Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

BACKGROUND

Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.

RESULTS

The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.

CONCLUSIONS

PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.

JAMI: a Java library for molecular interactions and data interoperability

Background

A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types.

Results

A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats.

Conclusion

Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI’s model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

Taxonomy and biogeography of Hemphillia (Gastropoda: Pulmonata: Arionidae) in North American rainforests, with description of a new species (Skade’s jumping-slug, Hemphillia skadei sp. nov.)

Species diversity of the genus Hemphillia Bland and W.G. Binney, 1872 (jumping-slugs) was studied across its range in western North America’s inland temperate rainforests. The taxonomic relationships among jumping-slug populations were clarified by integrating morphological, molecular, and biogeographic approaches. A new species, Skade’s jumping-slug (Hemphillia skadei sp. nov.), was discovered in this process and is described herein. We base this taxonomic decision on molecular comparison of representatives from other Hemphillia species and four morphological characters that distinguish H. skadei from its sister species, the pale jumping-slug (Hemphillia camelus Pilsbry and Vanatta, 1897). The distribution of H. skadei and H. camelus is described along with the notable lack of detection of the marbled jumping-slug (Hemphillia danielsi Vanatta, 1914) within the primary survey area.

Looking after the mouth - Evaluation of a pilot for a new approach to training care home carers in Kent, Surrey and Sussex

Objective This pilot study aimed to produce and evaluate training resources and training in oral health care, including oral hygiene, for carers in care homes in Surrey and Medway.Methods During two training days, for carers from these homes, short, interactive presentations were given on a range of topics relevant to oral health care and oral hygiene of older people, followed by practical training. Prior to any training all attendees completed a 39 question questionnaire to establish their baseline knowledge of oral health and hygiene. At the end of the training day they completed an evaluation form. Fourteen weeks later, they were visited at their place of work and completed the same questionnaire again. Differences in responses between baseline and after 14 weeks were statistically tested using the chi-squared test.Results Sixty-six carers attended the training sessions and 44 were followed up 14 weeks later. The results showed an improvement in carer knowledge at follow up. The majority of carers (36/44) spoke English as their first language. They had a mean age of 41 years, 37 were female and 7 male. They had worked as carers for a mean of 10.9 years (range 4 months-34 years). Over 90% stated that the training day fully met or exceeded their requirements and expectations.Conclusions The results indicated improvements in carer knowledge. However, the carers were atypical of carers in general, as they were self-selected and well-motivated. Nevertheless the content of the training day and the questionnaire should inform future work in this area.

Measuring Sarcopenia Severity in Older Adults and the Value of Effective Interventions

OBJECTIVES

Little is known about the severity and long-term health and economic consequences of sarcopenia. We developed a sarcopenia index to measure severity in older Americans and estimated the long-term societal benefits generated by effective interventions to mitigate severity.

DESIGN

Using a micro-simulation model, we quantified the potential societal value generated in the US in 2010-2040 by reductions in sarcopenia severity in older adults. All analyses were performed in Stata and SAS.

SETTING AND PARTICIPANTS

Secondary data from the National Health and Nutrition Examination Survey (NHANES) (N = 1634) and Health and Retirement Study (HRS) (N = 952) were used to develop a sarcopenia severity index in older adults.

MEASUREMENTS

Multi-trait multi-method and factor analyses were used to validate and calibrate the sarcopenia severity index, which was modeled as a function of gait speed, walking without an assistive device, and moderate physical activity.

RESULTS

In representative elderly populations, reducing sarcopenia severity by improving gait speed by 0.1 m/s in those with gait speed under 0.8 m/s generated a cumulative benefit of $65B by 2040 (2015 dollars). Improving walking ability in those with walking difficulty generated cumulative social benefit of $787B by 2040.

CONCLUSIONS

Reducing sarcopenia severity would generate significant health and economic benefits to society-almost $800B in the most optimistic scenarios.

Better Respiratory Education and Treatment Help Empower (BREATHE) study: Methodology and baseline characteristics of a randomized controlled trial testing a transitional care program to improve patient-centered care delivery among chronic obstructive pulmonary disease patients

BACKGROUND

Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of hospitalizations. Interventional studies focusing on the hospital-to-home transition for COPD patients are few. In the BREATHE (Better Respiratory Education and Treatment Help Empower) study, we developed and tested a patient and family-centered transitional care program that helps prepare hospitalized COPD patients and their family caregivers to manage COPD at home.

METHODS

In the study's initial phase, we co-developed the BREATHE transitional care program with COPD patients, family-caregivers, and stakeholders. The program offers tailored services to address individual patients' needs and priorities at the hospital and for 3months post discharge. We tested the program in a single-blinded RCT with 240 COPD patients who were randomized to receive the program or 'usual care'. Program participants were offered the opportunity to invite a family caregiver, if available, to enroll with them into the study. The primary outcomes were the combined number of COPD-related hospitalizations and Emergency Department (ED) visits per participant at 6months post discharge, and the change in health-related quality of life over the 6months study period. Other measures include 'all cause' hospitalizations and ED visits; patient activation; self-efficacy; and, self-care behaviors.

DISCUSSION

Unlike 1month transitional care programs that focus on patients' post-acute care needs, the BREATHE program helps hospitalized COPD patients manage the post discharge period as well as prepare them for long term self-management of COPD. If proven effective, this program may offer a timely solution for hospitals in their attempts to reduce COPD rehospitalizations.

Experimental Life-Cycle of Varestrongylus eleguneniensis (Nematoda: Protostrongylidae) in a Captive Reindeer (Rangifer tarandus tarandus) and a Muskox (Ovibos moschatus moschatus)

The life-cycle of a recently described protostrongylid lungworm, Varestrongylus eleguneniensis, which infects caribou, muskoxen, and moose from Arctic and boreal regions of North America, was completed experimentally for the first time. A native North American slug species, Deroceras laeve, was infected with the first-stage larvae (L1) isolated from the feces of wild muskoxen to generate third-stage larvae (L3). These were administered to a captive reindeer calf (250 L3) and an adult captive muskox (380 L3). The prepatent periods for the reindeer and muskox were 56 and 72 days, respectively. Patency lasted for only 19 days in the reindeer, and fecal larval counts were very low (0.09-1.53 larvae per gram of feces). Patency in the muskox was at least 210 days, and likely over 653 days, and the fecal larval counts were higher (0.06-17.8 larvae per gram of feces). This work provides the first experimental completion of the life-cycle of V. eleguneniensis.

Growth, morphometrics, and nutrient content of farmed eastern oysters, Crassostrea virginica (Gmelin), in New Hampshire, USA

When harvested, oysters represent a removal from the ecosystem of nutrients such as nitrogen (N) and carbon (C). A number of factors potentially affect nutrient content, but a quantitative understanding across the geographic range of the eastern oysters is lacking. The present study was designed to quantify the relationships among various metrics of farmed eastern oysters near its northern geographic range focusing on nutrient content. Hatchery-reared oysters were deployed in polyethylene bags at six sites, and were measured on multiple occasions from 2010-2012. A quadratic polynomial fit to the combined datasets for shell height indicated that on average a 'cocktail' size oyster (63 mm shell height) would be reached after 2 yr, and 'regular' size (76 mm) would require 3 yr. There were significant differences in growth rates and oyster nutrient content among the sites; means for %N in soft tissue ranged from 6.9 to 8.6, and 0.07 to 0.18 in shell. Percent N in soft tissue and shell were highest at two sites at the mouths of rivers with elevated dissolved inorganic N concentrations in the water. Grand means (all sites, seasons and years combined) of soft tissue N and C for regular size oysters were 7.3% and 38.5%, respectively; and for shell N and C were 0.13% and 12.0%, respectively. Our study extends the range of data on nutrient content of the eastern oyster to northern New England, and indicates that oyster size, seasonality, and nutrient concentration in ambient water potentially affect %N and %C content of oysters.

Splenorenal Arterial Bypass: Description of Technique and Case Example in an Instance of Renal Revascularization during Adrenalectomy for Adrenocortical Carcinoma

We present a patient with a 16 cm adrenocortical carcinoma that underwent a left adrenalectomy en bloc with resection of the involved segment of the left renal artery. A splenectomy and splenorenal bypass was performed to revascularize the left kidney. To our knowledge, this is the first instance in the literature of a splenorenal arterial bypass being reported for renal revascularization during an extirpative oncologic procedure. A 64-year-old male patient, with history significant for adrenocortical carcinoma, status post prior right adrenalectomy with partial right nephrectomy, presented for an elective left adrenalectomy. Preoperative work-up revealed an 11.4 × 13.2 × 16 cm left adrenal mass, most consistent with an adrenocortical carcinoma. At the time of surgery, the mass was found to be intimately adherent to the aorta at the takeoff of the left renal artery. Moreover, the left renal artery appeared to be coursing directly through the mass. The involved segment of the left renal artery was resected en bloc with the tumor. Because of concerns for a small and likely poorly functioning right renal remnant, a decision was made to attempt to salvage the left kidney. This was accomplished by performing a splenectomy and constructing a splenorenal bypass. Serial Duplex Doppler renal ultrasound studies were obtained over the first three postoperative days and demonstrated improved arterial waveforms. Serum creatinine reached a peak level of 3.76 mg/dL on postoperative day 3, and then began to slowly trend down to 3.37 mg/dL on the day of discharge (postoperative day7).

Factors Affecting Choice of Community Residential Care Setting

To investigate factors associated with residents’ choice of type of Medicaid-funded community residential care setting in western Washington State. Method: Prospective cohort design including residents new to any of three setting types (264 residents entering 170 different facilities), using data from state and Medicaid databases and in-person interviews. The authors used analysis of variance and multinomial logistic regression to examine bivariate associations and estimate effects of resident and facility characteristics on choice of facility type at baseline. Results: Several resident characteristics appear to be associated with choice of community residential care setting, including age, marital status, education, functional status, and reported memory and behavior problems. Facility policies differ significantly among types of facilities and also appear to be associated with choice of setting. Discussion: Selection processes operate in choice of community residential care setting, with residents choosing facility type based on the fit of their needs with facility characteristics.

An analysis of the association between prostate cancer risk loci, PSA levels, disease aggressiveness and disease-specific mortality

BACKGROUND

Genome-wide association studies have identified multiple single-nucleotide polymorphsims (SNPs) associated with prostate cancer (PCa). Although these SNPs have been clearly associated with disease risk, their relationship with clinical outcomes is less clear. Our aim was to assess the frequency of known PCa susceptibility alleles within a single institution ascertainment and to correlate risk alleles with disease-specific outcomes.

METHODS

We genotyped 1354 individuals treated for localised PCa between June 1988 and December 2007. Blood samples were prospectively collected and de-identified before being genotyped and matched to phenotypic data. We investigated associations between 61 SNPs and disease-specific end points using multivariable analysis and also determined if SNPs were associated with PSA at diagnosis.

RESULTS

Seven SNPs showed associations on multivariable analysis (P<0.05), rs13385191 with both biochemical recurrence (BR) and castrate metastasis (CM), rs339331 (BR), rs1894292, rs17178655 and rs11067228 (CM), and rs11902236 and rs4857841 PCa-specific mortality. After applying a Bonferroni correction for number of SNPs (P<0.0008), the only persistent significant association was between rs17632542 (KLK3) and PSA levels at diagnosis (P=1.4 × 10(-5)).

CONCLUSIONS

We confirmed that rs17632542 in KLK3 is associated with PSA at diagnosis. No significant association was seen between loci and disease-specific end points when accounting for multiple testing. This provides further evidence that known PCa risk SNPs do not predict likelihood of disease progression.