Flexible Long-Term Secure Archiving

Privacy and data protection have always been basic human needs in any society that makes use of written language. From simple personal correspondence over military communication to trade secrets or medical information, confidentiality has been of utmost importance. The implications of a leak of such sensitive information may prove devastating, as the previous examples illustrate perfectly. Furthermore reliability, that is, integrity and authenticitiy of information, is critical with risks reaching from annoying to lethal as can again be seen in the previous examples. This need for data protection has carried over from the analogue to the digital age seamlessly with the amount of data being generated, transmitted and stored increasing steadily and containing more and more personal details. And in regard of the developments in computational technology that recent years have seen, such as the ongoing improvements with respect to quantum computing as well as cryptoanalytical advances, the capabilities of attackers on the security of private information have never been more distinct. Thus the need for privacy and data protection has rarely been more dire

Development of high quality niche products from local chicken and pig genetic resources

This thesis indicates that the application of non-conventional and/or slow-growing pig and chicken genotypes alone does not guarantee a superior and/or distinctive meat color and quality of the products. It appears that the valorization of monogastric meat products through niche marketing is critically dependent on matching the respective genotype with appropriate production methods, thus, for instance, highlighting the need for producers to be discerning in regard to the choice of slaughter age and feeding strategy. In the case that these premises are implemented, a distinguished positioning of meat products derived from local pig and chicken genetic resources can be realized, and, expanded by standards that also take the social and economic dimensions of food value chains into account, translated into a common pool resource as a basis for an alternative food network. Efforts should then be directed toward the elaboration of stable distribution channels and effective governance structures in the respective food network.Zusammenfassend deutet diese Arbeit darauf hin, dass der Einsatz nicht-konventioneller und/oder langsam wachsender Schweine- und Hühnergenotypen an sich keine erhöhte bzw. unterscheidbare Fleischfarbe sowie -qualität bedingt. Es scheint, dass die Inwertsetzung der Fleischprodukte von Monogastriern durch Nischenvermarktung wesentlich von der Kombination der jeweiligen Genotypen mit geeigneten Produktionsmethoden abhängt, wodurch die Bedeutung einer gezielten, passgenauen Wahl des Schlachtalters und der Fütterungsstrategie durch den Produzenten hervorgehoben wird. Diese spezifische Kombination einer lokalen tiergenetischen Ressource mit entsprechenden Produktionsstandards bildet so ein normatives Gefüge, welches die Stabilität eines alternativen Wertschöpfungsnetzwerkes gewährleisten kann. Der Fokus sollte dann auf die nicht minder bedeutsame Entwicklung nachhaltiger Vertriebswege und effektiver Unternehmensstrukturen des betreffenden Produktions- und Vermarktungsnetzwerkes gelegt werden

Mistle: bringing spectral library predictions to metaproteomics with an efficient search index

Motivation Deep learning has moved to the forefront of tandem mass spectrometry-driven proteomics and authentic prediction for peptide fragmentation is more feasible than ever. Still, at this point spectral prediction is mainly used to validate database search results or for confined search spaces. Fully predicted spectral libraries have not yet been efficiently adapted to large search space problems that often occur in metaproteomics or proteogenomics. Results In this study, we showcase a workflow that uses Prosit for spectral library predictions on two common metaproteomes and implement an indexing and search algorithm, Mistle, to efficiently identify experimental mass spectra within the library. Hence, the workflow emulates a classic protein sequence database search with protein digestion but builds a searchable index from spectral predictions as an in-between step. We compare Mistle to popular search engines, both on a spectral and database search level, and provide evidence that this approach is more accurate than a database search using MSFragger. Mistle outperforms other spectral library search engines in terms of run time and proves to be extremely memory efficient with a 4- to 22-fold decrease in RAM usage. This makes Mistle universally applicable to large search spaces, e.g. covering comprehensive sequence databases of diverse microbiomes. Availability and implementation Mistle is freely available on GitHub at https://github.com/BAMeScience/Mistle

Carcass Grading for Local Vietnamese Ban Pigs and its Potential for a Quality Feedback System in a Short Food Supply Chain

AbstractIn-situ conservation of local pig breeds in Southeast Asia requires genetic improvement embedded in viable marketing concepts. Increasing demand offers marketing opportunities for indigenous Vietnamese Ban pork. This study sought to adjust estimation methods for grading light carcasses according to their leanness. Using data from the dissection of 45 carcasses, several models were fitted and evaluated. Although the predictive power of the equations was limited, Ban carcasses could be approximatively classified according to their lean content. Finally, a suggestion of how to include these measurements in a quality feedback system of a short food supply chain is made

Optimising contributions of goat farming to household economic success and food security in three production systems in Ethiopia

The study aims to analyse factors affecting contributions of goat farming to household economic success and food security in three goat production systems of Ethiopia. A study was conducted in three districts of Ethiopia representing arid agro-pastoral (AAP), semi-arid agro-pastoral (SAAP) and highland mixed crop-livestock (HMCL) systems involving 180 goat keeping households. Gross margin (GM) and net benefit (NB1 and NB2) were used as indicators of economic success of goat keeping. NB1 includes in-kind benefits of goats (consumption and manure), while NB2 additionally constitutes intangible benefits (insurance and finance). Household dietary diversity score (HDDS) was used as a proxy indicator of food security. GM was significantly affected by an off-take rate and flock size interaction (P0.001). The increment of GM due to increased off-take rate was more prominent for farmers with bigger flocks. Interaction between flock size and production system significantly (P0.001) affected both NB1 and NB2. The increment of NB1 and NB2 by keeping larger flocks was higher in AAP system, due to higher in-kind and intangible benefits of goats in this system. Effect of goat flock size as a predictor of household dietary diversity was not significant (P0.05). Nevertheless, a significant positive correlation (P0.05) was observed between GM from goats and HDDS in AAP system, indicating the indirect role of goat production for food security. The study indicated that extent of utilising tangible and intangible benefits of goats varied among production systems and these differences should be given adequate attention in designing genetic improvement programs

Discriminating the quality of local pork from crossbred pork from extensive production of ethnic minorities in mountainous northern Vietnam

Developing short food supply chains for products from local pig (Sus scrofa domesticus) breeds may offer chances for smallholders in rural areas to participate in niche markets and obtain additional income. Because the authenticity and distinctness of products are crucial for establishing marketing, this study compared selected product characteristics of pork from the Vietnamese Ban breed with pork from crossbreds, each derived at their typical market weight and from their respective extensive and semi-extensive production environment; thus resembling the combination, the products are available for customers. Traditional Ban pork could be effectively discriminated from crossbred pork through cut dimensions, exemplified by the significantly reduced loin eye area (P 0.001), and by the significantly reduced backfat thickness (P 0.001). Also, marbling fat was significantly decreased in local pork (P 0.001), whereas differences in further meat quality parameters were rather weakly expressed. The significantly higher share of polyunsaturated fatty acids in loins of traditionally produced Ban pigs (P = 0.003) could possibly result in a preferred nutritional value, but lower oxidative stability of the products. This study provides novel information to improve the marketing of specialty pork in Vietnam and comparable situations in the Southeast Asian Massif

Efficient and accurate modeling of electron photoemission in nanostructures with TDDFT

We derive and extend the time-dependent surface-flux method introduced in [L. Tao, A. Scrinzi, New J. Phys. 14, 013021 (2012)] within a time-dependent density-functional theory (TDDFT) formalism and use it to calculate photoelectron spectra and angular distributions of atoms and molecules when excited by laser pulses. We present other, existing computational TDDFT methods that are suitable for the calculation of electron emission in compact spatial regions, and compare their results. We illustrate the performance of the new method by simulating strong-field ionization of C60 fullerene and discuss final state effects in the orbital reconstruction of planar organic molecules

Effect of aliskiren on post-discharge outcomes among diabetic and non-diabetic patients hospitalized for heart failure: insights from the ASTRONAUT trial

Aims The objective of the Aliskiren Trial on Acute Heart Failure Outcomes (ASTRONAUT) was to determine whether aliskiren, a direct renin inhibitor, would improve post-discharge outcomes in patients with hospitalization for heart failure (HHF) with reduced ejection fraction. Pre-specified subgroup analyses suggested potential heterogeneity in post-discharge outcomes with aliskiren in patients with and without baseline diabetes mellitus (DM). Methods and results ASTRONAUT included 953 patients without DM (aliskiren 489; placebo 464) and 662 patients with DM (aliskiren 319; placebo 343) (as reported by study investigators). Study endpoints included the first occurrence of cardiovascular death or HHF within 6 and 12 months, all-cause death within 6 and 12 months, and change from baseline in N-terminal pro-B-type natriuretic peptide (NT-proBNP) at 1, 6, and 12 months. Data regarding risk of hyperkalaemia, renal impairment, and hypotension, and changes in additional serum biomarkers were collected. The effect of aliskiren on cardiovascular death or HHF within 6 months (primary endpoint) did not significantly differ by baseline DM status (P = 0.08 for interaction), but reached statistical significance at 12 months (non-DM: HR: 0.80, 95% CI: 0.64-0.99; DM: HR: 1.16, 95% CI: 0.91-1.47; P = 0.03 for interaction). Risk of 12-month all-cause death with aliskiren significantly differed by the presence of baseline DM (non-DM: HR: 0.69, 95% CI: 0.50-0.94; DM: HR: 1.64, 95% CI: 1.15-2.33; P < 0.01 for interaction). Among non-diabetics, aliskiren significantly reduced NT-proBNP through 6 months and plasma troponin I and aldosterone through 12 months, as compared to placebo. Among diabetic patients, aliskiren reduced plasma troponin I and aldosterone relative to placebo through 1 month only. There was a trend towards differing risk of post-baseline potassium ≥6 mmol/L with aliskiren by underlying DM status (non-DM: HR: 1.17, 95% CI: 0.71-1.93; DM: HR: 2.39, 95% CI: 1.30-4.42; P = 0.07 for interaction). Conclusion This pre-specified subgroup analysis from the ASTRONAUT trial generates the hypothesis that the addition of aliskiren to standard HHF therapy in non-diabetic patients is generally well-tolerated and improves post-discharge outcomes and biomarker profiles. In contrast, diabetic patients receiving aliskiren appear to have worse post-discharge outcomes. Future prospective investigations are needed to confirm potential benefits of renin inhibition in a large cohort of HHF patients without D

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Prevalence and risk factors of Strongyloides stercoralis in Takeo Province, Cambodia

The threadworm Strongyloides stercoralis, the most neglected helminth, affects an estimated 30-100 million people worldwide. Information on S. stercoralis infection is scarce in tropical and sub-tropical resource poor countries, including Cambodia. We determined S. stercoralis infection prevalence and risk factors for infection in the general population in Southern Cambodia.; A cross-sectional study was carried out between January and April 2011 among 2,861 participants living in 60 villages of Takeo province, using Koga-agar plate culture, the Baermann technique and the Kato-Katz technique on a single stool sample.; Eight intestinal helminth species were diagnosed. Hookworm (31.4%) and S. stercoralis (21.0%) occurred most frequently. Prevalence of S. stercoralis infection increased with age. In all age groups a higher prevalence was found among males than among females (OR: 1.7; 95% CI: 1.4 - 2.0; P > 0.001). Participants who had a latrine at home were significantly less frequently infected with S. stercoralis than those who did not (OR: 0.7; 95% CI: 0.4 - 0.8; P = 0.003). Muscle pain (OR: 1.3; 95% CI: 1.0 - 1.6; P = 0.028) and urticaria (OR: 1.4; 95% CI: 1.1 - 1.8; P = 0.001) were significantly associated with S. stercoralis infection.; S. stercoralis is highly prevalent among the general Cambodian population and should no longer be neglected. Access to adequate diagnosis and treatment is urgently needed