Bioefficacy of a mono-component protease in the diets of pigs and poultry: a meta-analysis of effect on ileal amino acid digestibility

A meta-analysis of the effect of a mono-component bacterial protease (RONOZYME® ProAct) on the apparent ileal digestibility of amino acids in poultry and swine diets was conducted to examine functional patterns, mean effects and variability of response. A total of 25 independently-conducted experiments were included comprising a total of 804 datapoints. The mean response to protease was +3.74% (SE 1.1%, P0.05). However, the inherent digestibility of amino acids in the control diet as a single explanatory term explained around 47% of the variance (P<0.001) in effect. When the inherent digestibility of amino acids in the control diet was less than 70% protease addition improved amino acid digestibility in 90% of cases with a mean improvement of around 10%. When the inherent digestibility of amino acids in the control diet was more than 90% there was a protease-mediated improvement in digestibility in only 60% of cases with a mean improvement of around 2%. It can be concluded that the inherent digestibility of amino acids in the diet without protease supplementation is the primary explanatory term for the efficacy of this exogenous protease, demonstrating that it is highly effective in improving the digestibility of amino acids across a wide range of feed ingredients. Benchmarking diets or feed ingredients as to their relative nutritional value would enhance the ability of nutritionists to determine the likely return on investment on use of bacterial proteases in their operatio

Numerical analysis of a singularly perturbed convection diffusion problem with shift in space

We consider a singularly perturbed convection-diffusion problem that has in addition a shift term. We show a solution decomposition using asymptotic expansions and a stability result. Based upon this we provide a numerical analysis of high order finite element method on layer adapted meshes. We also apply a new idea of using a coarser mesh in places where weak layers appear. Numerical experiments confirm our theoretical results.Comment: 17 pages, 1 figur

Greenʼs function estimates for a singularly perturbed convection–diffusion problem

We consider a singularly perturbed convection-diusion problem posed in the unit square with a horizontal convective direction. Its solutions exhibit parabolic and exponential boundary layers. Sharp estimates of the Green's function and its first- and second-order derivatives are derived in the L1 norm. The dependence of these estimates on the small diusion parameter is shown explicitly. The obtained estimates will be used in a forthcoming numerical analysis of the considered problem

On using Markov decision processes to model integration solutions for disparate resources in software ecosystems

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.The software ecosystem of an enterprise is usually composed of an heterogeneous set of applications, databases, documents, spreadsheets, and so on. Such resources are involved in the enterprise’s daily activities by supporting its business processes. As a consequence of market change and the enterprise evolution, new business processes emerge and the current ones have to be evolved to tackle the new requirements. It is not a surprise that different resources may be required to collaborate in a business process. However, most of these resources were devised without taking into account their integration with the others, i.e., they represent isolated islands of data and functionality. Thus, the goal of an integration solution is to enable the collaboration of different resources without changing them or increasing their coupling. The analysis of integration solutions to predict their behaviour and find possible performance bottlenecks is an important activity that contributes to increase the quality of the delivered solutions. Software engineers usually follow an approach that requires the construction of the integration solution, the execution of the actual integration solution, and the collection of data from this execution in order to analyse and predict their behaviour. This is a costly, risky, and time-consuming approach. This paper discusses the usage of Markov models for formal modelling of integration solutions aiming at enabling the simulation of the conceptual models of integration solutions still in the design phase. By using well-established simulation techniques and tools at an early development stage, this new approach contributes to reduce cost, risk, development time and improve software quality attributes such as robustness, scalability, and maintenance

PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra

Motivation: Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of independent variations and may therefore overwhelm computational resources. Results: We provide fast, cache-efficient search algorithms to screen large peptide search spaces including non-tryptic peptides, whole genomes, dozens of posttranslational modifications, unannotated point mutations and even unannotated splice sites. All these search spaces can be screened simultaneously. By optimizing the cache usage, we achieve a calculation speed that closely approaches the limits of the hardware. At the same time, we control the size of the overall search space by limiting the combinations of variations that can co-occur on the same peptide. Using a hypergeometric scoring scheme, we applied these algorithms to a dataset of 1 420 632 spectra. We were able to identify a considerable number of peptide variations within a modest amount of computing time on standard desktop computers. Availability: PepSplice is available as a C++ application for Linux, Windows and OSX at www.ti.inf.ethz.ch/pw/software/pepsplice/. It is open source under the revised BSD license. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

A systematic review of vitamin D status in populations worldwide

Vitamin D deficiency is associated with osteoporosis and is thought to increase the risk of cancer and CVD. Despite these numerous potential health effects, data on vitamin D status at the population level and within key subgroups are limited. The aims of the present study were to examine patterns of 25-hydroxyvitamin D (25(OH)D) levels worldwide and to assess differences by age, sex and region. In a systematic literature review using the Medline and EMBASE databases, we identified 195 studies conducted in forty-four countries involving more than 168000 participants. Mean population-level 25(OH)D values varied considerably across the studies (range 4·9-136·2nmol/l), with 37·3% of the studies reporting mean values below 50nmol/l. The highest 25(OH)D values were observed in North America. Although age-related differences were observed in the Asia/Pacific and Middle East/Africa regions, they were not observed elsewhere and sex-related differences were not observed in any region. Substantial heterogeneity between the studies precluded drawing conclusions on overall vitamin D status at the population level. Exploratory analyses, however, suggested that newborns and institutionalised elderly from several regions worldwide appeared to be at a generally higher risk of exhibiting lower 25(OH)D values. Substantial details on worldwide patterns of vitamin D status at the population level and within key subgroups are needed to inform public health policy development to reduce risk for potential health consequences of an inadequate vitamin D statu

Universality and its Origins at the Amorphous Solidification Transition

Systems undergoing an equilibrium phase transition from a liquid state to an amorphous solid state exhibit certain universal characteristics. Chief among these are the fraction of particles that are randomly localized and the scaling functions that describe the order parameter and (equivalently) the statistical distribution of localization lengths for these localized particles. The purpose of this Paper is to discuss the origins and consequences of this universality, and in doing so, three themes are explored. First, a replica-Landau-type approach is formulated for the universality class of systems that are composed of extended objects connected by permanent random constraints and undergo amorphous solidification at a critical density of constraints. This formulation generalizes the cases of randomly cross-linked and end-linked macromolecular systems, discussed previously. The universal replica free energy is constructed, in terms of the replica order parameter appropriate to amorphous solidification, the value of the order parameter is obtained in the liquid and amorphous solid states, and the chief universal characteristics are determined. Second, the theory is reformulated in terms of the distribution of local static density fluctuations rather than the replica order parameter. It is shown that a suitable free energy can be constructed, depending on the distribution of static density fluctuations, and that this formulation yields precisely the same conclusions as the replica approach. Third, the universal predictions of the theory are compared with the results of extensive numerical simulations of randomly cross-linked macromolecular systems, due to Barsky and Plischke, and excellent agreement is found.Comment: 10 pages, including 3 figures (REVTEX

Towards FAIRification of sensitive and fragmented rare disease patient data:challenges and solutions in European reference network registries

INTRODUCTION: Rare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR (‘FAIRification’) differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases. RESULTS: The FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs’ registries were collected and categorised into “training” (31), “community” (9), “modelling” (12), “implementation” (26), and “legal” (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were “training” (15) and “implementation” (9), followed by “community” (7), and then “modelling” (5) and “legal” (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the “training” challenges, which ranged from less-technical “coffee-rounds” to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the “implementation” challenges. CONCLUSION: This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13023-022-02558-5

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p

Surveyed common data access policies preferences amongst European Reference Networks

Background: Data sharing amongst existing Rare Disease (RD) registries, even though being a process that presents multiple barriers, would enrich and ease research, as well as facilitate interoperability between the registries themselves. Methods: To understand their preferences on sharing data, we surveyed 24 European Reference Networks (ERNs) from the RD Domain. Results: The answers show that most ERNs are willing to share a set of Common Data Elements for free with authenticated users at an aggregated or pseudonymized level the moment the data is collected. The one exception is the industry sector, to which ERNs prefer to ask for a fee. Objective: Our aim is to create a reference for how most RD registries are willing to share their data, improving the ability of other stakeholders to make informed decisions to make their data interoperable.</p