Estimation of different data compositions for early-season crop type classification
Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuracies around 155-day in Bole and 133-day in Luntai, which were earlier than the 32-day composition (170-day in both Bole and Luntai). Therefore, when the daily NDVI time series cannot be acquired, the 16-day composition is recommended in this study.
Spatial and Geographic Information Science
Hao et al. (2018) Estimation of different data compositions for early-season crop type classification. PeerJ 6:e4834 https://doi.org/10.7717/peerj.4834
Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress
Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection.
Choudhury et al. (2018) Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress. PeerJ 6:e4833 https://doi.org/10.7717/peerj.4833
Early and long-term results of minimally invasive mitral valve surgery through a right mini-thoracotomy approach: a retrospective propensity-score matched analysis
Background Minimally invasive mitral valve surgery (MVS) via right mini-thoracotomy has recently attracted a lot of attention. Minimally invasive MVS shows postoperative results that are comparable to those of conventional MVS through the median sternotomy as per various earlier studies. Methods Between 2000 and 2016, a total of 669 isolated mitral valve procedures for isolated mitral valve regurgitation were performed. A propensity score-matched analysis was generated for the elimination of the differences in relevant preoperative risk factors between the cohorts and included 227 patient pairs. Only degenerative mitral valve regurgitation was included. The aim of our study was to examine if the minimally MVS is superior to the conventional approach through sternotomy based on a retrospective propensity-matched analysis. The primary endpoints were early mortality and long-term survival. The secondary endpoints included postoperative complications. Results The in-hospital mortality rate was significantly higher within the conventional sternotomy cohort (3.1%, n = 7 vs 0.4%, n = 1 for the minimally invasive cohort; p = 0.032). The incidence of stroke and exploration for bleeding was comparable. In contrast, the necessity for dialysis was significantly lower in the minimally invasive cohort (p = 0.044). Postoperative pain was not significantly lower in the minimally invasive MVS cohort (p = 0.862). While patients who underwent minimally invasive MVS experienced longer bypass and cross-clamp times, their lengths of stay in the intensive care unit and in the hospital, did not differ from the conventionally operated collective (p = 0.779 and p = 0.516), respectively. The mitral valve repair rate of 81.1% in the minimally invasive cohort was significantly superior to that of the conventional approach, which was 46.3% (p < 0.0001). The one-, five-, and 10-year survival rates were significantly higher in the minimally invasive cohort compared to the conventional approach (96%, 90%, and 84% vs. 89%, 85%, and 70%; log rank p = 0.004). Conclusion Despite prolonged cardiopulmonary bypass and cross-clamping times, the minimally invasive MVS may be considered a safe approach that is equivalent to standard median sternotomy with lower early mortality and superior long-term survival.
Mkalaluh et al. (2018) Early and long-term results of minimally invasive mitral valve surgery through a right mini-thoracotomy approach: a retrospective propensity-score matched analysis. PeerJ 6:e4810 https://doi.org/10.7717/peerj.4810
Redescription of Phymolepis cuifengshanensis (Antiarcha: Yunnanolepididae) using high-resolution computed tomography and new insights into anatomical details of the endocranium in antiarchs
Background Yunnanolepidoids constitute either the most basal consecutive segments or the most primitive clade of antiarchs, a highly diversified jawed vertebrate group from the Silurian and Early Devonian periods. Although the general morphology of yunnanolepidoids is well established, their endocranial features remain largely unclear, thus hindering our further understanding of antiarch evolution, and early gnathostome evolution. Phymolepis cuifengshanensis, a yunnanolepidoid from the Early Devonian of southwestern China, is re-described in detail to reveal the information on endocranial anatomy and additional morphological data of head and trunk shields. Methods We scanned the material of P. cuifengshanensis using high-resolution computed tomography and generated virtual restorations to show the internal morphology of its dermal shield. The dorsal aspect of endocranium in P. cuifengshanensis was therefore inferred. The phylogenetic analysis of antiarchs was conducted based on a revised and expanded dataset that incorporates 10 new cranial characters. Results The lateroventral fossa of trunk shield and Chang’s apparatus are three-dimensionally restored in P. cuifengshanensis. The canal that is positioned just anterior to the internal cavity of Chang’s apparatus probably corresponds to the rostrocaudal canal of euantiarchs. The endocranial morphology of P. cuifengshanensis corroborates a general pattern for yunnanolepidoids with additional characters distinguishing them from sinolepids and euantiarchs, such as a developed cranio-spinal process, an elongated endolymphatic duct, and a long occipital portion. Discussion In light of new data from Phymolepis and Yunnanolepis, we summarized the morphology on the visceral surface of head shield in antiarchs, and formulated an additional 10 characters for the phylogenetic analysis. These cranial characters exhibit a high degree of morphological disparity between major subgroups of antiarchs, and highlight the endocranial character evolution in antiarchs.
Wang et al. (2018) Redescription of Phymolepis cuifengshanensis (Antiarcha: Yunnanolepididae) using high-resolution computed tomography and new insights into anatomical details of the endocranium in antiarchs. PeerJ 6:e4808 https://doi.org/10.7717/peerj.4808
A guideline for reporting experimental protocols in life sciences
Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements. This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline. As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology. By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria. Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol.
Giraldo et al. (2018) A guideline for reporting experimental protocols in life sciences. PeerJ 6:e4795 https://doi.org/10.7717/peerj.4795
Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?
That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (∼1,300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes.
Tonkin et al. (2018) Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?. PeerJ 6:e4898 https://doi.org/10.7717/peerj.4898
Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China
Background The spruce forests are dominant communities in northwest China, and play a key role in national carbon budgets. However, the patterns of carbon stock distribution and accumulation potential across stand ages are poorly documented. Methods We investigated the carbon stocks in biomass and soil in the natural spruce forests in the region by surveys on 39 plots. Biomass of tree components were estimated using allometric equations previously established based on tree height and diameter at breast height, while biomass in understory (shrub and herb) and forest floor were determined by total harvesting method. Fine root biomass was estimated by soil coring technique. Carbon stocks in various biomass components and soil (0–100 cm) were estimated by analyzing the carbon content of each component. Results The results showed that carbon stock in these forest ecosystems can be as high as 510.1 t ha−1, with an average of 449.4 t ha−1. Carbon stock ranged from 28.1 to 93.9 t ha−1 and from 0.6 to 8.7 t ha−1 with stand ages in trees and deadwoods, respectively. The proportion of shrubs, herbs, fine roots, litter and deadwoods ranged from 0.1% to 1% of the total ecosystem carbon, and was age-independent. Fine roots and deadwood which contribute to about 2% of the biomass carbon should be attached considerable weight in the investigation of natural forests. Soil carbon stock did not show a changing trend with stand age, ranging from 254.2 to 420.0 t ha−1 with an average of 358.7 t ha−1. The average value of carbon sequestration potential for these forests was estimated as 29.4 t ha−1, with the lower aged ones being the dominant contributor. The maximum carbon sequestration rate was 2.47 t ha−1 year−1 appearing in the growth stage of 37–56 years. Conclusion The carbon stock in biomass was the major contributor to the increment of carbon stock in ecosystems. Stand age is not a good predictor of soil carbon stocks and accurate evaluation of the soil carbon dynamics thus requires long-term monitoring in situ. The results not only revealed carbon stock status and dynamics in these natural forests but were helpful to understand the role of Natural Forest Protection project in forest carbon sequestration as well.
Yue et al. (2018) Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China. PeerJ 6:e4859 https://doi.org/10.7717/peerj.4859
Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study
Background The annual global deaths from viral hepatitis is 1.4 million. Pakistan has the second highest burden of hepatitis C in the world. There is dire need to evaluate the response of new direct acting antivirals for the treatment of hepatitis C patients in Pakistan. World Health Organization has developed a strategy to treat 80% of HCV patients by 2030. In Pakistan, HCV treatment rate is 1%. The aim of the study was to analyze the effect of Sofosbuvir plus Ribavirin therapy on HCV patients in Pakistan. Methods An observational study was conducted at Fauji Foundation Hospital Rawalpindi from November-2016 to July-2017. All the drugs were administered according to the guidelines of Asia Pacific Association for the Study of Liver (APASL) for the treatment of HCV patients. A total 327 chronic HCV patients were enrolled in the study and 304 completed the treatment. Patients belonged to three different groups including treatment: Naïve patients (n = 107), Non-Responder patients (n = 126) and patients who relapsed to Interferon therapy (n = 71). All the patients were given Sofosbuvir plus Ribavirin therapy for 24 weeks and the early virological response (EVR) and end treatment response (ETR) was calculated. Different parameters including patient age, viral load, viral genotype, blood picture, ultrasound findings and liver function tests were also studied. Results Out of 304 patients, 301 (99%) achieved EVR and 300 achieved ETR (98.7%). End treatment response was 95.6% in HCV genotype 1 and 98.9% in HCV genotype 3 patients. ETR was 99.06% in treatment Naïve, 99.20% in non-responders and 97.18% in previously relapsed patients. We did not find the association of any host and viral factor in the determination of EVR and ETR. Conclusion The Sofosbuvir plus Ribavirin treatment is highly effective, safe and cost-effective for the treatment of hepatitis C patients in Pakistan.
Jamil et al. (2018) Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study. PeerJ 6:e4853 https://doi.org/10.7717/peerj.4853
Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches
Background Among combat sports, Judo and Brazilian Jiu-Jitsu (BJJ) present elevated physical fitness demands from the high-intensity intermittent efforts. However, information regarding how metabolic and neuromuscular physical fitness is associated with technical-tactical performance in Judo and BJJ fights is not available. This study aimed to relate indicators of physical fitness with combat performance variables in Judo and BJJ. Methods The sample consisted of Judo (n = 16) and BJJ (n = 24) male athletes. At the first meeting, the physical tests were applied and, in the second, simulated fights were performed for later notational analysis. Results The main findings indicate: (i) high reproducibility of the proposed instrument and protocol used for notational analysis in a mobile device; (ii) differences in the technical-tactical and time-motion patterns between modalities; (iii) performance-related variables are different in Judo and BJJ; and (iv) regression models based on metabolic fitness variables may account for up to 53% of the variances in technical-tactical and/or time-motion variables in Judo and up to 31% in BJJ, whereas neuromuscular fitness models can reach values up to 44 and 73% of prediction in Judo and BJJ, respectively. When all components are combined, they can explain up to 90% of high intensity actions in Judo. Discussion In conclusion, performance prediction models in simulated combat indicate that anaerobic, aerobic and neuromuscular fitness variables contribute to explain time-motion variables associated with high intensity and technical-tactical variables in Judo and BJJ fights.
Coswig et al. (2018) Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches. PeerJ 6:e4851 https://doi.org/10.7717/peerj.4851
Purpose A literature review is presented that aims to summarize and compare current methods to evaluate sleep. Methods Current sleep assessment methods have been classified according to different criteria; e.g., objective (polysomnography, actigraphy…) vs. subjective (sleep questionnaires, diaries…), contact vs. contactless devices, and need for medical assistance vs. self-assessment. A comparison of validation studies is carried out for each method, identifying their sensitivity and specificity reported in the literature. Finally, the state of the market has also been reviewed with respect to customers’ opinions about current sleep apps. Results A taxonomy that classifies the sleep detection methods. A description of each method that includes the tendencies of their underlying technologies analyzed in accordance with the literature. A comparison in terms of precision of existing validation studies and reports. Discussion In order of accuracy, sleep detection methods may be arranged as follows: Questionnaire < Sleep diary < Contactless devices < Contact devices < Polysomnography A literature review suggests that current subjective methods present a sensitivity between 73% and 97.7%, while their specificity ranges in the interval 50%–96%. Objective methods such as actigraphy present a sensibility higher than 90%. However, their specificity is low compared to their sensitivity, being one of the limitations of such technology. Moreover, there are other factors, such as the patient’s perception of her or his sleep, that can be provided only by subjective methods. Therefore, sleep detection methods should be combined to produce a synergy between objective and subjective methods. The review of the market indicates the most valued sleep apps, but it also identifies problems and gaps, e.g., many hardware devices have not been validated and (especially software apps) should be studied before their clinical use.
Ibáñez et al. (2018) A survey on sleep assessment methods. PeerJ 6:e4849 https://doi.org/10.7717/peerj.4849