Exploiting protein language models for the precise classification of ion channels and ion transporters

This study introduces TooT-PLM-ionCT, a comprehensive framework that consolidates three distinct systems, each meticulously tailored for one of the following tasks: distinguishing ion channels (ICs) from membrane proteins (MPs), segregating ion transporters (ITs) from MPs, and differentiating ICs from ITs. Drawing upon the strengths of six Protein Language Models (PLMs)-ProtBERT, ProtBERT-BFD, ESM-1b, ESM-2 (650M parameters), and ESM-2 (15B parameters), TooT-PLM-ionCT employs a combination of traditional classifiers and deep learning models for nuanced protein classification. Originally validated on an existing dataset by previous researchers, our systems demonstrated superior performance in identifying ITs from MPs and distinguishing ICs from ITs, with the IC-MP discrimination achieving state-of-the-art results. In light of recommendations for additional validation, we introduced a new dataset, significantly enhancing the robustness and generalization of our models across bioinformatics challenges. This new evaluation underscored the effectiveness of TooT-PLM-ionCT in adapting to novel data while maintaining high classification accuracy. Furthermore, this study explores critical factors affecting classification accuracy, such as dataset balancing, the impact of using frozen versus fine-tuned PLM representations, and the variance between half and full precision in floating-point computations. To facilitate broader application and accessibility, a web server (https://tootsuite.encs.concordia.ca/service/TooT-PLM-ionCT) has been developed, allowing users to evaluate unknown protein sequences through our specialized systems for IC-MP, IT-MP, and IC-IT classification tasks.

Physical activity, organized sport participation and active transportation to school among Canadian youth by gender identity and sexual attraction

INTRODUCTION

Regular physical activity is associated with a wide range of health benefits in youth. While previous studies have identified disparities in physical activity among youth by gender identity and sexual attraction, these have seldom been explored in Canadian youth.

METHODS

Data from the 2019 Canadian Health Survey on Children and Youth were used to assess prevalence of and time spent in organized sports participation, total physical activity and active transportation by gender identity (non-cisgender vs. cisgender) among youth aged 12 to 17, and by sexual attraction (nonheterosexual attraction vs. heterosexual attraction) among youth aged 15 to 17.

RESULTS

There was no difference in average minutes of total physical activity per week between non-cisgender and cisgender Canadian youth. Non-cisgender youth (which represent 0.5% of the population) averaged significantly fewer minutes of organized sports per week than their cisgender counterparts. There was some evidence of increased active transportation to school among non-cisgender youth, but insufficient power to detect significant differences. Canadian youth reporting any nonheterosexual attraction (which represent 21.2% of the population, including mostly heterosexual youth) were less likely to be regularly physically active and participate in organized sports than youth reporting exclusive heterosexual attraction. Differences were larger among males than females. Males reporting nonheterosexual attraction were more likely to use active transportation to get to school than their heterosexual counterparts.

CONCLUSION

Non-cisgender youth and youth reporting nonheterosexual attraction tended to participate less in organized sports than their counterparts, but may have engaged in more active transportation. Mitigating the barriers associated with sport participation could increase physical activity among these groups.

Associations between school-level environment and individual-level factors of walking and cycling to school in Canadian youth

Identifying individual-level and school-level correlates of walking and cycling to school remains a public health priority as only one in four Canadian youth actively travels to school. This study aimed to estimate the prevalence of Canadian youth in grades 6 to 10 who walk, cycle, or use motorised transport to go to school, and to examine if school neighbourhood walkability, neighbourhood-level and individual-level correlates are associated with mode of transportation to school. Data come from the 2017/2018 Health Behaviour in School-aged Children study. The walkability of the schools' neighbourhood was measured using the Canadian Active Living Environments (Can-ALE) index. We observed that only 22.4% and 4.2% of youth walked and cycled to school, respectively. Most (73.4%) used motorised transport to school, including 53.2% of youth who lived less than 5 minutes from school. Schools located in neighbourhoods with higher Can-ALE classes (i.e., higher walkability) were positively associated with walking to school. No statistically significant association between school walkability and cycling to school was observed. Individual-level socioeconomic status (SES) was associated with walking, but not cycling, to school. Conversely, neighbourhood-level SES was associated with cycling, but not with walking, to school. Correlates of walking to school differed from those for cycling to school, suggesting that different approaches to promoting active transportation are needed.

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks

Transmembrane transport proteins (transporters) play a crucial role in the fundamental cellular processes of all organisms by facilitating the transport of hydrophilic substrates across hydrophobic membranes. Despite the availability of numerous membrane protein sequences, their structures and functions remain largely elusive. Recently, natural language processing (NLP) techniques have shown promise in the analysis of protein sequences. Bidirectional Encoder Representations from Transformers (BERT) is an NLP technique adapted for proteins to learn contextual embeddings of individual amino acids within a protein sequence. Our previous strategy, TooT-BERT-T, differentiated transporters from non-transporters by employing a logistic regression classifier with fine-tuned representations from ProtBERT-BFD. In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respectively.

Gender identity and sexual attraction among Canadian youth: findings from the 2019 Canadian Health Survey on Children and Youth

Gender identity and sexual attraction are important determinants of health. This study reports distributions of gender identity and sexual attraction among Canadian youth using data from the 2019 Canadian Health Survey on Children and Youth. Among youth aged 12 to 17, 0.2% are nonbinary and 0.2% are transgender. Among youth aged 15 to 17, 21.0%, comprising more females than males, report attraction not exclusive to the opposite gender. Given known associations between health and gender and sexual attraction, oversampling of sexual minority groups is recommended in future studies to obtain reliable estimates for identifying inequities and informing policy.

The Canadian Bikeway Comfort and Safety (Can-BICS) Classification System: A common naming convention for cycling infrastructure

There is no standard naming convention for cycling infrastructure across cities. Our aim was to develop a common nomenclature for cycling infrastructure in Canada, relevant to the context of public health practice. We drew on transportation engineering design guides and public health guidance to develop a bicycle facility classification system: the Canadian Bikeway Comfort and Safety (Can-BICS) classification system, a three-tiered classification scheme that groups five bicycle facilities based on safety performance and user comfort. Adopting consistent nomenclature as per the Can-BICS system will support regional and national surveillance efforts in public health, planning and sustainability.

Integrative approach for detecting membrane proteins

Background

Membrane proteins are key gates that control various vital cellular functions. Membrane proteins are often detected using transmembrane topology prediction tools. While transmembrane topology prediction tools can detect integral membrane proteins, they do not address surface-bound proteins. In this study, we focused on finding the best techniques for distinguishing all types of membrane proteins.

Results

This research first demonstrates the shortcomings of merely using transmembrane topology prediction tools to detect all types of membrane proteins. Then, the performance of various feature extraction techniques in combination with different machine learning algorithms was explored. The experimental results obtained by cross-validation and independent testing suggest that applying an integrative approach that combines the results of transmembrane topology prediction and position-specific scoring matrix (Pse-PSSM) optimized evidence-theoretic k nearest neighbor (OET-KNN) predictors yields the best performance.

Conclusion

The integrative approach outperforms the state-of-the-art methods in terms of accuracy and MCC, where the accuracy reached a 92.51% in independent testing, compared to the 89.53% and 79.42% accuracies achieved by the state-of-the-art methods.

Comparison of self-reported and accelerometer-measured physical activity among Canadian youth

BACKGROUND

Generally, correlation and agreement between self-reported and accelerometer-measured physical activity are low. The objective of this study is to compare estimates of physical activity from a newly developed Canadian questionnaire with measurements by accelerometer among 12- to 17-year-olds.

DATA AND METHODS

Physical activity was self-reported by domain (transportation, recreation, school, and occupational/household) as part of the new Physical Activity Youth Questionnaire (PAYQ) in the Canadian Health Measures Survey (CHMS; 2014-2017; n = 975) and the Canadian Community Health Survey (CCHS; 2015-2016; n=7,619). The CHMS also collected moderate-to-vigorous physical activity (MVPA) data using the Actical accelerometer. Descriptive statistics and correlation and agreement analyses were used to compare and contrast self-reported and accelerometer-measured physical activity variables. Linear regression was used to assess the association between physical activity and obesity.

RESULTS

The average daily MVPA measured by accelerometry was 49.7 minutes per day. According to the PAYQ, Canadian youth reported an average of 78.2 minutes of physical activity per day from all domains, including recreation (31.3 minutes per day), transportation (15.5 minutes per day), school (25.8 minutes per day), and occupational/household (5.6 minutes per day). According to accelerometer-measured MVPA, 23.1% of youth met the physical activity guideline. The inclusion of all domains of self-reported physical activity resulted in a higher percentage of youth meeting the physical activity guideline (58.6%) than was the case for the recreation domain only (18.5%) or the sum of the recreation and school domains (34.0%). Overall, self-reported and accelerometer-measured physical activity estimates were poorly correlated (R ⟨ 0.2).

DISCUSSION

Population-level estimates of physical activity and the percentage of youth meeting the physical activity guideline were well-aligned between the Actical and the PAYQ; however, large differences were evident at the individual level. Therefore, caution should be exercised in using data from these two methods since their values may not be interchangeable.

BENIN: Biologically enhanced network inference

Gene regulatory network inference is one of the central problems in computational biology. We need models that integrate the variety of data available in order to use their complementarity information to overcome the issues of noisy and limited data. BENIN: Biologically Enhanced Network INference is our proposal to integrate data and infer more accurate networks. BENIN is a general framework that jointly considers different types of prior knowledge with expression datasets to improve the network inference. The method states the network inference as a feature selection problem and uses a popular penalized regression method, the Elastic net, combined with bootstrap resampling to solve it. BENIN significantly outperforms the state-of-the-art methods on the simulated data from the DREAM 4 challenge when combining genome-wide location data, knockout gene expression data, and time series expression data.

TooT-T: discrimination of transport proteins from non-transport proteins

Background

Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and function is still not well characterized and understood, owing to the immense effort needed to characterize them. Therefore, there is a need for advanced computational techniques takes sequence information alone to distinguish membrane transporter proteins; this can then be used to direct new experiments and give a hint about the function of a protein.

Results

This work proposes an ensemble classifier TooT-T that is trained to optimally combine the predictions from homology annotation transfer and machine-learning methods to determine the final prediction. Experimental results obtained by cross-validation and independent testing show that combining the two approaches is more beneficial than employing only one.

Conclusion

The proposed model outperforms all of the state-of-the-art methods that rely on the protein sequence alone, with respect to accuracy and MCC. TooT-T achieved an overall accuracy of 90.07% and 92.22% and an MCC 0.80 and 0.82 with the training and independent datasets, respectively.

TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information

Transporters mediate the movement of compounds across the membranes that separate the cell from its environment and across the inner membranes surrounding cellular compartments. It is estimated that one third of a proteome consists of membrane proteins, and many of these are transport proteins. Given the increase in the number of genomes being sequenced, there is a need for computational tools that predict the substrates that are transported by the transmembrane transport proteins. In this paper, we present TranCEP, a predictor of the type of substrate transported by a transmembrane transport protein. TranCEP combines the traditional use of the amino acid composition of the protein, with evolutionary information captured in a multiple sequence alignment (MSA), and restriction to important positions of the alignment that play a role in determining the specificity of the protein. Our experimental results show that TranCEP significantly outperforms the state-of-the-art predictors. The results quantify the contribution made by each type of information used.

Oxytocin reduces post-stress sweet snack intake in women without attenuating salivary cortisol

Intranasal oxytocin produces anorectic effects on snack intake in men when tested in the absence of deprivation-induced hunger, but its effects on food intake in women without eating disorders have not been reported. Oxytocin may reduce food intake by reducing stress eating, since it inhibits ACTH release. The present study adopted a double-blind, repeated measures and fully concealed crossover protocol in which 38 women self-administered 24 IU of oxytocin or placebo intranasally, ate lunch, and underwent two consecutive stress tests. Snack intake was assessed 15-20 min after lunch, via a sham taste test. Salivary cortisol was measured throughout the test period every 15 min. Oxytocin significantly reduced sweet fatty snack intake independently of any effect on salivary cortisol, which declined over time at a similar rate after either drug or placebo. Ratings of sweet taste were slightly reduced by oxytocin, but only in self-reported stress eaters. These results differ from previous studies with men that found an effect of oxytocin on postprandial cortisol levels. However, previous research assayed the less active form of plasma cortisol and did not control for protein intake, which can drive elevated cortisol. The finding that oxytocin reduces snack intake in females after acute stress has important implications for appetite regulation and its treatment in obese people and in those with eating disorders.

Comparison of self-reported and accelerometer-measured physical activity in Canadian adults

BACKGROUND

Self-reported and accelerometer-measured physical activity levels generally exhibit low correlation and agreement. The objective of this study is to compare estimates of physical activity among adults from a newly developed Canadian questionnaire with those obtained objectively by accelerometry.

DATA AND METHODS

Data for 18- to 79-year-olds (N = 2,372) were collected in 2014 and 2015 as part of the Canadian Health Measures Survey (CHMS). Moderate-to-vigorous physical activity (MVPA) was reported on the household questionnaire by domain (transportation, recreation, and occupational or household) as part of the new Physical Activity Adult Questionnaire (PAAQ) and measured objectively using the Actical accelerometer. Correlation and mean difference analyses were used to assess the relationships between measured and reported physical activity variables. Linear regression was used to test the association between measured and reported physical activity and measures of obesity.

RESULTS

On average, Canadian adults reported more physical activity than they accumulated on an accelerometer (49 minutes versus 23 minutes per day). The highest correlation observed was between accelerometer-measured MVPA and the sum of self-reported recreation and transportation activity (R = 0.36, p ⟨ 0.0001). The sum of activity from all domains (recreation + transportation + occupational or household) exhibited a lower correlation with measured variables because the occupational or household domain was negatively correlated with MVPA (R = -0.04). The occupational or household domain was positively correlated with light-intensity physical activity (R = 0.20, p ⟨ 0.0001). Respondents in the least active quintile were more likely than those in the most active quintile to report more activity than was measured by the accelerometer. On average, the most active quintile reported less activity than was measured by the accelerometer.

DISCUSSION

The newly developed Canadian physical activity questionnaire exhibited modest correlation and agreement with accelerometer-measured physical activity among adults. Accelerometers and questionnaires provide complementary information, about different aspects of physical activity (actual movement versus perceived time). Consequently, one should exercise caution in using estimates derived from these methods interchangeably.

Characteristics of people with severe mental illness who obtain employment

Aims and method

We explored sociodemographic and clinical factors associated with obtaining employment for people with severe mental illness. Standardised validated interviews and questionnaires were administered to participants who had been recruited into a randomised controlled trial of supported employment.

Results

Older age and diagnosis of schizophrenia were found to be independent predictors of unemployment in the previous year. Other factors of unemployment such as ethnicity and educational level were not associated with obtaining employment.

Clinical implications

Older people and those with a diagnosis of schizophrenia may need additional targeted help in obtaining employment if they are to be helped to meet their vocational aims. Further research is needed to determine how this can be done most effectively.

Implementing a nursing systems framework in a developing country

AIM

To test the effect on patient mortality of implementing a nursing systems framework across a national health system.

BACKGROUND

There have been five previous observational studies that have tested the effect of a nursing systems framework on clinical outcomes for patients. Implementation of a nursing systems framework in the health system of a developing country has not been evaluated.

DESIGN

Quasi-experimental (before and after) study.

METHOD

A nursing systems framework consisting of six themes: (i) Professionalisation; (ii) Education; (iii) Structure; (iv) Quality of nursing care; (v) An academic health system; and (vi) Communication (Professional), was implemented across the national health system of Qatar in March 2015. Routine administrative data were extracted (March 2014-February 2016) for elective admissions. Our primary and secondary outcomes were, respectively, all cause mortality at discharge and readmission to hospital (within 28 days of discharge). We split the data into two time periods: before (March 2014-February 2015) and after (March 2015-February 2016) the implementation of the nursing systems framework. Multivariable regression modelling was used to examine the effect of the framework on patient mortality, after adjusting for key confounding variables (patient age, episode acuity, intensive care admission and length of stay).

FINDINGS

Data were extracted for 318 548 patients (year 1 = 130 829; year 2 = 187 725). After adjusting for confounding, there was a significant association between the implementation of the nursing systems framework, mortality and readmission.

CONCLUSION AND IMPLICATIONS FOR NURSING POLICY AND PRACTICE

Our observations suggest that the implementation of a nursing systems framework may be important in improving outcomes for patients in emerging health systems.

Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance

OBJECTIVES

Candida parapsilosis is a healthcare-related fungal pathogen particularly common among immunocompromised patients. Our understanding of antifungal resistance mechanisms in C. parapsilosis remains very limited. We previously described an azole-resistant strain of C. parapsilosis (BC014R_PSC), obtained following exposure in vitro to posaconazole. Resistance was associated with overexpression of ergosterol biosynthetic genes (ERG genes), together with the transcription factors UPC2 (CPAR2-207280) and NDT80 (CPAR2-213640). The aim of this study was to identify the mechanisms underlying posaconazole resistance of the BC014R_PSC strain.

METHODS

To identify the causative mutation, we sequenced the genomes of the susceptible (BC014S) and resistant (BC014R_PSC) isolates, using Illumina technology. Ergosterol content was assessed in both strains by mass spectrometry. UPC2 and NDT80 genes were deleted in BC014R_PSC strain. Mutants were characterized regarding their azole susceptibility profile and ERG gene expression.

RESULTS

One homozygous missense mutation (R135I) was found in ERG3 (CPAR2-105550) in the azole-resistant isolate. We show that Erg3 activity is completely impaired, resulting in a build up of sterol intermediates and a failure to generate ergosterol. Deleting UPC2 and NDT80 in BC014R_PSC reduces the expression of ERG genes and restores susceptibility to azole drugs.

CONCLUSIONS

A missense mutation in the ERG3 gene results in azole resistance and up-regulation of ERG genes expression. We propose that this mutation prevents the formation of toxic intermediates when cells are treated with azoles. Resistance can be reversed by deleting Upc2 and Ndt80 transcription factors. UPC2 plays a stronger role in C. parapsilosis azole resistance than does NDT80.

An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures

Computational design of RNA sequences that fold into targeted secondary structures has many applications in biomedicine, nanotechnology and synthetic biology. An RNA molecule is made of different types of secondary structure elements and an important RNA element named pseudoknot plays a key role in stabilizing the functional form of the molecule. However, due to the computational complexities associated with characterizing pseudoknotted RNA structures, most of the existing RNA sequence designer algorithms generally ignore this important structural element and therefore limit their applications. In this paper we present a new algorithm to design RNA sequences for pseudoknotted secondary structures. We use NUPACK as the folding algorithm to compute the equilibrium characteristics of the pseudoknotted RNAs, and describe a new adaptive defect weighted sampling algorithm named Enzymer to design low ensemble defect RNA sequences for targeted secondary structures including pseudoknots. We used a biological data set of 201 pseudoknotted structures from the Pseudobase library to benchmark the performance of our algorithm. We compared the quality characteristics of the RNA sequences we designed by Enzymer with the results obtained from the state of the art MODENA and antaRNA. Our results show our method succeeds more frequently than MODENA and antaRNA do, and generates sequences that have lower ensemble defect, lower probability defect and higher thermostability. Finally by using Enzymer and by constraining the design to a naturally occurring and highly conserved Hammerhead motif, we designed 8 sequences for a pseudoknotted cis-acting Hammerhead ribozyme. Enzymer is available for download at https://bitbucket.org/casraz/enzymer.

GH safety workshop position paper: a critical appraisal of recombinant human GH therapy in children and adults

Recombinant human GH (rhGH) has been in use for 30 years, and over that time its safety and efficacy in children and adults has been subject to considerable scrutiny. In 2001, a statement from the GH Research Society (GRS) concluded that 'for approved indications, GH is safe'; however, the statement highlighted a number of areas for on-going surveillance of long-term safety, including cancer risk, impact on glucose homeostasis, and use of high dose pharmacological rhGH treatment. Over the intervening years, there have been a number of publications addressing the safety of rhGH with regard to mortality, cancer and cardiovascular risk, and the need for long-term surveillance of the increasing number of adults who were treated with rhGH in childhood. Against this backdrop of interest in safety, the European Society of Paediatric Endocrinology (ESPE), the GRS, and the Pediatric Endocrine Society (PES) convened a meeting to reappraise the safety of rhGH. The ouput of the meeting is a concise position statement.

A review of genomic data warehousing systems

To facilitate the integration and querying of genomics data, a number of generic data warehousing frameworks have been developed. They differ in their design and capabilities, as well as their intended audience. We provide a comprehensive and quantitative review of those genomic data warehousing frameworks in the context of large-scale systems biology. We reviewed in detail four genomic data warehouses (BioMart, BioXRT, InterMine and PathwayTools) freely available to the academic community. We quantified 20 aspects of the warehouses, covering the accuracy of their responses, their computational requirements and development efforts. Performance of the warehouses was evaluated under various hardware configurations to help laboratories optimize hardware expenses. Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW (http://warehousebenchmark.fungalgenomics.ca/benchmark/) to build custom warehouse profiles and tailor our results to their specific needs.

Impact of US Brown Swiss genetics on milk quality from low-input herds in Switzerland: interactions with grazing intake and pasture type

This study investigated the effect of, and interactions between, contrasting crossbreed genetics (US Brown Swiss [BS] × Improved Braunvieh [BV] × Original Braunvieh [OB]) and feeding regimes (especially grazing intake and pasture type) on milk fatty acid (FA) profiles. Concentrations of total polyunsaturated FAs, total omega-3 FAs and trans palmitoleic, vaccenic, α-linolenic, eicosapentaenoic and docosapentaenoic acids were higher in cows with a low proportion of BS genetics. Highest concentrations of the nutritionally desirable FAs, trans palmitoleic, vaccenic and eicosapentaenoic acids were found for cows with a low proportion of BS genetics (0-24% and/or 25-49%) on high grazing intake (75-100% of dry matter intake) diets. Multivariate analysis indicated that the proportion of OB genetics is a positive driver for nutritionally desirable monounsaturated and polyunsaturated FAs while BS genetics proportion was positive driver for total and undesirable individual saturated FAs. Significant genetics × feeding regime interactions were also detected for a range of FAs.

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

BACKGROUND

Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them.

RESULTS

SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data.

CONCLUSIONS

SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/.

Improving the fatty acid profile of winter milk from housed cows with contrasting feeding regimes by oilseed supplementation

Many studies show concentrations of nutritionally desirable fatty acids in bovine milk are lower when cows have no access to grazing, leading to seasonal fluctuations in milk quality if cows are housed for part of the year. This study investigated the potential to improve the fatty acid profiles of bovine milk by oilseed supplementation (rolled linseed and rapeseed) during a period of indoor feeding in both organic and conventional production systems. Both linseed and rapeseed increased the concentrations of total monounsaturated fatty acids, vaccenic acid, oleic acid and rumenic acid in milk, but decreased the concentration of the total and certain individual saturated fatty acids. Linseed resulted in greater changes than rapeseed, and also significantly increased the concentrations of α-linolenic acid, total polyunsaturated fatty acids and total omega-3 fatty acids. The response to oilseed supplementation, with respect to increasing concentrations of vaccenic acid and omega-3 fatty acids, appeared more efficient for organic compared with conventional diets.

Implications of parent and child quality of life assessments for decisions about growth hormone treatment in eligible children

OBJECTIVE

To determine differences between parents and children in ratings of child health-related quality of life (HRQL) prior to growth hormone treatment.

METHOD

HRQL measures were collected from 144 children and their caregivers. Inclusion criteria were aged between 10 and 16 years, diagnosed with Turner's syndrome, acquired or idiopathic growth hormone deficiency (AGHD or IGHD) and eligible to begin human GH treatment (GHT), or non-growth hormone deficient (GHD) short stature.

RESULTS

Parents rated children to have poorer physical and psychosocial HRQL than children rated themselves. Differences depended on the measure used. Parents rated children with IGHD and non-GHD short stature better than children rated themselves, but they rated children with AGHD or Turner's much worse than children rated themselves in terms of physical but not psychosocial functioning.

CONCLUSIONS

Decisions to prescribe GHT should include children's perspectives of HRQL whenever possible. Differences between parents and children are most likely in conditions that involve more complex medical needs (AGHD and Turner's). Generic and disease-specific HRQL measures may vary in sensitivity to HRQL differences between groups. More work is required to evaluate HRQL among younger children.

Retrospective chart review in a cohort of patients with urticarial dermatitis

Urticarial dermatitis is a poorly understood skin condition while it seems to be much more common than the paucity of reports suggest. It manifests with severely pruritic papules and plaques that resemble eczematous and urticarial lesions morphologically. The key clues to diagnosis are the urticarial appearance and overlap with an eczematous reaction. Here, we present a series of 19 cases (13 women and six men) with urticarial dermatitis clinically and histologically. The patients' average age was 58 and most of the cases were idiopathic. Trunk and proximal extremities were the most common sites involved followed by the distal extremities. Poor response to potent topical corticosteroids and antihistamines was usual and many patients required oral prednisone or other immunosuppressant agents or phototherapy.

The EnzymeTracker: an open-source laboratory information management system for sample tracking

BACKGROUND

In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems.

RESULTS

In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking.

CONCLUSIONS

The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license.

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.

Mycobacterium abscessus infection complicating a professional tattoo

A healthy 23-year-old man presented with a tender papular eruption confined to the grey pigment of a recently acquired professional tattoo. Atypical mycobacterial infection was suspected and culture of a tissue specimen grew Mycobacterium abscessus. He was successfully treated with minocycline and subsequently, clarithromycin. We present a brief review of M. abscessus infection, with a particular focus on its role in nosocomial infections and in the post-tattoo setting.

Fat composition of organic and conventional retail milk in northeast England

This study of UK retail milk identified highly significant variations in fat composition. The survey, conducted over 2 yr replicating summer and winter, sampled 22 brands, 10 of which indicated organic production systems. Results corroborate earlier farm-based findings considering fat composition of milk produced under conventional and organic management. Organic milk had higher concentrations of beneficial fatty acids (FA) than conventional milk, including total polyunsaturated fatty acids (PUFA; 39.4 vs. 31.8 g/kg of total FA), conjugated linoleic acid cis-9,trans-11 (CLA9; 7.4 v 5.6 g/kg of FA), and α-linolenic acid (α-LN; 6.9 vs. 4.4 g/kg of FA). As expected, purchase season had a strong effect on fat composition: compared with milk purchased in winter, summer milk had a lower concentration of saturated fatty acids (682 vs. 725 g/kg of FA) and higher concentrations of PUFA (37.6 vs. 32.8 g/kg of FA), CLA9 (8.1 vs. 4.7 g/kg of FA), and α-LN (6.5 vs. 4.6 g/kg of FA). Differences identified between sampling years were more surprising: compared with that in yr 2, milk purchased in year 1 had higher concentrations of PUFA (37.5 vs. 32.9 g/kg of FA), α-LN (6.0 vs. 5.1 g/kg of FA), and linoleic acid (19.9 vs. 17.5 g/kg of FA) and lower concentrations of C16:0 and C14:0 (332 vs. 357 and 110 vs. 118 g/kg of FA, respectively). Strong interactions were identified between management and season as well as between season and year of the study. As in the earlier farm studies, differences in fat composition between systems were greater for summer compared with winter milk. Large between-year differences may be due to changes in weather influencing milk composition through forage availability, quality, and intake. If climate change predictions materialize, both forage and dairy management may have to adapt to maintain current milk quality. Considerable variation existed in milk fat composition between brands.

Milk quality as affected by feeding regimens in a country with climatic variation

To investigate the influence of climatic conditions and season on milk composition, bulk tank milk was sampled on 5 occasions during a period of 15 mo from 20 Swedish dairy farms. These farms included 5 organic and 5 conventional farms in central Sweden and 7 traditional conventional farms and 3 conventional farms growing maize for silage in southern Sweden. Feed data and milk yield were recorded and milk was analyzed for content of fatty acids, carotenoids, and tocopherol. Differences between milk from the 2 regions and between summer and winter seasons were shown. Milk from central Sweden differed from milk from southern Sweden in that it had a higher content of carotenoids, tocopherol, short-chain fatty acids (C4-C14), C18:0, and C18:3 n-3 and a lower content of C16. Summer milk samples had a lower fat content and contained higher amounts of C18:1 cis-9 and conjugated linoleic acid cis-9,trans-11, and lower amounts of C4 to C16 compared with winter milk. Differences between farm types from central Sweden were lower content of conjugated linoleic acid cis-9,trans-11 and higher content of C18:3 n-3 in organic milk compared with conventional milk. In southern Sweden the use of maize silage caused lower milk content of carotenoids and C18:3 n-3 when compared with traditional feeding. Differences in milk composition could be related to climatic differences because legumes are more dominating in the leys of central Sweden and maize growing is limited to southern Sweden.

Effectiveness and cost-effectiveness of height-screening programmes during the primary school years: a systematic review

OBJECTIVE

To determine the effectiveness and cost-effectiveness of height screening (of children aged 4 to 11) to identify height-related conditions.

DESIGN

Systematic review and economic modelling.

SETTING AND INTERVENTION

We included published and unpublished screening studies of any design, except case reports, conducted in any setting that measured children's height as part of a population-level assessment. Studies were identified by electronic database searches, contact with experts and from bibliographies of retrieved studies.

PARTICIPANTS

Children aged between 4 and 11 years.

OUTCOME MEASURES

Diagnostic yield of height-related conditions and change in quality of life, as measured by quality-adjusted life years (QALYs), for early versus late treatment of underlying conditions.

RESULTS

Twelve studies described a height-screening programme and provided data on the diagnostic yield of newly diagnosed height-related conditions. Where reported, yield for growth-hormone deficiency (per 1000 children screened) ranged from 0.05 (1 in 20,000) to 0.62 (approximately 1 in 1500) and for Turner syndrome (per 1000 children screened) was between 0.02 (1 in 50,000) and 0.07 (approximately 1 in 14,000). As a secondary gain, children with other potentially treatable conditions were identified; diagnostic yields ranged from 0.22 to 1.84 per 1000 children screened. Three studies did not detect any new cases, but all of these studies had methodological limitations. Economic modelling suggested that height screening is associated with health improvements and is cost effective for a willingness to pay threshold of pound 30,000 per QALY.

CONCLUSIONS

This review indicates the utility and acceptable cost-effectiveness of height screening arising from increased detection of height-related disorders and secondary pick-up of other undiagnosed conditions. Further research is needed to obtain more reliable data on quality of life gains and costs associated with early interventions for height-related conditions. The exact role of height-screening programmes in improving child health remains to be determined.

A systematic review of the routine monitoring of growth in children of primary school age to identify growth-related conditions

OBJECTIVES

To clarify the role of growth monitoring in primary school children, including obesity, and to examine issues that might impact on the effectiveness and cost-effectiveness of such programmes.

DATA SOURCES

Electronic databases were searched up to July 2005. Experts in the field were also consulted.

REVIEW METHODS

Data extraction and quality assessment were performed on studies meeting the review's inclusion criteria. The performance of growth monitoring to detect disorders of stature and obesity was evaluated against National Screening Committee (NSC) criteria.

RESULTS

In the 31 studies that were included in the review, there were no controlled trials of the impact of growth monitoring and no studies of the diagnostic accuracy of different methods for growth monitoring. Analysis of the studies that presented a 'diagnostic yield' of growth monitoring suggested that one-off screening might identify between 1:545 and 1:1793 new cases of potentially treatable conditions. Economic modelling suggested that growth monitoring is associated with health improvements [incremental cost per quality-adjusted life-year (QALY) of 9500 pounds] and indicated that monitoring was cost-effective 100% of the time over the given probability distributions for a willingness to pay threshold of 30,000 pounds per QALY. Studies of obesity focused on the performance of body mass index against measures of body fat. A number of issues relating to human resources required for growth monitoring were identified, but data on attitudes to growth monitoring were extremely sparse. Preliminary findings from economic modelling suggested that primary prevention may be the most cost-effective approach to obesity management, but the model incorporated a great deal of uncertainty.

CONCLUSIONS

This review has indicated the potential utility and cost-effectiveness of growth monitoring in terms of increased detection of stature-related disorders. It has also pointed strongly to the need for further research. Growth monitoring does not currently meet all NSC criteria. However, it is questionable whether some of these criteria can be meaningfully applied to growth monitoring given that short stature is not a disease in itself, but is used as a marker for a range of pathologies and as an indicator of general health status. Identification of effective interventions for the treatment of obesity is likely to be considered a prerequisite to any move from monitoring to a screening programme designed to identify individual overweight and obese children. Similarly, further long-term studies of the predictors of obesity-related co-morbidities in adulthood are warranted. A cluster randomised trial comparing growth monitoring strategies with no growth monitoring in the general population would most reliably determine the clinical effectiveness of growth monitoring. Studies of diagnostic accuracy, alongside evidence of effective treatment strategies, could provide an alternative approach. In this context, careful consideration would need to be given to target conditions and intervention thresholds. Diagnostic accuracy studies would require long-term follow-up of both short and normal children to determine sensitivity and specificity of growth monitoring.