scholarly journals The Dfam community resource of transposable element families, sequence models, and genome annotations

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis J. Wheeler ◽  
Arian F. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Open Access Database ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into

AbstractDfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0–3.3 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

scholarly journals The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations

2020 ◽  
Author(s):  
Jessica Storer ◽  
Robert Hubley ◽  
Jeb Rosen ◽  
Travis Wheeler ◽  
Arian F.A. Smit
Keyword(s):  
Transposable Element ◽  
De Novo ◽  
Consensus Sequence ◽  
Model Organisms ◽  
Community Resource ◽  
Genome Annotations ◽  
Protein Alignments ◽  
Insight Into ◽  
Proof Of Principle

Abstract The 3.0-3.2 releases of Dfam (https://dfam.org) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam’s new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

scholarly journals Comparative analysis of whole flower transcriptomes in the Zingiberales

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5490 ◽  
Author(s):  
Ana Maria R. Almeida ◽  
Alma Piñeyro-Nelson ◽  
Roxana B. Yockteng ◽  
Chelsea D. Specht
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Model Organisms ◽  
Comparative Approach ◽  
Careful Study ◽  
Sequencing Technologies ◽  
Outgroup Species ◽  
Floral Diversification ◽  
Genomic Scale ◽  
Insight Into

The advancement of next generation sequencing technologies (NGS) has revolutionized our ability to generate large quantities of data at a genomic scale. Despite great challenges, these new sequencing technologies have empowered scientists to explore various relevant biological questions on non-model organisms, even in the absence of a complete sequenced reference genome. Here, we analyzed whole flower transcriptome libraries from exemplar species across the monocot order Zingiberales, using a comparative approach in order to gain insight into the evolution of the molecular mechanisms underlying flower development in the group. We identified 4,153 coding genes shared by all floral transcriptomes analyzed, and 1,748 genes that are only retrieved in the Zingiberales. We also identified 666 genes that are unique to the ginger lineage, and 2,001 that are only found in the banana group, while in the outgroup species Dichorisandra thyrsiflora J.C. Mikan (Commelinaceae) we retrieved 2,686 unique genes. It is possible that some of these genes underlie lineage-specific molecular mechanisms of floral diversification. We further discuss the nature of these lineage-specific datasets, emphasizing conserved and unique molecular processes with special emphasis in the Zingiberales. We also briefly discuss the strengths and shortcomings of de novo assembly for the study of developmental processes across divergent taxa from a particular order. Although this comparison is based exclusively on coding genes, with particular emphasis in transcription factors, we believe that the careful study of other regulatory mechanisms, such as non-coding RNAs, might reveal new levels of complexity, which were not explored in this work.

scholarly journals The state of artificial intelligence-based FDA-approved medical devices and algorithms: an online database

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Stan Benjamens ◽  
Pranavsingh Dhunnoo ◽  
Bertalan Meskó
Keyword(s):  
Artificial Intelligence ◽  
Medical Devices ◽  
De Novo ◽  
Online Database ◽  
Medical Technologies ◽  
The Us ◽  
Open Access Database ◽  
Regulatory Bodies ◽  
Premarket Approval ◽  
Insight Into

Abstract At the beginning of the artificial intelligence (AI)/machine learning (ML) era, the expectations are high, and experts foresee that AI/ML shows potential for diagnosing, managing and treating a wide variety of medical conditions. However, the obstacles for implementation of AI/ML in daily clinical practice are numerous, especially regarding the regulation of these technologies. Therefore, we provide an insight into the currently available AI/ML-based medical devices and algorithms that have been approved by the US Food & Drugs Administration (FDA). We aimed to raise awareness of the importance of regulatory bodies, clearly stating whether a medical device is AI/ML based or not. Cross-checking and validating all approvals, we identified 64 AI/ML based, FDA approved medical devices and algorithms. Out of those, only 29 (45%) mentioned any AI/ML-related expressions in the official FDA announcement. The majority (85.9%) was approved by the FDA with a 510(k) clearance, while 8 (12.5%) received de novo pathway clearance and one (1.6%) premarket approval (PMA) clearance. Most of these technologies, notably 30 (46.9%), 16 (25.0%), and 10 (15.6%) were developed for the fields of Radiology, Cardiology and Internal Medicine/General Practice respectively. We have launched the first comprehensive and open access database of strictly AI/ML-based medical technologies that have been approved by the FDA. The database will be constantly updated.

The state of artificial intelligence-based FDA-approved medical devices and algorithms: An online database (Preprint)

2020 ◽  
Author(s):  
Bertalan Mesko ◽  
Stan Benjamens ◽  
Pranavsingh Dhunnoo
Keyword(s):  
Artificial Intelligence ◽  
Medical Devices ◽  
De Novo ◽  
Online Database ◽  
Medical Technologies ◽  
Open Access Database ◽  
Regulatory Bodies ◽  
Premarket Approval ◽  
Insight Into ◽  
The U.S

BACKGROUND At the beginning of the artificial intelligence (A.I.) era, the expectations are high, and experts foresee that A.I. shows potential for diagnosing, managing and treating a wide variety of medical conditions. However, the obstacles for implementation of A.I. in daily clinical practice are numerous, especially regarding the regulation of these technologies. OBJECTIVE Therefore, we provide an insight into the currently available A.I.-based medical devices and algorithms that have been approved by the U.S. Food & Drugs Administration (FDA). We aimed to raise awareness about the importance of regulatory bodies, clearly stating whether a medical device is A.I.-based or not. METHODS Cross-checking and validating all approvals, we identified 64 A.I.-based, FDA approved medical devices and algorithms. Out of those, only 29 (45%) mentioned any A.I.-related expressions in the official FDA announcement. RESULTS The majority (85.9%) was approved by the FDA with a 510(k) clearance, while 8 (12.5%) received de novo pathway clearance and one (1.6%) premarket approval (PMA) clearance. Most of these technologies, notably 30 (46.9%), 16 (25.0%) and 10 (15.6%) were developed for the fields of Radiology, Cardiology and Internal Medicine / General Practice respectively. CONCLUSIONS We launched the first comprehensive and open access database of strictly A.I.-based medical technologies that have been approved by the FDA. The database will be constantly updated. 

Turkish Muslims in a German city: Entrepreneurial and residential self-determination

2015 ◽  
Vol 12 (1) ◽  
pp. 1-12
Author(s):  
Sarah Hackett
Keyword(s):  
Residential Patterns ◽  
Academic Literature ◽  
Self Employment ◽  
German City ◽  
Post War ◽  
Oral History Interviews ◽  
The City ◽  
Insight Into ◽  
Term Objective

Drawing upon a collection of oral history interviews, this paper offers an insight into entrepreneurial and residential patterns and behaviour amongst Turkish Muslims in the German city of Bremen. The academic literature has traditionally argued that Turkish migrants in Germany have been pushed into self-employment, low-quality housing and segregated neighbourhoods as a result of discrimination, and poor employment and housing opportunities. Yet the interviews reveal the extent to which Bremen’s Turkish Muslims’ performances and experiences have overwhelmingly been the consequences of personal choices and ambitions. For many of the city’s Turkish Muslim entrepreneurs, self-employment had been a long-term objective, and they have succeeded in establishing and running their businesses in the manner they choose with regards to location and clientele, for example. Similarly, interviewees stressed the way in which they were able to shape their housing experiences by opting which districts of the city to live in and by purchasing property. On the whole, they perceive their entrepreneurial and residential practices as both consequences and mediums of success, integration and a loyalty to the city of Bremen. The findings are contextualised within the wider debate regarding the long-term legacy of Germany’s post-war guest-worker system and its position as a “country of immigration”.

Is 3 years adequate for tracking completely occluded coiled aneurysms?

2020 ◽  
Vol 133 (3) ◽  
pp. 758-764
Author(s):  
Eung Koo Yeon ◽  
Young Dae Cho ◽  
Dong Hyun Yoo ◽  
Su Hwan Lee ◽  
Hyun-Seung Kang ◽  
...  
Keyword(s):  
De Novo ◽  
Careful Monitoring ◽  
Surveillance Period ◽  
Radiological Data ◽  
De Novo Aneurysm ◽  
Low Probability ◽  
Almost All ◽  
Annual Risk

OBJECTIVEThe authors conducted a study to ascertain the long-term durability of coiled aneurysms completely occluded at 36 months’ follow-up given the potential for delayed recanalization.METHODSIn this retrospective review, the authors examined 299 patients with 339 aneurysms, all shown to be completely occluded at 36 months on follow-up images obtained between 2011 and 2013. Medical records and radiological data acquired during the extended monitoring period (mean 74.3 ± 22.5 months) were retrieved, and the authors analyzed the incidence of (including mean annual risk) and risk factors for delayed recanalization.RESULTSA total of 5 coiled aneurysms (1.5%) occluded completely at 36 months showed recanalization (0.46% per aneurysm-year) during the long-term surveillance period (1081.9 aneurysm-years), 2 surfacing within 60 months and 3 developing thereafter. Four showed minor recanalization, with only one instance of major recanalization. The latter involved the posterior communicating artery as an apparent de novo lesion, arising at the neck of a firmly coiled sac, and was unrelated to coil compaction or growth. Additional embolization was undertaken. In a multivariate analysis, a second embolization for a recurrent aneurysm (HR = 22.088, p = 0.003) independently correlated with delayed recanalization.CONCLUSIONSAlmost all coiled aneurysms (98.5%) showing complete occlusion at 36 months postembolization proved to be stable during extended observation. However, recurrent aneurysms were predisposed to delayed recanalization. Given the low probability yet seriousness of delayed recanalization and the possibility of de novo aneurysm formation, careful monitoring may be still considered in this setting but at less frequent intervals beyond 36 months.

Moving Songs

2019 ◽  
pp. 590-606
Author(s):  
Sally Treloyn ◽  
Matthew Dembal Martin ◽  
Rona Goonginda Charles
Keyword(s):  
Cultural Heritage ◽  
Knowledge Transmission ◽  
Intercultural Relationships ◽  
Cultural Negotiation ◽  
Intercultural Collaboration ◽  
Present Collection ◽  
Intergenerational Knowledge ◽  
Early Phases ◽  
Insight Into

Repatriation has become almost ubiquitous in ethnomusicological research on Australian Indigenous song. This article provides insights into processes of a repatriation-centered song revitalization project in the Kimberley, northwest Australia. Authored by an ethnomusicologist and two members of the Ngarinyin cultural heritage community, the article provides firsthand accounts of the early phases of a long-term repatriation-centered project referred to locally as the Junba Project. The authors provide a sample of narratives and dialogues that deliver insight into experiences of the work of identifying recordings “in the archive” and cultural negotiation and use of recordings “on Country.” The entanglement of local epistemological frameworks with past and present collection, archival research, repatriation, and dissemination for intergenerational knowledge transmission between spirits, Country, and the living, is explored, showing how recordings move song knowledge from community to archive to community and from generation to generation, and move people in present-day communities. The chapter considers how these “moving songs” allow an interrogation of the fraught endeavor of intercultural collaboration in the pursuit of revitalizing Indigenous song traditions. It positions repatriation as a method that can support intergenerational knowledge transmission and as a method to consider past and present intercultural relationships within research projects and between cultural heritage communities and collecting institutions.

scholarly journals Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

2021 ◽  
Author(s):  
José Cerca ◽  
Marius F. Maurstad ◽  
Nicolas C. Rochette ◽  
Angel G. Rivera‐Colón ◽  
Niraj Rayamajhi ◽  
...  
Keyword(s):  
De Novo ◽  
Model Organisms

scholarly journals Long-term outcomes of fully covered self-expandable metal stents versus plastic stents in chronic pancreatitis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sang Hoon Lee ◽  
Yeon Suk Kim ◽  
Eui Joo Kim ◽  
Hee Seung Lee ◽  
Jeong Youp Park ◽  
...  
Keyword(s):  
Chronic Pancreatitis ◽  
Clinical Efficacy ◽  
De Novo ◽  
Plastic Stents ◽  
Metal Stents ◽  
Plastic Stent ◽  
Sems Group ◽  
Spontaneous Migration

AbstractChronic pancreatitis (CP) related main pancreatic duct (MPD) stricture has been a challenge for endoscopists. Fully covered self-expandable metal stents (FC-SEMS) has been tried in CP patients, but the efficacy and safety are still controversial. Thus, we aim to compare the long-term clinical efficacy of FC-SEMS vs. plastic stent placement in persistent MPD strictures secondary to CP. Between 2007 and 2018, 80 chronic pancreatitis patients (58 males, median age 49 years), who underwent endoscopic placement of FC-SEMS (n = 26) and plastic stent (n = 54) for persistent MPD strictures after at least 3 months of initial single plastic stenting, were retrospectively analyzed during a median follow-up duration of 33.7 months. As a result, MPD stricture resolution rate was statistically higher in FC-SEMS group (87.0% vs. 42.0%, p < 0.001). Although immediate complications occurred similarly (38.5% vs. 37.0%, p = 0.902), spontaneous migration (26.9%) and de novo strictures (23.1%) were pronounced delayed complications in FC-SEMS group. Pain relief during follow-up was significantly higher in FC-SEMS group (76.9% vs. 53.7%, p = 0.046). The total procedure cost was similar in both groups ($1,455.6 vs. $1,596.9, p = 0.486). In comparison with plastic stent, FC-SEMS placement for persistent MPD strictures had favorable long-term clinical efficacy, with its typical complications like spontaneous migration and de novo strictures.

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