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Category: Hindfoot; Other Introduction/Purpose: Subtalar arthrodesis (SA) is a common procedure to treat end-stage subtalar osteoarthritis. We set out in order to determine whether a combined direct fixation of both anterior and posterior facets during SA might influence union and complications compared to isolated fixation of the posterior facet. Our hypothesis was that a combined fixation increases the union rate and reduces the complication rate. Methods: In this PRISMA-compliant PROSPERO-registered systematic review, we included studies reporting data after SA stabilized with screws in adults. The characteristics of the cohort, study design, surgical details, nonunion and complication rate at the longest follow-up were recorded. The modified Coleman Methodology Score (mCMS) was applied to appraise the quality of studies. Two groups were compared: an ANT/POST group (screws positioned both in the anterior and posterior facet) and an ONLY POST group (isolated posterior facet fixation). Results: Eighteen series (685 feet: ANT/POST=96, ONLY POST=589) were selected. The median follow-up was 28 months (IQR, 12-42). The pooled proportion showed a similar nonunion rate (6% vs 10%;p=0.46) and complication rate (14% vs 19%,p=0.47) in the ANT/POST group as compared to the ONLY POST group. The pooled proportion of reoperation was not different either (ANT/POST: 7% vs ONLY POST: 10%,p=0.37). Kernel regression suggested a correlation between the proportion of open/arthroscopic procedures and the nonunion rate (p=0.025) with a median nonunion rate at 10.9% and 5.9% for open and arthroscopic procedures, respectively. Mean CMS was 40.4 points (poor quality). Conclusion: This proportional meta-analysis suggested that a combined direct fixation of anterior and posterior facets during subtalar arthrodesis does not significantly influence the risk of nonunion nor affects the risk of complication and reoperation as compared to isolated posterior facet fixation.

Abstract Bringing floating offshore wind turbines (FOWTs) to a real industrial maturity and reducing the levelized cost of floating wind energy are key to significantly increasing the penetration of renewables in the energy mix of Mediterranean countries, especially if in combination with suitable energy storage systems, such as those involving green hydrogen production. The present study analyses techno‐economic aspects of some of the technologies related to FOWTs and hydrogen production by means of offshore‐generated energy, aiming to evaluate the potential of a floating wind farm integrated with a power‐to‐gas energy storage system in a specific installation site near the Sardinian shores. In comparison to the pioneering studies to date, a more detailed computational model is used, able to account for several critical factors like a better description of metocean conditions, constraints on grid capacity, and a state‐of‐the‐art model to define the farm layout. Concerning hydrogen production, a comparison between the statistical approach, which is commonly used in the field, and a fully time‐dependent method is performed. Proposed results obtained with the statistic and the time‐dependent approach show values ranging between 3.79 and 5.47€/kg, respectively. These outcomes are thought to provide an interesting comparison between different fidelity approaches and realistic reference values for the levelized cost of hydrogen by floating wind in the Mediterranean Sea.

In this paper we extend to two-dimensional data two recently introduced one-dimensional compressibility measures: the $\gamma $ measure defined in terms of the smallest string attractor, and the $\delta $ measure defined in terms of the number of distinct substrings of the input string. Concretely, we introduce the two-dimensional measures $\gamma _{2D}$ and $\delta _{2D}$ , as natural generalizations of $\gamma $ and $\delta $ , and we initiate the study of their properties. Among other things, we prove that $\delta _{2D}$ is monotone and can be computed in linear time, and we show that, although it is still true that $\delta _{2D}\leq \gamma _{2D}$ , the gap between the two measures can be $\Omega (\sqrt {n})$ and therefore asymptotically larger than the gap between $\gamma $ and $\delta $ . To complete the scenario of two-dimensional compressibility measures, we introduce the measure $b_{2D}$ which generalizes to two dimensions the notion of optimal parsing. We prove that, somewhat surprisingly, the relationship between $b_{2D}$ and $\gamma _{2D}$ is significantly different than in the one-dimensional case. As an application of our results we provide the first analysis of the space usage of the two-dimensional block tree introduced in [Brisaboa et al., Two-dimensional block trees, The computer Journal, 2024]. Our analysis shows that the space usage can be bounded in terms of both $\gamma _{2D}$ and $\delta _{2D}$ . Finally, using insights from our analysis, we design the first linear time and space algorithm for constructing the two-dimensional block tree for arbitrary matrices.

We revisit the fundamental problem of compressing an integer dictionary that supports efficient ${\mathsf {rank}}$ and ${\mathsf {select}}$ operations by exploiting simultaneously two kinds of regularities arising in real data: repetitiveness and approximate linearity. We attack this problem by proposing two novel compressed indexing approaches that extend the classic Lempel-Ziv compression scheme and the more recent block tree data structure with new algorithms and data structures that allow them to also capture regularities in terms of the approximate linearity in the data. Finally, we corroborate these theoretical results with a wide set of experiments on real and synthetic datasets, which allow us to show that our approaches achieve new interesting space-time trade-offs that characterise them as more robust in most practical scenarios compared to the known data structures that exploit only one of the two regularities.

Abstract High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such indexes is a challenge. Fortunately, many of these genomic databases are highly-repetitive—a characteristic that can be exploited to ease the computation of the Burrows-Wheeler Transform (BWT), which underlies many popular indexes. In this paper, we introduce a preprocessing algorithm, referred to as prefix-free parsing, that takes a text T as input, and in one-pass generates a dictionary D and a parse P of T with the property that the BWT of T can be constructed from D and P using workspace proportional to their total size and O(|T|)-time. Our experiments show that D and P are significantly smaller than T in practice, and thus, can fit in a reasonable internal memory even when T is very large. In particular, we show that with prefix-free parsing we can build an 131-MB run-length compressed FM-index (restricted to support only counting and not locating) for 1000 copies of human chromosome 19 in 2 h using 21 GB of memory, suggesting that we can build a 6.73 GB index for 1000 complete human-genome haplotypes in approximately 102 h using about 1 TB of memory.

Abstract Background Sequencing technologies produce larger and larger collections of biosequences that have to be stored in compressed indices supporting fast search operations. Many compressed indices are based on the Burrows–Wheeler Transform (BWT) and the longest common prefix (LCP) array. Because of the sheer size of the input it is important to build these data structures in external memory and time using in the best possible way the available RAM. Results We propose a space-efficient algorithm to compute the BWT and LCP array for a collection of sequences in the external or semi-external memory setting. Our algorithm splits the input collection into subcollections sufficiently small that it can compute their BWT in RAM using an optimal linear time algorithm. Next, it merges the partial BWTs in external or semi-external memory and in the process it also computes the LCP values. Our algorithm can be modified to output two additional arrays that, combined with the BWT and LCP array, provide simple, scan-based, external memory algorithms for three well known problems in bioinformatics: the computation of maximal repeats, the all pairs suffix–prefix overlaps, and the construction of succinct de Bruijn graphs. Conclusions We prove that our algorithm performs $${\mathcal {O}}(n\, \mathsf {maxlcp})$$ O(nmaxlcp) sequential I/Os, where n is the total length of the collection and $$\mathsf {maxlcp}$$ maxlcp is the maximum LCP value. The experimental results show that our algorithm is only slightly slower than the state of the art for short sequences but it is up to 40 times faster for longer sequences or when the available RAM is at least equal to the size of the input.

Abstract Background De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. Given the high number of sequences obtained from NGS approaches, a critical step in any analysis workflow is the assembly of reads to reconstruct transcripts thus reducing the complexity of the analysis. Despite many available tools show a good sensitivity, there is a high percentage of false positives due to the high number of assemblies considered and it is likely that the high frequency of false positive is underestimated by currently used benchmarks. The reconstruction of not existing transcripts may false the biological interpretation of results as – for example – may overestimate the identification of “novel” transcripts. Moreover, benchmarks performed are usually based on RNA-seq data from annotated genomes and assembled transcripts are compared to annotations and genomes to identify putative good and wrong reconstructions, but these tests alone may lead to accept a particular type of false positive as true, as better described below. Results Here we present a novel methodology of de novo assembly, implemented in a software named STAble (Short-reads Transcriptome Assembler). The novel concept of this assembler is that the whole reads are used to determine possible alignments instead of using smaller k-mers, with the aim of reducing the number of chimeras produced. Furthermore, we applied a new set of benchmarks based on simulated data to better define the performance of assembly method and carefully identifying true reconstructions. STAble was also used to build a prototype workflow to analyse metatranscriptomics data in connection to a steady state metabolic modelling algorithm. This algorithm was used to produce high quality metabolic interpretations of small gene expression sets obtained from already published RNA-seq data that we assembled with STAble. Conclusions The presented results, albeit preliminary, clearly suggest that with this approach is possible to identify informative reactions not directly revealed by raw transcriptomic data.

Polymorphic Tandem Repeat (PTR) is a common form of polymorphism in the human genome. A PTR consists in a variation found in an individual (or in a population) of the number of repeating units of a Tandem Repeat (TR) locus of the genome with respect to the reference genome. Several phenotypic traits and diseases have been discovered to be strongly associated with or caused by specific PTR loci. PTR are further distinguished in two main classes: Short Tandem Repeats (STR) when the repeating unit has size up to 6 base pairs, and Variable Number Tandem Repeats (VNTR) for repeating units of size above 6 base pairs. As larger and larger populations are screened via high throughput sequencing projects, it becomes technically feasible and desirable to explore the association between PTR and a panoply of such traits and conditions. In order to facilitate these studies, we have devised a method for compiling catalogs of PTR from assembled genomes, and we have produced a catalog of PTR for genic regions (exons, introns, UTR and adjacent regions) of the human genome (GRCh38). We applied four different TR discovery software tools to uncover in the first phase 55,223,485 TR (after duplicate removal) in GRCh38, of which 373,173 were determined to be PTR in the second phase by comparison with five assembled human genomes. Of these, 263,266 are not included by state-of-the-art PTR catalogs. The new methodology is mainly based on a hierarchical and systematic application of alignment-based sequence comparisons to identify and measure the polymorphism of TR. While previous catalogs focus on the class of STR of small total size, we remove any size restrictions, aiming at the more general class of PTR, and we also target fuzzy TR by using specific detection tools. Similarly to other previous catalogs of human polymorphic loci, we focus our catalog toward applications in the discovery of disease-associated loci. Validation by cross-referencing with existing catalogs on common clinically-relevant loci shows good concordance. Overall, this proposed census of human PTR in genic regions is a shared resource (web accessible), complementary to existing catalogs, facilitating future genome-wide studies involving PTR.