivated us to develop yet another generation of platforms coined “Rosemary”. At the core of Rosemary the three fundamental SG functions, namely related to data, computing, and collaboration management, are integrated together. Our earlier studies showed that complete integration between these functions is a feature that is usually overlooked in the existing SG platforms. Rosemary provides a generic data model, RESTful API, and responsive UI that can be customized through programming to build customized SGs. Moreover, Rosemary is designed and implemented to be flexible to changes in e-Infrastructures and user community requirements. The software frameworks, tools and libraries employed in the realization of Rosemary streamline the development, deployment and operation of customized SGs for the users needs. The code of Rosemary is open source, available at https://github.com/AMCeScience/Rosemary-Vanilla. So far the platform has been used to implement prototypes of three SGs for high-throughput analysis and management of neuroimaging data, sharing of data in in-vitro fertilization research, and provenance tracking of DNA sequencing data. This paper presents the design considerations, data model, and system architecture of Rosemary and highlights some of the features that are intrinsic to its design and implementation with examples from the three prototypes.

scholarly journals Conservative management of uterine adenosarcoma: lessons learned from 20 years of follow-up

2019 ◽  
Vol 300 (5) ◽  
pp. 1383-1389 ◽  
Author(s):  
Ariadne L’Heveder ◽  
Benjamin P. Jones ◽  
Srdjan Saso ◽  
Jen Barcroft ◽  
Robert Richardson ◽  
...  
Keyword(s):  
Conservative Management ◽  
Laparoscopic Hysterectomy ◽  
Endometrial Biopsy ◽  
Lessons Learned ◽  
Low Grade ◽  
Retrospective Case ◽  
Pelvic Magnetic Resonance Imaging ◽  
Vitro Fertilization

Abstract Purpose Uterine adenosarcomas (UAs) account for 5–8% of cases of uterine sarcomas. Treatment includes total abdominal hysterectomy (TAH) and bilateral salpingo-oophorectomy (BSO). Fertility preservation is an emerging concept in gynaecology oncology and is particularly relevant in UA, where cases are diagnosed as young as 15-year-old. This manuscript demonstrates a case of UA which was treated conservatively, achieved successful livebirths and underwent completion hysterectomy after two decades of follow-up. Method This was a retrospective case note review. Results An 18-year-old nulliparous woman presented with abnormal vaginal bleeding. Ultrasound identified an endometrial polyp, which was histologically diagnosed as low-grade adenosarcoma. She was advised to undergo TAH and BSO, but instead decided to preserve her fertility and opted for conservative management. She was monitored with pelvic ultrasound, hysteroscopy and endometrial biopsy bi-annually, with annual pelvic magnetic resonance imaging for 10 years which was uneventful. 11 years post-operatively she conceived following in-vitro fertilization (IVF) but suffered a miscarriage at 16 weeks likely due to cervical incompetence. She subsequently conceived with twins. She delivered spontaneously preterm at 28 weeks. Both children are alive and well. After 20 years of follow-up, she underwent a laparoscopic hysterectomy with no evidence of recurrence. She remains disease free. Conclusion Whilst radical completion surgery should be advised in UA, this case, in addition to all published conservatively managed cases of UA, demonstrates that conservative management is possible in appropriately selected women. Intensive monitoring post-operatively is essential owing to the risk of recurrence; however, this may pose deleterious side effects which require consideration.

scholarly journals Using quantitative reconstitution to investigate multi-component condensates

RNA ◽  
2021 ◽  
pp. rna.079008.121
Author(s):  
Simon L Currie ◽  
Michael K Rosen
Keyword(s):  
Stress Granules ◽  
Lessons Learned ◽  
Sequencing Data ◽  
Processing Bodies ◽  
P Bodies ◽  
Multiple Components ◽  
In Vitro Reconstitution ◽  
Condensate Formation ◽  
Liquid Liquid Phase Separation

Many biomolecular condensates are thought to form via liquid-liquid phase separation (LLPS) of multivalent macromolecules. For those that form through this mechanism, our understanding has benefitted significantly from biochemical reconstitutions of key components and activities. Reconstitutions of RNA-based condensates to date have mostly been based on relatively simple collections of molecules. However, proteomics and sequencing data indicate that natural RNA-based condensates are enriched in hundreds to thousands of different components, and genetic data suggest multiple interactions can contribute to condensate formation to varying degrees. In this perspective we describe recent progress in understanding RNA-based condensates through different levels of biochemical reconstitutions, as a means to bridge the gap between simple in vitro reconstitution and cellular analyses. Complex reconstitutions provide insight into the formation, regulation, and functions of multi-component condensates. We focus on two RNA-protein condensate case studies: stress granules and RNA processing bodies (P bodies), and examine the evidence for cooperative interactions among multiple components promoting LLPS. An important concept emerging from these studies is that composition and stoichiometry regulate biochemical activities within condensates. Based on the lessons learned from stress granules and P bodies we discuss forward-looking approaches to understand the thermodynamic relationships between condensate components, with the goal of developing predictive models of composition and material properties, and their effects on biochemical activities. We anticipate that quantitative reconstitutions will facilitate understanding of the complex thermodynamics and functions of diverse RNA-protein condensates.

Triploidy in a Live-Born Extremely Low Birth Weight Twin: Clinical Aspects

2020 ◽  
Author(s):  
Liliya Vakrilova ◽  
Stanislava Hitrova-Nikolova ◽  
Irena Bradinova
Keyword(s):  
Left Lung ◽  
Extremely Low Birth Weight ◽  
Clinical Aspects ◽  
Severe Respiratory Distress ◽  
Vitro Fertilization ◽  
Gestational Week ◽  
Polymerase Chain ◽  
Fluorescent Polymerase Chain Reaction ◽  
Second Twin

AbstractTriploidy is a rare chromosomal aberration characterized by a karyotype with 69 chromosomes. Triploid fetuses usually are miscarried in early pregnancy. We present a case of a triploid twin and a genetically unaffected co-twin, conceived through in vitro fertilization. A discordant growth was registered at 20 weeks of gestation. Cesarean section was performed at 355/7 gestational week. The second twin was extremely growth restricted female (780 g) with oligohydramnios and severe respiratory distress, and died at 20 hours of age. The autopsy revealed unilobar left lung, bilobar right lung, and cysts of the terminal bronchioles. Quantitative fluorescent polymerase chain reaction detected triploidy compatible pattern. So, early intrauterine growth restriction may be a sign of triploidy, which must be proven by pre or postnatal genetic testing.

Predictive Model for Live Birth at 12 Months After Starting In-Vitro Fertilization Treatment

MedPharmRes ◽  
2018 ◽  
Vol 2 (2) ◽  
pp. 5-20
Author(s):  
Vu Ho ◽  
Toan Pham ◽  
Tuong Ho ◽  
Lan Vuong
Keyword(s):  
In Vitro Fertilization ◽  
Live Birth ◽  
Cox Regression ◽  
Financial Burden ◽  
Oocyte Retrieval ◽  
Operating Characteristics ◽  
Vitro Fertilization ◽  
Cox Regression Analysis ◽  
Significant Difference

IVF carries a considerable physical, emotional and financial burden. Therefore, it would be useful to be able to predict the likelihood of success for each couple. The aim of this retrospective cohort study was to develop a prediction model to estimate the probability of a live birth at 12 months after one completed IVF cycle (all fresh and frozen embryo transfers from the same oocyte retrieval). We analyzed data collected from 2600 women undergoing in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) at a single center in Vietnam between April 2014 and December 2015. All patients received gonadotropin-releasing hormone (GnRH) antagonist stimulation, followed by fresh and/or frozen embryo transfer (FET) on Day 3. Using Cox regression analysis, five predictive factors were identified: female age, total dose of recombinant follicle stimulating hormone used, type of trigger, fresh or FET during the first transfer, and number of subsequent FET after the first transfer. The area under the receiver operating characteristics curve for the final model was 0.63 (95% confidence interval [CI] 0.60‒0.65) and 0.60 (95% CI 0.57‒0.63) for the validation cohort. There was no significant difference between the predicted and observed probabilities of live birth (Hosmer-Lemeshow test, p > 0.05). The model developed had similar discrimination to existing models and could be implemented in clinical practice.

Sign in / Sign up

Export Citation Format

Share Document