A Faster Implementation of Online Run-Length Burrows-Wheeler Transform

Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in $O(n\lg r)$ time and $O(r\lg n)$ bits of space, where $n$ is the length of input string $S$ received so far and $r$ is the number of runs in the BWT of the reversed $S$. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.Comment: In Proc. IWOCA201

Composite repetition-aware data structures

In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these measures. We describe two data structures whose size depends on multiple measures of repetition at once, and that provide competitive tradeoffs between the time for counting and reporting all the exact occurrences of a pattern, and the space taken by the structure. The key component of our constructions is the run-length encoded BWT (RLBWT), which takes space proportional to the number of BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it with data structures from LZ77 indexes, which take space proportional to the number of LZ77 factors, and with the compact directed acyclic word graph (CDAWG), which takes space proportional to the number of extensions of maximal repeats. The combination of CDAWG and RLBWT enables also a new representation of the suffix tree, whose size depends again on the number of extensions of maximal repeats, and that is powerful enough to support matching statistics and constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from previous version

Fast Label Extraction in the CDAWG

The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive datasets, like collections of genomes from similar species, in which $e$ grows significantly more slowly than $n$. We reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to count the number of occurrences of a pattern of length $m$, using an existing data structure that takes an amount of space proportional to the size of the CDAWG. This implies a reduction from $O(m\log{\log{n}}+\mathtt{occ})$ to $O(m+\mathtt{occ})$ in the time needed to locate all the $\mathtt{occ}$ occurrences of the pattern. We also reduce from $O(k\log{\log{n}})$ to $O(k)$ the time needed to read the $k$ characters of the label of an edge of the suffix tree of $T$, and we reduce from $O(m\log{\log{n}})$ to $O(m)$ the time needed to compute the matching statistics between a query of length $m$ and $T$, using an existing representation of the suffix tree based on the CDAWG. All such improvements derive from extracting the label of a vertex or of an arc of the CDAWG using a straight-line program induced by the reversed CDAWG.Comment: 16 pages, 1 figure. In proceedings of the 24th International Symposium on String Processing and Information Retrieval (SPIRE 2017). arXiv admin note: text overlap with arXiv:1705.0864

Effects of erythropoietin in murine-induced pluripotent cell-derived panneural progenitor cells

Induced cell fate changes by reprogramming of somatic cells offers an efficient strategy to generate autologous pluripotent stem (iPS) cells from any adult cell type. The potential of iPS cells to differentiate into various cell types is well established, however the efficiency to produce functional neurons from iPS cells remains modest. Here, we generated panneural progenitor cells (pNPCs) from mouse iPS cells and investigated the effect of the neurotrophic growth factor erythropoietin (EPO) on their survival, proliferation and neurodifferentiation. Under neural differentiation conditions, iPS-derived pNPCs gave rise to microtubule-associated protein-2 positive neuronlike cells (34% to 43%) and platelet-derived growth factor receptor positive oligodendrocytelike cells (21% to 25%) while less than 1% of the cells expressed the astrocytic marker glial fibrillary acidic protein. Neuronlike cells generated action potentials and developed active presynaptic terminals. The pNPCs expressed EPO receptor (EPOR) mRNA and displayed functional EPOR signaling. In proliferating cultures, EPO (0.1–3 U/mL) slightly improved pNPC survival but reduced cell proliferation and neurosphere formation in a concentration-dependent manner. In differentiating cultures EPO facilitated neurodifferentiation as assessed by the increased number of β-III-tubulin positive neurons. Our results show that EPO inhibits iPS pNPC self-renewal and promotes neurogenesis

THE RESULTS OF PANCREATIC RESECTIONS AND LONG- TERM SURVIVAL FOR PANCREATIC DUCTAL ADENOCARCINOMA : A SINGLE-INSTITUTION EXPERIENCE

Objectives: Since the early 1990s, low long-term survival rates following pancreatic surgery for pancreatic ductal adenocarcinoma have challenged us to improve treatment. In this series, we aim to show improved survival from pancreatic ductal adenocarcinoma during the era of centralized pancreatic surgery. Methods: Analysis of all pancreatic resections performed at Helsinki University Hospital and survival of pancreatic ductal adenocarcinoma patients during 2000-2013 were included. Post-operative complications such as fistulas, reoperations, and mortality rates were recorded. Patient and tumor characteristics were compared with survival data. Results: Of the 853 patients undergoing pancreatic surgery, 581 (68%) were pancreaticoduodenectomies, 195 (21%) distal resections, 28 (3%) total pancreatectomies, and 49 (6%) other procedures. Mortality after pancreaticoduodenectomy was 2.1%. The clinically relevant B/C fistula rate was 7% after pancreaticoduodenectomy and 13% after distal resection, and the re-operation rate was 5%. The 5- and 10-year survival rates for pancreatic ductal adenocarcinoma were 22% and 14%; for T1-2, N0 and R0 tumors, the corresponding survival rates were 49% and 31%. Carbohydrate antigen 19-9 >75 kU/L, carcinoembryonic antigen >5 mu g/L, N1, lymph-node ratio >20%, R1, and lack of adjuvant therapy were independent risk factors for decreased survival. Conclusion: After centralization of pancreatic surgery in southern Finland, we have managed to enable pancreatic ductal adenocarcinoma patients to survive markedly longer than in the early 1990s. Based on a 1.7-million population in our clinic, mortality rates are equal to those of other high-volume centers and long-term survival rates for pancreatic ductal adenocarcinoma have now risen to some of the highest reported.Peer reviewe

Minimum size and positioning of imaging field for CBCT scans of impacted maxillary canines

Objectives: In children and adolescents, cone-beam computed tomography (CBCT) is frequently used for localization of unerupted or impacted teeth in the anterior maxilla. CBCT causes a higher radiation dose than conventional intraoral and panoramic imaging. The objective was to analyze the location of impacted canines in a three-dimensional coordinate and thereby optimize the CBCT field-of-view (FOV), for radiation dose reduction.Materials and methods: Location of 50 impacted maxillary canines of children under 17 years was retrospectively evaluated from CBCT scans. The minimum and maximum distances of any part of the right- and left-side canines to three anatomic reference planes were measured to assess the adequate size and position of a cylindrical image volume.Results: A cylinder sized 39.0 (diameter)×33.2 (height) mm, with its top situated 13.8 mm above the hard palate, its medial edge 8.4 mm across the midline, and anterior edge 2.5 mm in front of the labial surface of maxillary central incisors fitted all the analyzed canines.Conclusions: In this sample, the FOV required for imaging maxillary impacted canines was smaller than the smallest FOV offered by common CBCT devices. We encourage development of indication-specific CBCT imaging programs and aids to facilitate optimum patient positioning.Clinical relevance: An impacted maxillary canine is a common dental problem and a frequent indication for 3D imaging particularly in growing individuals. This article focuses on the optimization of CBCT of impacted canines. Our recommendation of a reduced FOV promotes radiation safety.</p

Focal brain trauma in the cryogenic lesion model in mice

The method to induce unilateral cryogenic lesions was first described in 1958 by Klatzo. We describe here an adaptation of this model that allows reliable measurement of lesion volume and vasogenic edema by 2, 3, 5-triphenyltetrazolium chloride-staining and Evans blue extravasation in mice. A copper or aluminium cylinder with a tip diameter of 2.5 mm is cooled with liquid nitrogen and placed on the exposed skull bone over the parietal cortex (coordinates from bregma: 1.5 mm posterior, 1.5 mm lateral). The tip diameter and the contact time between the tip and the parietal skull determine the extent of cryolesion. Due to an early damage of the blood brain barrier, the cryogenic cortical injury is characterized by vasogenic edema, marked brain swelling, and inflammation. The lesion grows during the first 24 hours, a process involving complex interactions between endothelial cells, immune cells, cerebral blood flow, and the intracranial pressure. These contribute substantially to the damage from the initial injury. The major advantage of the cryogenic lesion model is the circumscribed and highly reproducible lesion size and location

A Cross-Site Analysis of Neotropical Bird Hunting Profiles

© The Author(s) 2017. Subsistence hunting of neotropical birds is common and widespread in the tropical forests of Latin America. Although its sustainability under different scenarios is subject to debate, hunting has already contributed to the decline and local extirpation of several taxa and is considered to be a significant threat to a range of large-bodied species. Gaining a better understanding of the variability of hunting patterns, as well as the factors that can potentially be used to predict them, is important if we are to develop conservation strategies that target the species most likely to be experiencing declines. In this article, we examine the avian hunting profiles of 65 communities in the neotropics. We describe their variability and look at the relationship between a hunting profile and (a) its geographical location, (b) the community’s age, (c) the community’s population size, and (d) the year in which the survey was carried out. We find that there is a significant but weak relationship between a community’s geographic location and the composition of its bird hunting profile, and that prey profiles can be considerably different even among close neighbors. We found no relationship between a community’s age or size and the mean biomass of bird prey hunted. Our results challenge the assumption that older and larger settlements have a predictable impact upon avian prey communities and suggest that cultural preferences or the starting availability of prey species can change rapidly over short distances

Cognition in adults with Williams syndrome — A 20-year follow-up study

Background: Williams syndrome (WBS) is a genetic multisystem disorder. The main symptom is borderline (intelligence quotient, IQ 70–79) or abnormally low intelligence (IQ Methods: We followed 25 adults (age at baseline 19–68, median 38) with genetically confirmed WBS for about 20 years. The study subjects underwent medical and neuropsychological assessments at the baseline and at the end of follow‐up.Results: The mean VIQ remained quite stable from early adulthood up to 40 years of age after which it declined. The mean PIQ kept on improving from early adulthood until 50 years of age after which it gradually declined. At the end of the study, all study subjects had at least two longstanding health problems out of which hypertension, psychiatric disorder, and scoliosis or kyphosis occurred most frequently. At end of the study, two patients suffered from vascular dementia. Seven patients died during the follow‐up.Conclusions: In adults with WBS, the course of cognition is uneven across the cognitive profile. Their verbal functions both develop and deteriorate earlier than performance/nonverbal functions. Frequent somatic co‐morbidities may increase risk to shortened life span.</p