title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1662
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Segmentation and classification of colon glands with deep convolutional neural networks and total variation regularization
link: https://peerj.com/articles/3874
last-modified: 2017-10-03
description: Segmentation of histopathology sections is a necessary preprocessing step for digital pathology. Due to the large variability of biological tissue, machine learning techniques have shown superior performance over conventional image processing methods. Here we present our deep neural network-based approach for segmentation and classification of glands in tissue of benign and malignant colorectal cancer, which was developed to participate in the GlaS@MICCAI2015 colon gland segmentation challenge. We use two distinct deep convolutional neural networks (CNN) for pixel-wise classification of Hematoxylin-Eosin stained images. While the first classifier separates glands from background, the second classifier identifies gland-separating structures. In a subsequent step, a figure-ground segmentation based on weighted total variation produces the final segmentation result by regularizing the CNN predictions. We present both quantitative and qualitative segmentation results on the recently released and publicly available Warwick-QU colon adenocarcinoma dataset associated with the GlaS@MICCAI2015 challenge and compare our approach to the simultaneously developed other approaches that participated in the same challenge. On two test sets, we demonstrate our segmentation performance and show that we achieve a tissue classification accuracy of 98% and 95%, making use of the inherent capability of our system to distinguish between benign and malignant tissue. Our results show that deep learning approaches can yield highly accurate and reproducible results for biomedical image analysis, with the potential to significantly improve the quality and speed of medical diagnoses.
creator: Philipp Kainz
creator: Michael Pfeiffer
creator: Martin Urschler
uri: https://doi.org/10.7717/peerj.3874
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Kainz et al.

title: Development and validation of near-infrared spectroscopy for the prediction of forage quality parameters in Lolium multiflorum
link: https://peerj.com/articles/3867
last-modified: 2017-10-03
description: Italian ryegrass (Lolium multiflorum) is an important cool-season, annual forage crop for the grassland rotation system in Southern China. The primary aim of breeding programs is always to seek to improve forage quality in the animal productivity system; however, it is time- and labor-consuming when analyzed excessive large number of samples. The main objectives of this study were to construct near-infrared reflectance spectroscopy (NIRS) models to predict the forage chemistry quality of Italian ryegrass including the concentrations of crude protein (CP), acid detergent fiber (ADF), neutral detergent fiber (NDF), and water soluble carbohydrate (WSC). The results showed that a broader range of CP, NDF, ADF and WSC contents (%DM) were obtained (4.45–30.60, 21.29–60.47, 11.66–36.17 and 3.95–51.52, respectively) from the samples selected for developing NIRS models. In addition, the critical wavelengths identified in this study to construct optimal NIRS models were located in 4,247–6,102 and 4,247–5,450 cm-1 for CP and NDF content, and both wavelengths 5,446–6,102 and 4,247–4,602 cm-1 could for ADF and WSC. Finally, the optimal models were developed based on the laboratory data and the spectral information by partial least squares (PLS) regression, with relatively high coefficients of determination (R2CV, CP = 0.99, NDF = 0.94, ADF = 0.92, WSC = 0.88), ratio of prediction to devitation (RPD, CP = 8.58, NDF = 4.25, ADF = 3.64, WSC = 3.10). The further statistics of prediction errors relative to laboratory (PRL) and the range error ratio (RER) give excellent assessments of the models with the PRL ratios lower than 2 and the RER values greater than 10. The NIRS models were validated using a completely independent set of samples and have coefficients of determination (R2V, CP = 0.99, NDF = 0.91, ADF = 0.95, WSC = 0.91) and ratio of prediction to deviation (RPD, CP = 9.37, NDF = 3.44, ADF = 4.40, WSC = 3.39). The result suggested that routine screening for forage quality parameters with large numbers of samples is available with the NIRS model in Italian ryegrass breeding programs, as well as facilitating graziers to monitor the forage development stage for improving grazing efficiency.
creator: Zhongfu Yang
creator: Gang Nie
creator: Ling Pan
creator: Yan Zhang
creator: Linkai Huang
creator: Xiao Ma
creator: Xinquan Zhang
uri: https://doi.org/10.7717/peerj.3867
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Yang et al.

title: Assessment on the coupling effects of drip irrigation and organic fertilization based on entropy weight coefficient model
link: https://peerj.com/articles/3855
last-modified: 2017-10-03
description: Water and fertilizer are two important factors influencing crop growth, development and yield formation. To investigate their combined effects on the soil-plant system, and to find out the optimal water and organic fertilizer coupling strategy for tomato (Solanum lycopersicum L), an experiment was carried out from May to October in 2016 in the south of China. The experiment consisted of three drip irrigation quotas (150, 180, 210 m3/ha) and three organic fertilizer application amounts (2,800, 3,600, 4,400 kg/ha). A water-fertilizer treatment (abbreviated as CK) that is in line with local practice was used for comparison. The tomato marketable yield, sugar/acid ratio (SAR) and irrigation water use efficiency (IWUE), as well as the soil salinity and available nutrient concentrations were measured. The results showed that the marketable yield was highly significantly (p < 0.01) affected by irrigation or fertilization. The SAR of tomato were significantly (p < 0.05) affected by irrigation or/and fertilization. The fertilization had an highly significant (p < 0.01) effect on the concentrations of soil nutrients (N, P, K), while the coupling effect of irrigation and fertilization was not pronounced. According to the multi-index analysis and the computed result by the entropy weight coefficient model, a 180 m3/ha irrigation quota in combination with 4,400 kg/ha organic fertilizer application amount was the optimal water-fertilizer coupling strategy which owned the most satisfactory comprehensive benefits. The marketable yield, SAR and IWUE under this optimal strategy were 122.4 t/ha, 9.2, 32.4 kg/m3, respectively, and by 28.0%, 29.6% and 28.1% higher compared to that under CK.
creator: Fenglin Zhong
creator: Maomao Hou
creator: Bizhu He
creator: Iouzen Chen
uri: https://doi.org/10.7717/peerj.3855
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Zhong et al.

title: A preliminary survey of zoantharian endosymbionts shows high genetic variation over small geographic scales on Okinawa-jima Island, Japan
link: https://peerj.com/articles/3740
last-modified: 2017-10-03
description: Symbiotic dinoflagellates (genus Symbiodinium) shape the responses of their host reef organisms to environmental variability and climate change. To date, the biogeography of Symbiodinium has been investigated primarily through phylogenetic analyses of the ribosomal internal transcribed spacer 2 region. Although the marker can approximate species-level diversity, recent work has demonstrated that faster-evolving genes can resolve otherwise hidden species and population lineages, and that this diversity is often distributed over much finer geographical and environmental scales than previously recognized. Here, we use the noncoding region of the chloroplast psbA gene (psbAncr) to examine genetic diversity among clade C Symbiodinium associating with the common reef zoantharian Palythoa tuberculosa on Okinawa-jima Island, Japan. We identify four closely related Symbiodinium psbAncr lineages including one common generalist and two potential specialists that appear to be associated with particular microhabitats. The sea surface temperature differences that distinguish these habitats are smaller than those usually investigated, suggesting that future biogeographic surveys of Symbiodinium should incorporate fine scale environmental information as well as fine scale molecular data to accurately determine species diversity and their distributions.
creator: Hatsuko Noda
creator: John Everett Parkinson
creator: Sung-Yin Yang
creator: James Davis Reimer
uri: https://doi.org/10.7717/peerj.3740
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Noda et al.

title: Framework for community functioning: synthesis of stress gradient and resource partitioning concepts
link: https://peerj.com/articles/3885
last-modified: 2017-10-02
description: To understand how communities function and generate abundance, I develop a framework integrating elements from the stress gradient and resource partitioning concepts. The framework suggests that guild abundance depends on environmental and spatial factors but also on inter-guild interactions (competitor or facilitator richness), which can alter the fundamental niche of constituent species in negative (competition) or positive direction (facilitation). Consequently, the environmental and spatial mechanisms driving guild abundance would differ across guilds and interaction modes. Using continental data on stream diatoms and physico-chemistry, the roles of these mechanisms were tested under three interaction modes—shared preference, distinct preference, and facilitative, whereby pairs of guilds exhibited, respectively, a dominance-tolerance tradeoff along a eutrophication gradient, specialization along a pH gradient, or a donor-recipient relationship along a nitrogen gradient. Representative of the shared preference mode were the motile (dominant) and low profile (tolerant) guilds, of the distinct preference mode—the acidophilous and alkaliphilous (low profile) guilds, and of the facilitative mode—nitrogen fixers (donors) and motile species (recipients). In each mode, the influences of environment, space (latitude and longitude), and competitor or facilitator richness on guild density were assessed by variance partitioning. Pure environment constrained most strongly the density of the dominant, the acidophilous, and the recipient guild in the shared preference, distinct preference, and facilitative mode, respectively, while spatial effects were important only for the low profile guild. Higher competitor richness was associated with lower density of the tolerant guild in the shared preference mode, both guilds in the distinct preference mode, and the donor guild in the facilitative mode. Conversely, recipient density in the facilitative mode increased with donor richness in stressful nitrogen-poor environments. Thus, diatom guild abundance patterns were determined primarily by biotic and/or environmental impacts and, with the exception of the low profile guild, were insensitive to spatial effects. This framework identifies major sources of variability in diatom guild abundance with implications for the understanding of biodiversity-ecosystem functioning.
creator: Sophia I. Passy
uri: https://doi.org/10.7717/peerj.3885
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Passy

title: Elevated serum osteoprotegerin may predict peripheral arterial disease after kidney transplantation: a single-center prospective cross-sectional study in Taiwan
link: https://peerj.com/articles/3847
last-modified: 2017-10-02
description: BackgroundOsteoprotegerin (OPG) is a potential biomarker for severity and complications of cardiovascular diseases. Peripheral arterial disease (PAD) is associated with an increased risk of death in kidney transplantation (KT) patients. This prospective cross-sectional study evaluated the relationship between serum OPG and PAD in KT patients.MethodsSeventy-four KT patients were enrolled for this PAD study. Fasting blood samples were obtained to measure serum OPG levels by using enzyme-linked immunosorbent assay kits. The ankle-brachial index (ABI) of less than 0.9 was applied for PAD diagnosis.ResultsThirteen patients (17.6%) were diagnosed with PAD. Diabetes (P = 0.025), smoking (P = 0.010), and increased OPG levels (P = 0.001) were significantly more frequent in the PAD group. Multivariate logistic regression analysis showed that serum OPG (odds ratio [OR], 1.336; 95% CI [1.108–1.611]; P = 0.002) and diabetes (OR, 7.120; 95% CI [1.080–46.940]; P = 0.041) were independent predictors of PAD in KT patients. The area under the receiver operating characteristic (ROC) curve determined that the probability of a serum OPG level of 7.117 pg/L in predicting PAD in KT patients was 0.799 (95% CI [0.690–0.884]; P < 0.001).DiscussionExploration of reliable biomarkers for early identification of vascular risk is crucial for KT patients. Elevated serum OPG levels may predict PAD in KT patients with cutoff value of 7.117 pg/L.
creator: Yen-Cheng Chen
creator: Bang-Gee Hsu
creator: Ching-Chun Ho
creator: Chung-Jen Lee
creator: Ming-Che Lee
uri: https://doi.org/10.7717/peerj.3847
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Chen et al.

title: Diverse responses of Symbiodinium types to menthol and DCMU treatment
link: https://peerj.com/articles/3843
last-modified: 2017-10-02
description: To understand the mechanism of photosynthetic inhibition and generation of reactive oxygen species (ROS) in Symbiodinium types under stress, chemicals such as dichlorophenyl dimethylurea (DCMU) are widely used. Moreover, DCMU and recently menthol were used to generate aposymbiotic cnidarian hosts. While the effects of DCMU on Symbiodinium cells have been extensively studied, no studies have shown the mechanism behind menthol-induced coral bleaching. Moreover, no study has compared the effects of DCMU and menthol treatments on photosystem II (PSII) activity and generation of ROS in different Symbiodinium types. In this study, we utilized five freshly isolated Symbiodinium types (S. minutum (B1), S. goreaui (C1), C3, C15, and S. trenchii (D1a)) to compare the effects of DCMU and menthol treatments. Symbiodinium cells were exposed to DCMU and menthol at different concentrations for 4 h. Results showed that values of the 50% inhibitory concentration (IC50) for PSII inhibition were 0.72∼1.96 mM for menthol-treated cells compared to 29∼74 pM for DCMU-treated cells. Diverse responses of Symbiodinium types were displayed in terms of PSII tolerance to menthol (S. minutum > S. trenchii = C15 > C3 = S. goreaui), and also in the response curves. In contrast, responses were not so diverse when the different types were treated with DCMU. Three of five menthol-treated Symbiodinium types showed instant and significant ROS generation when PSII activity was inhibited, compared to no ROS being generated in DCMU-treated Symbiodinium types. Both results indicated that menthol inhibited Symbiodinium PSII activity through Symbiodinium type-dependent mechanisms, which were also distinct from those with DCMU treatment. This study further confirmed that photosynthetic functions Symbiodinium have diverse responses to stress even within the same clade.
creator: Jih-Terng Wang
creator: Shashank Keshavmurthy
creator: Tzu-Ying Chu
creator: Chaolun Allen Chen
uri: https://doi.org/10.7717/peerj.3843
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Wang et al.

title: Harnessing mtDNA variation to resolve ambiguity in ‘Redfish’ sold in Europe
link: https://peerj.com/articles/3746
last-modified: 2017-10-02
description: Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples.
creator: Peter Shum
creator: Lauren Moore
creator: Christophe Pampoulie
creator: Cristina Di Muri
creator: Sara Vandamme
creator: Stefano Mariani
uri: https://doi.org/10.7717/peerj.3746
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Shum et al.

title: Comparative study of Cd uptake and tolerance of two Italian ryegrass (Lolium multiflorum) cultivars
link: https://peerj.com/articles/3621
last-modified: 2017-10-02
description: Cadmium (Cd) is one of the most toxic heavy metals and is difficult to be removed from contaminated soil and water. Italian ryegrass (Lolium multiflorum), as an energy crop, exhibits a valuable potential to develop Cd polluted sites due to its use as a biofuel rather than as food and forage. Previously, via a screening for Cd-tolerant ryegrass, the two most extreme cultivars (IdyII and Harukaze) with high and low Cd tolerance during seed germination, respectively, were selected. However, the underlying mechanism for Cd tolerance was not well investigated. In this study, we comparatively investigated the growth, physiological responses, and Cd uptake and translocation of IdyII and Harukaze when the seedlings were exposed to a Cd (0–100 μM) solution for 12 days. As expected, excess Cd inhibited seedling growth and was accompanied by an accumulation of malondialdehyde (MDA) and reduced photosynthetic pigments in both cultivars. The effects of Cd on the uptake and translocation of other nutrient elements (Zn, Fe, Mn and Mg) were dependent on Cd concentrations, cultivars, plant tissues and elements. Compared with Harukaze, IdyII exhibited better performance with less MDA and higher pigment content. Furthermore, IdyII was less efficient in Cd uptake and translocation compared to Harukaze, which might be explained by the higher non-protein thiols content in its roots. Taken together, our data indicate that IdyII is more tolerant than Harukaze, which partially resulted from the differences in Cd uptake and translocation.
creator: Zhigang Fang
creator: Laiqing Lou
creator: Zhenglan Tai
creator: Yufeng Wang
creator: Lei Yang
creator: Zhubing Hu
creator: Qingsheng Cai
uri: https://doi.org/10.7717/peerj.3621
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Fang et al.

title: Growth of hybrid open access, 2009–2016
link: https://peerj.com/articles/3878
last-modified: 2017-09-29
description: Hybrid Open Access is an intermediate form of OA, where authors pay scholarly publishers to make articles freely accessible within journals, in which reading the content otherwise requires a subscription or pay-per-view. Major scholarly publishers have in recent years started providing the hybrid option for the vast majority of their journals. Since the uptake usually has been low per journal and scattered over thousands of journals, it has been very difficult to obtain an overview of how common hybrid articles are. This study, using the results of earlier studies as well as a variety of methods, measures the evolution of hybrid OA over time. The number of journals offering the hybrid option has increased from around 2,000 in 2009 to almost 10,000 in 2016. The number of individual articles has in the same period grown from an estimated 8,000 in 2009 to 45,000 in 2016. The growth in article numbers has clearly increased since 2014, after some major research funders in Europe started to introduce new centralized payment schemes for the article processing charges (APCs).
creator: Bo-Christer Björk
uri: https://doi.org/10.7717/peerj.3878
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Björk