Contextualizing digital reformatting in the history of preservation knowledge: timeline and research directions

This research builds a timeline of the development of preservation knowledge drawn from key texts in the field of the history of preservation in order to establish the larger historical and cultural trends shaping digital reformatting as a sociotechnical practice in information institutions. The timeline integrates key events, inventions and standards in the development of preservation knowledge from the 19th century to the present time, and charts and periodizes particular intellectual trends that integrate technological and institutional change into the development of preservation knowledge, focusing primarily on the U.S. context. From these trends, the author identifies a potential area of future research on digital reformatting that draws on perspectives from research in the sociology of standards

Militarized Refugee Populations: Humanitarian Challenges in the Former Yugoslavia

This paper examines the conditions under which refugee flows cause conflict to spread across borders. In order to develop propositions, the paper studies a group of Bosnian Muslim refugees who formed an army to retake their hometown. The situation of those refugees suggests that external political conditions, especially support from the refugee receiving state, determined the ability of the refugees to mobilize militarily. The presence of non-civilian elements among the refugees and the influence of powerful refugee leaders acted as necessary, but not sufficient, conditions that led to violence. The Bosnian Muslim case confirms that the actions of humanitarian agencies are constrained by the level of available resources and the attitude of the receiving state. Within those constraints, UNHCR and NGOs may attempt to prevent, reduce, or ignore political violence that involves refugees

Refugee-Related Political Violence: When? Where? How Much?

Lack of information about the nature and extent of refugee involvement in political violence has long hindered researchers and policymakers. This paper presents new time series data in order to analyze the frequency, persistence, intensity, and type of political violence involving refugees for the years 1987 to 1998. The analysis reveals a number of interesting, and surprising, trends that contradict the conventional wisdom about refugee militarization. Overall, while absolute numbers of refugees involved in political violence have decreased, the number of states affected remains constant. The difference results from smaller refugee populations becoming involved in political violence. Another significant finding contradicts the assumption that political violence affects most refugee areas. In fact, very few refugee situations experience political violence. In most years, over one hundred states host refugees, yet 95% of all refugee-related violence usually takes place, on average, in fewer than fifteen states. The findings from this dataset reveal trends in refugee-related violence and change the terms of the current discourse on refugees and political violence

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

Summary: The analysis of genetic data often requires a combination of several approaches using different and sometimes incompatible programs. In order to facilitate data exchange and file conversions between population genetics programs, we introduce PGDSpider, a Java program that can read 27 different file formats and export data into 29, partially overlapping, other file formats. The PGDSpider package includes both an intuitive graphical user interface and a command-line version allowing its integration in complex data analysis pipelines. Availability: PGDSpider is freely available under the BSD 3-Clause license on http://cmpg.unibe.ch/software/PGDSpider/ Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Unicameral Bone Cyst in the Proximal Humerus with Secondary Infection in an 18 -Month-Old Foal

An 18-month-old warmblood filly was 4/5 lame on the front right limb at referral and showed severe swelling of the right shoulder region and pain during manipulation of the shoulder region. Radiography revealed a roundish 5 × 7 cm radiolucent area with defined borders within the greater tubercle and the presence of a fracture of the lateral tubercle associated with the cyst. Cellular blood count was 27,500 WBC/μL and serum biochemical analyses revealed fibrinogen of 855 mg/dL. The fractured bone was removed surgically; the cyst debrided and filled with autologous cancellous bone graft. Three and five weeks after surgery the filly was reoperated on because of an osseous sequestrum and a periostal defect on the distal dorsolateral aspect of the pastern of the right hind limb and a septic synovitis of the DFTS of the left hind limb. Fifteen month after surgery the filly was not lame and was introduced to training. Unicameral bone cysts (UBC) are well described lesions, often associated to pathologic fracture in the proximal humerus of children but, until present, no scientific report exists of UBC in the foal. The prompt surgical management had a favorable outcome

Reference-guided de novo assembly approach improves genome reconstruction for related species.

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly

BMP2 and TGF-β Cooperate Differently during Synovial-Derived Stem-Cell Chondrogenesis in a Dexamethasone-Dependent Manner

Recent studies highlighting mesenchymal stem cell (MSC) epigenetic memory suggest that a different differentiation medium may be required depending on the tissue of origin. As synovial-derived stem cells (SDSCs) attract interest we aimed to investigate the influence of TGF-β1, BMP-2 and dexamethasone on SDSC chondrogenesis in vitro. We demonstrate that dexamethasone-free medium led to enhanced chondrogenic differentiation at both the mRNA and matrix level. The greatest COL2A1/COL10A1 ratio was detected in cells exposed to a combination medium containing 10 ng/mL BMP-2 and 1 ng/mL TGF-β1 in the absence of dexamethasone, and this was reflected in the total amount of glycosaminoglycans produced. In summary, dexamethasone-free medium containing BMP-2 and TGF-β1 may be the most suitable when using SDSCs for cartilage tissue regeneration

Drop on a Bent Fibre

Inspired by the huge droplets attached on cypress tree leaf tips after rain, we find that a bent fibre can hold significantly more water in the corner than a horizontally placed fibre (typically up to three times or more). The maximum volume of the liquid that can be trapped is remarkably affected by the bending angle of the fibre and surface tension of the liquid. We experimentally find the optimal included angle ($\sim {36}{^\circ}$) that holds the most water. Analytical and semi-empirical models are developed to explain these counter-intuitive experimental observations and predict the optimal angle. The data and models could be useful for designing microfluidic and fog harvesting devices

Avoiding the pitfalls of gene set enrichment analysis with SetRank.

The purpose of gene set enrichment analysis (GSEA) is to find general trends in the huge lists of genes or proteins generated by many functional genomics techniques and bioinformatics analyses. Here we present SetRank, an advanced GSEA algorithm which is able to eliminate many false positive hits. The key principle of the algorithm is that it discards gene sets that have initially been flagged as significant, if their significance is only due to the overlap with another gene set. The algorithm is explained in detail and its performance is compared to that of other methods using objective benchmarking criteria. Furthermore, we explore how sample source bias can affect the results of a GSEA analysis. The benchmarking results show that SetRank is a highly specific tool for GSEA. Furthermore, we show that the reliability of results can be improved by taking sample source bias into account. SetRank is available as an R package and through an online web interface