The Curation of Genetic Variants: Difficulties and Possible Solutions

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China

¹⁴C AMS at SUERC: improving QA data from the 5 MV tandem AMS and 250 kV SSAMS

In 2003, a National Electrostatics Corporation (NEC) 5MV tandem accelerator mass spectrometer was installed at SUERC, providing the radiocarbon laboratory with 14C measurements to 4–5‰ repeatability. In 2007, a 250kV single-stage accelerator mass spectrometer (SSAMS) was added to provide additional 14C capability and is now the preferred system for 14C analysis. Changes to the technology and to our operations are evident in our copious quality assurance data: typically, we now use the 134-position MC-SNICS source, which is filled to capacity. Measurement of standards shows that spectrometer running without the complication of on-line δ13C evaluation is a good operational compromise. Currently, 3‰ 14C/13C measurements are routinely achieved for samples up to nearly 3 half-lives old by consistent sample preparation and an automated data acquisition algorithm with sample random access for measurement repeats. Background and known-age standard data are presented for the period 2003–2008 for the 5MV system and 2007–2008 for the SSAMS, to demonstrate the improvements in data quality

INTERPRETATION OF THE BOUGUER GRAVITY ANOMALIES OF THE ERZURUM-HORASAN-PASİNLER BASIN (EAST ANATOLIA) WITH SAXOV-NYGAARD METHOD

Saxov-Nygaard varyasyon (SN) yöntemi, yer altı jeolojik yapısının fiziksel özelliklerindeki (yoğunluk) küçük değişimler sebebiyle gravite alanlarında meydana gelen küçük farklılıkları ayırt etmek için kullanılan yöntemlerden birisidir. Bu çalışmada, bu yöntemle elde edilen rezidüel anomaliler ve bunlara sebep olan yer altı kütlelerinin derinliği arasındaki ilişki incelenmiştir. Yapılan model ve arazi çalışmaları sonucu yöntemin küçük yoğunluk değişimleri sebebiyle Bouguer anomalilerinde meydana gelen gözle görülmeyen değişimleri iyi bir şekilde ortaya çıkardığı ve kütlelerin derinlikleri hakkında bilgi elde edildiği görülmüştür. Saxov-Nygaard variation method is used in order to separate small variations in the gravity fields owing to small changes of the physical properties (density) of the subsurface geological structure. In this study, the residual anomaly obtained with this method and the relationships between the anomaly mass and depth caused by subsurface mass. According to do model and area studies using this method, it is seen that small variations in the Bouguer gravity anomalies owing to small density variations appear slightly. Moreover, this method gives the depth information about anomaly masses

Cues and knowledge structures used by mental-health professionals when making risk assessments

Background: Research into mental-health risks has tended to focus on epidemiological approaches and to consider pieces of evidence in isolation. Less is known about the particular factors and their patterns of occurrence that influence clinicians’ risk judgements in practice. Aims: To identify the cues used by clinicians to make risk judgements and to explore how these combine within clinicians’ psychological representations of suicide, self-harm, self-neglect, and harm to others. Method: Content analysis was applied to semi-structured interviews conducted with 46 practitioners from various mental-health disciplines, using mind maps to represent the hierarchical relationships of data and concepts. Results: Strong consensus between experts meant their knowledge could be integrated into a single hierarchical structure for each risk. This revealed contrasting emphases between data and concepts underpinning risks, including: reflection and forethought for suicide; motivation for self-harm; situation and context for harm to others; and current presentation for self-neglect. Conclusions: Analysis of experts’ risk-assessment knowledge identified influential cues and their relationships to risks. It can inform development of valid risk-screening decision support systems that combine actuarial evidence with clinical expertise

Using XML and XSLT for flexible elicitation of mental-health risk knowledge

Current tools for assessing risks associated with mental-health problems require assessors to make high-level judgements based on clinical experience. This paper describes how new technologies can enhance qualitative research methods to identify lower-level cues underlying these judgements, which can be collected by people without a specialist mental-health background. Methods and evolving results: Content analysis of interviews with 46 multidisciplinary mental-health experts exposed the cues and their interrelationships, which were represented by a mind map using software that stores maps as XML. All 46 mind maps were integrated into a single XML knowledge structure and analysed by a Lisp program to generate quantitative information about the numbers of experts associated with each part of it. The knowledge was refined by the experts, using software developed in Flash to record their collective views within the XML itself. These views specified how the XML should be transformed by XSLT, a technology for rendering XML, which resulted in a validated hierarchical knowledge structure associating patient cues with risks. Conclusions: Changing knowledge elicitation requirements were accommodated by flexible transformations of XML data using XSLT, which also facilitated generation of multiple data-gathering tools suiting different assessment circumstances and levels of mental-health knowledge

Did female prisoners with mental disorders receive psychiatric treatment before imprisonment?

© 2015 Mundt et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.BackgroundThroughout the world, high prevalence rates of mental disorders have been found in prison populations, especially in females. It has been suggested that these populations do not access psychiatric treatment. The aim of this study was to establish rates of psychiatric in- and outpatient treatments prior to imprisonment in female prisoners and to explore reasons for discontinuation of such treatments.Methods150 consecutively admitted female prisoners were interviewed in Berlin, Germany. Socio-demographic characteristics, mental disorders, and previous psychiatric in- and outpatient treatments were assessed by trained researchers. Open questions were used to explore reasons for ending previous psychiatric treatment.ResultsA vast majority of 99 prisoners (66%; 95% CI: 58¿73) of the total sample reported that they had previously been in psychiatric treatment, 80 (53%; 95 CI: 45¿61) in inpatient treatment, 62 (41%; 95 CI: 34¿49) in outpatient treatment and 42 (29%; 21¿39) in both in- and outpatient treatments. All prisoners with psychosis and 72% of the ones with any lifetime mental health disorder had been in previous treatment. The number of inpatient treatments and imprisonments were positively correlated (rho¿=¿0.27; p¿<¿0.01). Inpatient treatment was described as successfully completed by 56% (N¿=¿41) of those having given reasons for ending such treatment, whilst various reasons were reported for prematurely ending outpatient treatments.ConclusionThe data do not support the notion of a general `mental health treatment gap¿ in female prisoners. Although inpatient care is often successfully completed, repeated inpatient treatments are not linked with fewer imprisonments. Improved transition from inpatient to outpatient treatment and services that engage female prisoners to sustained outpatient treatments are needed