Miracle-dz/UniFAR-FTUs huggingface dataset:
A targeted next‐generation sequencing toolkit for exon‐based cichlid phylogenomics

Cichlid fishes (family Cichlidae) are models for evolutionary and ecological research. Massively parallel sequencing approaches have been successfully applied to study relatively recent diversification in groups of African and Neotropical cichlids, but such technologies have yet to be used for addressing larger‐scale phylogenetic questions of cichlid evolution. Here, we describe a process for identifying putative single‐copy exons from five African cichlid genomes and sequence the targeted exons for a range of divergent (>tens of millions of years) taxa with probes designed from a single reference species (Oreochromis niloticus, Nile tilapia). Targeted sequencing of 923 exons across 10 cichlid species that represent the family's major lineages and geographic distribution resulted in a complete taxon matrix of 564 exons (649 549 bp), representing 559 genes. Maximum likelihood and Bayesian analyses in both species tree and concatenation frameworks yielded the same fully resolved and highly supported topology, which matched the expected backbone phylogeny of the major cichlid lineages. This work adds to the body of evidence that it is possible to use a relatively divergent reference genome for exon target design and successful capture across a broad phylogenetic range of species. Furthermore, our results show that the use of a third‐party laboratory coupled with accessible bioinformatics tools makes such phylogenomics projects feasible for research groups that lack direct access to genomic facilities. We expect that these resources will be used in further cichlid evolution studies and hope the protocols and identified targets will also be useful for phylogenetic studies of a wider range of organisms.
Barcoding : composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, twostage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls. cuhk.edu. hk/vipbarcoding/.
Fatigue in non-alcoholic fatty liver disease (NAFLD) is significant and associates with inactivity and excessive daytime sleepiness but not with liver disease severity or insulin resistance

Objective: To quantify fatigue in non-alcoholic fatty liver disease (NAFLD), to determine whether perceived fatigue reflects impairment of physical function and to explore potential causes. Patients and methods: A cohort study was carried out on 156 consecutive patients with histologically proven NAFLD studied in two cohorts. Phase 1 determined the perceived fatigue experienced by NAFLD patients (assessed using the Fatigue Impact Scale (FIS)) in comparison with normal and liver disease controls, and the relationship to physical function (actigraphy). In phase 2, biological associations of fatigue in NAFLD were explored. Results: Fatigue was markedly higher in NAFLD patients than in controls (mean (SD) FIS 51 (38) vs 8 (12), p<0.001). NAFLD patients showed significantly lower physical activity over 6 days (7089 (2909) mean steps/day vs 8676 (2894), p = 0.02). A significant inverse correlation was seen between FIS and physical activity (r2 = 0.1, p = 0.02). Fatigue experienced by NAFLD patients was similar to that in primary biliary cirrhosis (n = 36) (FIS 64 (9) vs 61 (2), p = NS). No association was seen between FIS and biochemical and histological markers of liver disease severity or insulin resistance (homeostasis model assessment (HOMA)) (r2<0.005). Significant association was seen between fatigue severity and daytime somnolence (Epworth Sleepiness Scale) (r2 = 0.2, p<0.001). Conclusion: Fatigue is a significant problem in NAFLD, is similar in degree to that in primary biliary cirrhosis patients and is associated with impairment in physical function. Fatigue in NAFLD appears to be unrelated to either severity of underlying liver disease or insulin resistance, but is associated with significant daytime somnolence.
Identifying the ichthyoplankton of a coral reef using DNA barcodes

Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large‐scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being <5 mm. Among the 505 individuals DNA barcoded, 373 larvae (i.e. 75%) were identified to the species level. A total of 106 species were detected, among which 11 corresponded to pelagic and bathypelagic species, while 95 corresponded to species observed at the adult stage on neighbouring reefs. This study highlights the benefits and pitfalls of using standardized molecular systems for species identification and illustrates the new possibilities enabled by DNA barcoding for future work on coral reef fish larval ecology.
What is Known About Caries in Relation to Restorations as a Reason for Replacement? a Review

In the past 20 years, a great many studies have identified secondary caries to be the most common reason for the replacement of restorations. This review raises the question whether clinicians use 'secondary caries' as a catch-all into which they put a variety of reasons for replacement, or whether they do have professionally based reasons for focusing on caries adjacent to restorations. There is no consensus among researchers concerning the nature of secondary caries, but it is possible to identify two major-and conflicting-trends : One adheres to a critical approach concerning the frequency of replacements and recommends a much more conservative evaluation of existing fillings. In contrast, the other trend focuses on the clinical undetectable microleakage as the major risk factor for the initiation and uncontrolled dentinal spread of secondary caries. Since the latter trend offers a reasonable explanation for the clinicians' concern about invisible 'secondary caries', and hence reinforces the tendency to replacement, it is relevant to reconsider the conventional concept that microleakage leads to the initiation of secondary caries. Available data indicate that visible gaps and marginal discrepancies are poorly related to secondary caries, and that secondary caries is a localized phenomenon caused by localized conditions for the evolution of cariogenic plaque. Consequently, secondary caries is not a universal attack along the entire interface between tooth and restoration, but rather a new lesion or a re-beginning of caries on the surface due to local conditions for plaque formation with cariogenic potential. It is concluded that reinforcement of a new and more appropriate professional behavior should be based on diffusion of existing knowledge of dental caries as a disease rather than on simplified criteria for the placement and replacement of dental restorations.
Long-term results and risk factor analysis for recurrence after curative endoscopic therapy in 349 patients with high-grade intraepithelial neoplasia and mucosal adenocarcinoma in Barrett’s oesophagus

Objective: Endoscopic therapy is increasingly being used in the treatment of high-grade intraepithelial neoplasia (HGIN) and mucosal adenocarcinoma (BC) in patients with Barrett’s oesophagus. This report provides 5 year follow-up data from a large prospective study investigating the efficacy and safety of endoscopic treatment in these patients and analysing risk factors for recurrence. Design: Prospective case series. Setting: Academic tertiary care centre. Patients: Between October 1996 and September 2002, 61 patients with HGIN and 288 with BC were included (173 with short-segment and 176 with long-segment Barrett’s oesophagus) from a total of 486 patients presenting with Barrett’s neoplasia. Patients with submucosal or more advanced cancer were excluded. Interventions: Endoscopic therapy. Main outcome measures: Rate of complete remission and recurrence rate, tumour-associated death. Results: Endoscopic resection was performed in 279 patients, photodynamic therapy in 55, and both procedures in 13; two patients received argon plasma coagulation. The mean follow-up period was 63.6 (SD 23.1) months. Complete response (CR) was achieved in 337 patients (96.6%); surgery was necessary in 13 (3.7%) after endoscopic therapy failed. Metachronous lesions developed during the follow-up in 74 patients (21.5%); 56 died of concomitant disease, but none died of BC. The calculated 5 year survival rate was 84%. The risk factors most frequently associated with recurrence were piecemeal resection, long-segment Barrett’s oesophagus, no ablative therapy of Barrett’s oesophagus after CR, time until CR achieved >10 months and multifocal neoplasia. Conclusions: This study showed that endoscopic therapy was highly effective and safe, with an excellent long-term survival rate. The risk factors identified may help stratify patients who are at risk for recurrence and those requiring more intensified follow-up.
Impact of enrichment conditions on cross‐species capture of fresh and degraded DNA

By combining high‐throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination‐rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on‐target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.
Autonomous Decentralized Kernel Cache Architecture for Multi Ontology Based Information Extraction on Microsoft Windows

Ontology Based Information Extraction (OBIE) is being adopted in various domains in order to improve the system's precision and recall. Though use of multiple ontologies in different semantic based Information Extraction systems helps to improve the system extraction accuracy but the performance of system degrades significantly. This paper proposes autonomous decentralized kernel cache architecture to improve the query time for OBIE systems that utilize multiple ontologies. In order to minimize performance bottlenecks we propose caching most frequently used relations of the ontologies in the autonomous and decentralized kernel cache in order to reduce the query time against different semantic queries. Results show performance improvement for different queries made on YAGO2s and DBpedia ontologies using the proposed kernel based Onto-Cache.
Targeted gene enrichment and high‐throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates

Recent studies have advocated biomonitoring using DNA techniques. In this study, two high‐throughput sequencing (HTS)‐based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene‐enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene‐enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene‐enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification‐based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high‐throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co‐occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field‐collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population‐level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.
Characteristics of Adherence to Plastic Tissue Culture Plates of Coagulase-Negative Staphylococci Exposed to Subinhibitory Concentrations of Antimicrobial Agents

Adherence and hydrophobic properties characteristic of 6-h cultures of coagulase-negative staphylococci on plastic tissue culture plates were determined after the organisms had been treated for up to an additional 6 h with subinhibitory concentrations of antimicrobial agents. Clindamycin, erythromycin, norfloxacin, tunicamycin, and vancomycin had no effect. Cephalothin, chloramphenicol, gentamicin, imipenem, methicillin, novobiocin, polymyxin B, rifampin, and tobramycin had varied effects. Most changes induced by these agents resulted in differing degrees of inhibition of adherence. However, an increase in adherence of 65 ^o was observed for one strain, RP14 (ATCC 35981), with rifampin treatment. Hydrophobicity of coagulase-negative staphylococci treated with antimicrobial agents measured by using a biphasic system with hexadecane showed excellent correlation with adherence (r = .958, P < .0005), a result suggesting that adherence of these bacteria in this system depends heavily on hydrophobic surface moieties. Transmission electron microscopy of drug-treated coagulase-negative staphylococci revealed only an increase in cell-wall thickness, regardless of whether adherence was increased or decreased.
Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis

Objective: To investigate differential intestinal gene expression in patients with ulcerative colitis and in controls. Design: Genome-wide expression study (41 058 expression sequence tags, 215 biopsies). Setting: Western General Hospital, Edinburgh, UK, and Genentech, San Francisco, USA. Patients: 67 patients with ulcerative colitis and 31 control subjects (23 normal subjects and 8 patients with inflamed non-inflammatory bowel disease biopsies). Interventions: Paired endoscopic biopsies were taken from 5 specific anatomical locations for RNA extraction and histology. The Agilent microarray platform was used and confirmation of results was undertaken by real time polymerase chain reaction and immunohistochemistry. Results: In healthy control biopsies, cluster analysis showed differences in gene expression between the right and left colon. (χ2 = 25.1, p<0.0001). Developmental genes, homeobox protein A13 (HOXA13), (p = 2.3×10−16), HOXB13 (p<1×10−45), glioma-associated oncogene 1 (GLI1) (p = 4.0×10−24), and GLI3 (p = 2.1×10−28) primarily drove this separation. When all ulcerative colitis biopsies and control biopsies were compared, 143 sequences had a fold change of >1.5 in the ulcerative colitis biopsies (0.01>p>10−45) and 54 sequences had a fold change of <−1.5 (0.01>p>10−20). Differentially upregulated genes in ulcerative colitis included serum amyloid A1 (SAA1) (p<10−45) the alpha defensins 5 and 6 (DEFA5 and 6) (p = 0.00003 and p = 6.95×10−7, respectively), matrix metalloproteinase 3 (MMP3) (p = 5.6×10−10) and MMP7 (p = 2.3×10−7). Increased DEFA5 and 6 expression was further characterised to Paneth cell metaplasia by immunohistochemistry and in situ hybridisation. Sub-analysis of the inflammatory bowel disease 2 (IBD2) and IBD5 loci, and the ATP-binding cassette (ABC) transporter genes revealed a number of differentially regulated genes in the ulcerative colitis biopsies. Conclusions: Key findings are the expression gradient in the healthy adult colon and the involvement of novel gene families, as well as established candidate genes in the pathogenesis of ulcerative colitis.
Expression of taste molecules in the upper gastrointestinal tract in humans with and without type 2 diabetes

Objective: Nutrient feedback from the small intestine modulates upper gastrointestinal function and energy intake; however, the molecular mechanism of nutrient detection is unknown. In the tongue, sugars are detected via taste T1R2 and T1R3 receptors and signalled via the taste G-protein α-gustducin (Gαgust) and the transient receptor potential ion channel, TRPM5. These taste molecules are also present in the rodent small intestine, and may regulate gastrointestinal function. Subjects and methods: Absolute transcript levels for T1R2, T1R3, Gαgust and TRPM5 were quantified in gastrointestinal mucosal biopsies from subjects with and without type 2 diabetes; immunohistochemistry was used to locate Gαgust. Effects of luminal glucose on jejunal expression of taste molecules were also quantified in mice. Results: T1R2, T1R3, Gαgust and TRPM5 were preferentially expressed in the proximal small intestine in humans, with immunolabelling for Gαgust localised to solitary cells dispersed throughout the duodenal villous epithelium. Expression of T1R2, T1R3, TRPM5 (all p<0.05) and Gαgust (p<0.001) inversely correlated with blood glucose concentration in type 2 diabetes subjects but, as a group, did not differ from control subjects. Transcript levels of T1R2 were reduced by 84% following jejunal glucose perfusion in mice (p<0.05). Conclusions: Taste molecules are expressed in nutrient detection regions of the proximal small intestine in humans, consistent with a role in “tasting”. This taste molecule expression is decreased in diabetic subjects with elevated blood glucose concentration, and decreased by luminal glucose in mice, indicating that intestinal “taste” signalling is under dynamic metabolic and luminal control.