A genetic programming approach to oral cancer prognosis
Background The potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis. Method GP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP. Result The result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis. Discussion Some of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.
Tan et al. (2016) A genetic programming approach to oral cancer prognosis. PeerJ 4:e2482 https://doi.org/10.7717/peerj.2482
Evaluation of the effectiveness of insecticide trunk injections for control of Latoia lepida (Cramer) in the sweet olive tree Osmanthus fragrans
The screening of suitable insecticides is a key factor in successfully applying trunk injection technology to ornamental plants. In this study, six chemical pesticides were selected and injected into the trunks of Osmanthus fragrans to control the nettle caterpillar, Latoia lepida (Lepidoptera: Limacodidae), using a no-pressure injection system. The absorption rate of the insecticides, the leaf loss due to insect damage, and the mortality and frass amount of L. lepida larvae were evaluated after 77 and 429 days. The results showed that 4% imidacloprid + carbosulfan and 21% abamectin + imidacloprid + omethoate had the fastest conductivity and were completely absorbed into the trunkswithin14 days; however, the efficiencies of these insecticides in controlling L. lepidawere extremely low. Additionally, the treatment 10% emamectin benzoate + clothianidin and 2.5% emamectin benzoate was almost completely absorbed within 30 days and exhibited a longer duration of insecticide efficiency (>80% mortality) in the upper and lower leaves of the canopy. Treatment with these insecticides also resulted in significantly lower leaf loss and frass amounts. We conclude that emamectin benzoate and emamectin benzoate + clothianidin have a rapid uptake into O. fragrans, and are effective as insecticides over long durations. Hence, they may be a suitable control option for L. lepida in O. fragrans plants.
Huang et al. (2016) Evaluation of the effectiveness of insecticide trunk injections for control of Latoia lepida (Cramer) in the sweet olive tree Osmanthus fragrans. PeerJ 4:e2480 https://doi.org/10.7717/peerj.2480
Successful population establishment from small introductions appears to be less common than believed
Although small populations are at high risk of extinction, there are regular reports in the scientific literature of purported small, isolated, persistent populations. One source of evidence of the viability of small populations comes from the alleged successful introduction of species to areas outside their original range from introductions of few individuals. We reviewed the examples from introduction compendia on deliberate translocations of birds, and the original sources, to identify and evaluate purported examples of successful establishments from small introductions. We found 23 purportedly successful introductions from few (<30) individuals. After assessing original sources, we found that two of the claims were substantiated; the rest were ambiguous or could be rejected as examples, primarily due to a lack of evidence in original sources of the number of birds released and because of supplemental individuals from other releases, releases in nearby regions, and the possibility of natural invasion. Our results suggest that reports of successful establishment of birds from introductions of few individuals have been overstated. These results strengthen the relationship previously reported between propagule pressure and likelihood of establishment, and support the lack of viability of small populations presumed by population theory. We suggest that analyses of introduction failure and success would benefit from excluding studies where introduction effort is unknown or unreliably documented.
Corbett King et al. (2016) Successful population establishment from small introductions appears to be less common than believed. PeerJ 4:e2440 https://doi.org/10.7717/peerj.2440
A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis
Inferring growth for aquatic species is dependent upon accurate descriptions of age-length relationships, which may be degraded by measurement error in observed ages. Ageing error arises from biased and/or imprecise age determinations as a consequence of misinterpretation by readers or inability of ageing structures to accurately reflect true age. A Bayesian errors-in-variables (EIV) approach (i.e., measurement-error modeling) can account for ageing uncertainty during nonlinear growth curve estimation by allowing observed ages to be parametrically modeled as random deviates. Information on the latent age composition then comes from the specified prior distribution, which represents the true age structure of the sampled fish population. In this study, weakfish growth was modeled by means of traditional and measurement-error von Bertalanffy growth curves using otolith- or scale-estimated ages. Age determinations were assumed to be log-normally distributed, thereby incorporating multiplicative error with respect to ageing uncertainty. The prior distribution for true age was assumed to be uniformly distributed between ±4 of the observed age (yr) for each individual. Measurement-error growth models described weakfish that reached larger sizes but at slower rates, with median length-at-age being overestimated by traditional growth curves for the observed age range. In addition, measurement-error models produced slightly narrower credible intervals for parameters of the von Bertalanffy growth function, which may be an artifact of the specified prior distributions. Subjectivity is always apparent in the ageing of fishes and it is recommended that measurement-error growth models be used in conjunction with otolith-estimated ages to accurately capture the age-length relationship that is subsequently used in fisheries stock assessment and management.
Hatch et al. (2016) A comparison between traditional and measurement-error growth models for weakfish Cynoscion regalis. PeerJ 4:e2431 https://doi.org/10.7717/peerj.2431
New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti)
The Ziphiidae (beaked whales) represent a large group of open-ocean odontocetes (toothed cetaceans), whose elusive and deep diving behavior prevents direct observation in their natural habitat. Despite their generally large body size, broad geographical distribution, and high species number, ziphiids thus remain poorly known. Furthermore, the evolutionary processes that have led to their extreme adaptations and impressive extant diversity are still poorly understood. Here we report new fossil beaked whales from the late Miocene of the Pisco Formation (southern Peru). The best preserved remains here described are referred to two new genera and species, the Messinian Chavinziphius maxillocristatus and the Tortonian Chimuziphius coloradensis, based on skull remains from two marine vertebrate-rich localities: Cerro Los Quesos and Cerro Colorado, respectively. C. maxillocristatus is medium sized retains a complete set of functional lower teeth, and bears robust rostral maxillary crests similar to those of the extant Berardius. By contrast, C. coloradensis is small and characterized by large triangular nasals and moderately thickened premaxillae that dorsally close the mesorostral groove. Both species confirm the high past diversity of Ziphiidae, the richest cetacean family in terms of the number of genera and species. Our new phylogenetic and biogeographical analyses depart markedly from earlier studies in dividing beaked whales into two major clades: the Messapicetus clade, which, along with other stem ziphiids, once dominated the southeastern Pacific and North Atlantic; and crown Ziphiidae, the majority of which are found in deep-water regions of the Southern Ocean, with possible subsequent dispersal both globally (Mesoplodon and Ziphius) and to the cooler waters of the northern oceans (Berardius and Hyperoodon). Despite this relatively clear separation, both lineages seem to follow similar evolutionary trends, including (1) a progressive reduction of dentition; (2) an increase in the compactness and thickness of the rostral bones; (3) similar changes in facial morphology (e.g., elevation of the vertex); and (4) an increase of body size. We suggest that these trends may be linked to a convergent ecological shift to deep diving and suction feeding.
Bianucci et al. (2016) New beaked whales from the late Miocene of Peru and evidence for convergent evolution in stem and crown Ziphiidae (Cetacea, Odontoceti). PeerJ 4:e2479 https://doi.org/10.7717/peerj.2479
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
Background The bacterial 16S rRNA gene has historically been used in defining bacterial taxonomy and phylogeny. However, there are currently no high-throughput methods to sequence full-length 16S rRNA genes present in a sample with precision. Results We describe a method for sequencing near full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform and test it using DNA from human skin swab samples. Proof of principle of the approach is demonstrated, with the generation of 1,604 sequences greater than 1,300 nt from a single Nano MiSeq run, with accuracy estimated to be 100-fold higher than standard Illumina reads. The reads were chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. Conclusions This method could be scaled up to generate many thousands of sequences per MiSeq run and could be applied to other sequencing platforms. This has great potential for populating databases with high quality, near full-length 16S rRNA gene sequences from under-represented taxa and environments and facilitates analyses of microbial communities at higher resolution.
Burke et al. (2016) A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq. PeerJ 4:e2492 https://doi.org/10.7717/peerj.2492
Spermatozoon ultrastructure in two monorchiid digeneans
Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris share several characters such as the presence of two axonemes of different lengths showing the 9+“1” pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, granules of glycogen and similar morphologies of the anterior and posterior extremities. The slight differences between the male gamete of O. dinema and P. selaris are the length of the first axoneme and the position of the second mitochondrion. This study also elucidates the general morphology of the spermatozoon in all monorchiid species described so far, which corresponds to a unique spermatozoon type. Other interesting finds concern the spermatological similarities between monorchiid spermatozoa and the mature spermatozoon reported in the apocreadiid Neoapocreadium chabaudi. These similarities allow us to suggest a close phylogenetical relationship between the Monorchiidae and the Apocreadiidae, although more studies are needed, especially in the unexplored taxa.
Quilichini et al. (2016) Spermatozoon ultrastructure in two monorchiid digeneans. PeerJ 4:e2488 https://doi.org/10.7717/peerj.2488
CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients
Introduction Rituximab (RTX) is a B cell-depleting agent approved for the treatment of granulomatosis with polyangiitis (GPA). RTX reduces antibody producing precursor plasma cells and inhibits B and T cells interaction. Infections related to T cell immunodeficiency are not infrequent during RTX treatment. Our study investigated CD4 cell count and CD4/CD8 ratio in GPA patients during the first two years of long-term RTX treatment. Methods A single centre cohort study of 35 patients who received median total cumulative dose of cyclophosphamide (CYC) of 15 g and were treated with RTX 2 g followed by retreatment with either 2 g once annually or 1 g biannually. Serum levels of total immunoglobulin (Ig) and lymphocytes subsets were recorded at RTX initiation and at 3, 6, 12, 18 and 24 months. Low CD4 count and inverted CD4/CD8 ratio were defined as CD4 < 0.3 × 109/l and ratio < 1. Results The CD4 cell count and CD4/CD8 ratio decreased slightly following the initial RTX treatment and then increased gradually during maintenance treatment. While the proportion of patients with low CD4 cell count decreased from 43% at baseline to 18% at 24 months, the ratio remained inverted in 40%. Oral daily prednisolone dose at baseline, CYC exposure and the maintenance regimen did not influence the CD4 cell count and ratio. Being older (p = 0.012) and having a higher CRP (p = 0.044) and ESR (p = 0.024) at baseline significantly increased the risk of inverted CD4/CD8 ratio at 24 months. Inverted ratio at baseline associated with lower total Ig levels during the study. Conclusions Overall, the CD4 and CD4/CD8 ratio increased during maintenance RTX therapy in GPA with no discernible impact of other immunosuppressive therapy. However the increase in CD4 was not followed by an increase in the CD4/CD8 ratio, especially in older patients. Inverted CD4/CD8 ratio associated with lower Ig levels, suggesting a more profound B cell depleting effect of RTX with a relative increase in CD8+ lymphocytes.
Besada et al. (2016) CD4 cell count and CD4/CD8 ratio increase during rituximab maintenance in granulomatosis with polyangiitis patients. PeerJ 4:e2487 https://doi.org/10.7717/peerj.2487
Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth
Background Parenteral nutrition associated cholestasis (PNAC) is a frequently observed pathology in extremely low birth weight (ELBW) infants. Its pathogenesis is determined by the composition and duration of parenteral nutrition (PN) as well as the tolerance of enteral feeds (EF). “Aggressive” nutrition is increasingly used in ELBW infants to improve postnatal growth. Little is known about the effect of “aggressive” nutrition on the incidence of PNAC. We analyzed the influence of implementing an “aggressive” nutritional regimen on the incidence of PNAC and growth in a cohort of ELBW infants. Methods ELBW infants were nourished using a “conservative” (2005–6; n = 77) or “aggressive” (2007–9; n = 85) nutritional regimen that differed in the composition of PN after birth as well as the composition and timing of advancement of EFs. We analyzed the incidence of PNAC (conjugated bilirubin > 1.5 mg/dl (25 µmol/l)) corrected for confounders of cholestasis (i.e., NEC and/or gastrointestinal surgery, sepsis, birth weight, Z-score of birth weight, time on PN and male sex), growth until discharge (as the most important secondary outcome) and neonatal morbidities. Results The incidence of PNAC was significantly lower during the period of “aggressive” vs. “conservative “nutrition (27% vs. 46%, P < 0.05; adjusted OR 0.275 [0.116–0.651], P < 0.01). Body weight (+411g), head circumference (+1 cm) and length (+1 cm) at discharge were significantly higher. Extra-uterine growth failure (defined as a Z-score difference from birth to discharge lower than −1) was significantly reduced for body weight (85% vs. 35%), head circumference (77% vs. 45%) and length (85% vs. 65%) (P < 0.05). The body mass index (BMI) at discharge was significantly higher (11.1 vs. 12.4) using “aggressive” nutrition and growth became more proportionate with significantly less infants being discharged below the 10th BMI percentile (44% vs. 9%), while the percentage of infants discharged over the 90th BMI percentile (3% vs. 5%) did not significantly increase. Discussion “Aggressive” nutrition of ELBW infants was associated with a significant decrease of PNAC and marked improvement of postnatal growth.
Repa et al. (2016) Aggressive nutrition in extremely low birth weight infants: impact on parenteral nutrition associated cholestasis and growth. PeerJ 4:e2483 https://doi.org/10.7717/peerj.2483
Overland movement in African clawed frogs (Xenopus laevis): a systematic review
African clawed frogs (Xenopus laevis) are often referred to as ‘purely aquatic’ but there are many publications which suggest extensive overland movements. Previous reviews which considered the topic have not answered the following questions: (1) is there evidence for overland dispersal in native and invasive ranges; (2) what is the range of distances moved overland; (3) when does overland movement occur; and (4) is there evidence of breeding migratory behaviour? A systematic review was chosen to synthesise and critically analyse all literature on the overland movement in Xenopus laevis. Database searches resulted in 57 documents which revealed a paucity of empirical studies, with 28 containing no data, and 19 having anecdotal content. Overwhelming evidence shows that both native and invasive populations of X. laevis move overland, with well documented examples for several other members of the genus (X. borealis, X. gilli, X. muelleri, X. fraseriand X. tropicalis). Reports of distances moved overland were from 40 m to 2 km, with no apparent difference between native and invasive ranges. Overland movements are not confined to wet seasons or conditions, but the literature suggests that moving overland does not occur in the middle of the day. Migrations to temporary water-bodies for breeding have been suggested, but without any corroborating data.
Measey (2016) Overland movement in African clawed frogs (Xenopus laevis): a systematic review. PeerJ 4:e2474 https://doi.org/10.7717/peerj.2474