Early Detection of Encroaching Woody Juniperus virginiana and Its Classification in Multi-Species Forest Using UAS Imagery and Semantic Segmentation Algorithms

Woody plant encroachment into grasslands ecosystems causes significantly ecological destruction and economic losses. Effective and efficient management largely benefits from accurate and timely detection of encroaching species at an early development stage. Recent advances in unmanned aircraft systems (UAS) enabled easier access to ultra-high spatial resolution images at a centimeter level, together with the latest machine learning based image segmentation algorithms, making it possible to detect small-sized individuals of target species at early development stage and identify them when mixed with other species. However, few studies have investigated the optimal practical spatial resolution of early encroaching species detection. Hence, we investigated the performance of four popular semantic segmentation algorithms (decision tree, DT; random forest, RF; AlexNet; and ResNet) on a multi-species forest classification case with UAS-collected RGB images in original and down-sampled coarser spatial resolutions. The objective of this study was to explore the optimal segmentation algorithm and spatial resolution for eastern redcedar (Juniperus virginiana, ERC) early detection and its classification within a multi-species forest context. To be specific, firstly, we implemented and compared the performance of the four semantic segmentation algorithms with images in the original spatial resolution (0.694 cm). The highest overall accuracy was 0.918 achieved by ResNet with a mean interaction over union at 85.0%. Secondly, we evaluated the performance of ResNet algorithm with images in down-sampled spatial resolutions (1 cm to 5 cm with 0.5 cm interval). When applied on the down-sampled images, ERC segmentation performance decreased with decreasing spatial resolution, especially for those images coarser than 3 cm spatial resolution. The UAS together with the state-of-the-art semantic segmentation algorithms provides a promising tool for early-stage detection and localization of ERC and the development of effective management strategies for mixed-species forest management

TiAVox: Time-aware Attenuation Voxels for Sparse-view 4D DSA Reconstruction

Four-dimensional Digital Subtraction Angiography (4D DSA) plays a critical role in the diagnosis of many medical diseases, such as Arteriovenous Malformations (AVM) and Arteriovenous Fistulas (AVF). Despite its significant application value, the reconstruction of 4D DSA demands numerous views to effectively model the intricate vessels and radiocontrast flow, thereby implying a significant radiation dose. To address this high radiation issue, we propose a Time-aware Attenuation Voxel (TiAVox) approach for sparse-view 4D DSA reconstruction, which paves the way for high-quality 4D imaging. Additionally, 2D and 3D DSA imaging results can be generated from the reconstructed 4D DSA images. TiAVox introduces 4D attenuation voxel grids, which reflect attenuation properties from both spatial and temporal dimensions. It is optimized by minimizing discrepancies between the rendered images and sparse 2D DSA images. Without any neural network involved, TiAVox enjoys specific physical interpretability. The parameters of each learnable voxel represent the attenuation coefficients. We validated the TiAVox approach on both clinical and simulated datasets, achieving a 31.23 Peak Signal-to-Noise Ratio (PSNR) for novel view synthesis using only 30 views on the clinically sourced dataset, whereas traditional Feldkamp-Davis-Kress methods required 133 views. Similarly, with merely 10 views from the synthetic dataset, TiAVox yielded a PSNR of 34.32 for novel view synthesis and 41.40 for 3D reconstruction. We also executed ablation studies to corroborate the essential components of TiAVox. The code will be publically available.Comment: 10 pages, 8 figure

Characterization of Cajanus scarabaeoides growing in Yuanjiang county of Yunnan province in China

In Yuanjiang, Yunnan, China, C. scarabaeoides is found in abundance in open grasslands and dry scrub vegetation on hill slopes and ridges between cultivated fields. It is also located along roadsides, foot paths or convex rides where reasonable amount of sunlight is available. This creeper-climber, supported by grass and small shrubs have: either straight or winding branches which are woody at the base; pinnately trifoliate leaves with white-pubescent lower and upper surfaces; obovate end leaflet; short racemes; indeterminate and sporadic flowering habit; oblong, purple to dark purple pods; rectangular to rounded seeds; and yellow or creamish yellow flowers with dense sun-red veins. Its mean protein content is 21.88% in the seed and 13.23% in the dried leaves. It may be used as medicine for diarrhoea in cattle, and as a traditional Chinese medicine for improving indigestion and diuresis

A Set of Novel Microsatellite Markers Developed for Luculia yunnanensis (Rubiaceae), an Endangered Plant Endemic to Yunnan, China

The genus Luculia Sweet contains about five species of small trees or shrubs and is a member of the family Rubiaceae (tribe Cinchoneae). Luculia yunnanensis is an endangered ornamental shrub endemic to southwest China. Only two natural populations of L. yunnanensis exist in the wild according to our field investigation. It can be inferred that L. yunnanensis is facing a very high risk of extinction in the wild and an urgent conservation strategy is required. By using a modified biotin-sterptavidin capture method, 24 primer sets were identified in two wild populations. Of these primers, 11 displayed polymorphisms and 13 were monomorphic. The number of alleles per locus ranged from two to four, values for observed and expected heterozygosities ranged from 0.000 to 0.833 and from 0.431 to 0.771, with averages of 0.389 and 0.614, respectively. These markers will be useful for further investigation of conservation of resources, selecting parental types in cross-breeding, evolution of this species at the molecular level and related research in Luculia species

knnAUC: an open-source R package for detecting nonlinear dependence between one continuous variable and one binary variable

Abstract Background Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). Results We addressed this problem by using knnAUC (k-nearest neighbors AUC test, the R package is available at https://sourceforge.net/projects/knnauc/ ). In the knnAUC software framework, we first resampled a dataset to get the training and testing dataset according to the sample ratio (from 0 to 1), and then constructed a k-nearest neighbors algorithm classifier to get the yhat estimator (the probability of y = 1) of testy (the true label of testing dataset). Finally, we calculated the AUC (area under the curve of receiver operating characteristic) estimator and tested whether the AUC estimator is greater than 0.5. To evaluate the advantages of knnAUC compared to seven other popular methods, we performed extensive simulations to explore the relationships between eight different methods and compared the false positive rates and statistical power using both simulated and real datasets (Chronic hepatitis B datasets and kidney cancer RNA-seq datasets). Conclusions We concluded that knnAUC is an efficient R package to test non-linear dependence between one continuous variable and one binary dependent variable especially in computational biology area.https://deepblue.lib.umich.edu/bitstream/2027.42/146514/1/12859_2018_Article_2427.pd

Wild relatives of pigeonpea in China

Wild relatives play an important role in the genetic improvement of cultivated crops. Breeders turn their attention to the wild relatives of crops after unsuccessful search for some unique trait in the cultivated germplasm. According to van der Maesen (1986) the genus Cajanus has 32 species. Of these, the Indian subcontinent harbors 18 species. ICRISAT has the global responsibility of collection, maintenance, and evaluation of germplasm of the wild relatives of pigeonpea. At present a total of 213 accessions, representing 20 Cajanus species are conserved for use in the breeding programs

World Data Centre for Microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide

The World Data Centre for Microorganisms (WDCM) was established 50 years ago as the data center of the World Federation for Culture Collections (WFCC) Microbial Resource Center (MIRCEN). WDCM aims to provide integrated information services using big data technology for microbial resource centers and microbiologists all over the world. Here, we provide an overview of WDCM including all of its integrated services. Culture Collections Information Worldwide (CCINFO) provides metadata information on 708 culture collections from 72 countries and regions. Global Catalogue of Microorganism (GCM) gathers strain catalogue information and provides a data retrieval, analysis, and visualization system of microbial resources. Currently, GCM includes more than 368,000 strains from 103 culture collections in 43 countries and regions. Analyzer of Bioresource Citation (ABC) is a data mining tool extracting strain related publications, patents, nucleotide sequences and genome information from public data sources to form a knowledge base. Reference Strain Catalogue (RSC) maintains a database of strains listed in International Standards Organization (ISO) and other international or regional standards. RSC allocates a unique identifier to strains recommended for use in diagnosis and quality control, and hence serves as a valuable cross-platform reference. WDCM provides free access to all these services at www.wdcm.org.National High Technology Research and Development Program of China [2014AA021501, 2014AA021503, 2015AA020108]; International S&T Cooperation Program of China (ISTCP) [2015DFG32550]; Bureau of Science & Technology for Development of Chinese Academy of Sciences (Strategic bio-resources information center) and Field Cloud Project of Chinese Academy of Sciences [XXH12503-05-01]. Funding for open access charge: National High Technology Research and Development Program of China [2014AA021501, 2014AA021503, 2015AA020108]; International S&T Cooperation Program of China (ISTCP) [2015DFG32550] ; Bureau of Science & Technology for Development of Chinese Academy of Sciences [Strategic bio-resources information center]; Field Cloud Project of Chinese Academy of Sciences [XXH12503-05-01]

Predictive model for inflammation grades of chronic hepatitis B: Large‐scale analysis of clinical parameters and gene expressions

BackgroundLiver biopsy is the gold standard to assess pathological features (eg inflammation grades) for hepatitis B virus‐infected patients although it is invasive and traumatic; meanwhile, several gene profiles of chronic hepatitis B (CHB) have been separately described in relatively small hepatitis B virus (HBV)‐infected samples. We aimed to analyse correlations among inflammation grades, gene expressions and clinical parameters (serum alanine amino transaminase, aspartate amino transaminase and HBV‐DNA) in large‐scale CHB samples and to predict inflammation grades by using clinical parameters and/or gene expressions.MethodsWe analysed gene expressions with three clinical parameters in 122 CHB samples by an improved regression model. Principal component analysis and machine‐learning methods including Random Forest, K‐nearest neighbour and support vector machine were used for analysis and further diagnosis models. Six normal samples were conducted to validate the predictive model.ResultsSignificant genes related to clinical parameters were found enriching in the immune system, interferon‐stimulated, regulation of cytokine production, anti‐apoptosis, and etc. A panel of these genes with clinical parameters can effectively predict binary classifications of inflammation grade (area under the ROC curve [AUC]: 0.88, 95% confidence interval [CI]: 0.77‐0.93), validated by normal samples. A panel with only clinical parameters was also valuable (AUC: 0.78, 95% CI: 0.65‐0.86), indicating that liquid biopsy method for detecting the pathology of CHB is possible.ConclusionsThis is the first study to systematically elucidate the relationships among gene expressions, clinical parameters and pathological inflammation grades in CHB, and to build models predicting inflammation grades by gene expressions and/or clinical parameters as well.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/139116/1/liv13427.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/139116/2/liv13427_am.pd

The Precambrian Khondalite Belt in the Daqingshan area, North China Craton: evidence for multiple metamorphic events in the Palaeoproterozoic era

High-grade pelitic metasedimentary rocks (khondalites) are widely distributed in the northwestern part of the North China Craton and were named the ‘Khondalite Belt’. Prior to the application of zircon geochronology, a stratigraphic division of the supracrustal rocks into several groups was established using interpretative field geology. We report here SHRIMP U–Pb zircon ages and Hf-isotope data on metamorphosed sedimentary and magmatic rocks at Daqingshan, a typical area of the Khondalite Belt. The main conclusions are as follows: (1) The early Precambrian supracrustal rocks belong to three sequences: a 2.56–2.51 Ga supracrustal unit (the previous Sanggan ‘group’), a 2.51–2.45 Ga supracrustal unit (a portion of the previous upper Wulashan ‘group’) and a 2.0–1.95 Ga supracrustal unit (including the previous lower Wulashan ‘group’, a portion of original upper Wulashan ‘group’ and the original Meidaizhao ‘group’) the units thus do not represent a true stratigraphy; (2) Strong tectono-thermal events occurred during the late Neoarchaean to late Palaeoproterozoic, with four episodes recognized: 2.6–2.5, 2.45–2.37, 2.3–2.0 and 1.95–1.85 Ga, with the latest event being consistent with the assembly of the Palaeoproterozoic supercontinent Columbia; (3) During the late Neoarchaean to late Palaeoproterozoic (2.55–2.5, 2.37 and 2.06 Ga) juvenile, mantle-derived material was added to the crust

Efficacy and pharmacoeconomic advantages of Fufang Huangbai Fluid hydropathic compress in diabetic foot infections: a comparative clinical study with antimicrobial calcium alginate wound dressing

Objective: To compare the intervention effects and pharmacoeconomic advantages of Fufang Huangbai Fluid (FFHB) hydropathic compress versus Antimicrobial Calcium Alginate Wound Dressing (ACAWD) in the treatment of diabetic foot infections (DFI).Methods: Patients with DF who were hospitalized in the peripheral vascular Department of Dongzhimen Hospital of Beijing University of Chinese Medicine from December 2020 to February 2022 and met the inclusion and excluding criteria were allocated into the experimental group and control group through minimization randomization. The experimental group was treated with FFHB hydropathic compress for 2 weeks, while the control group was treated with ACAWD for the same duration. The wound healing of both groups was monitored for 1 month post-discharge. Clinical data from all eligible patients were collected, and differences in various indices between cohorts were analyzed.Results: 22 in the experimental group (including two fell off) and 20 in the control group. After the treatment, the negative rate of wound culture in the experimental group was 30% and that in the control group was 10%, There was no significant difference in the negative rate of wound culture and change trend of minimum inhibitory concentration (MIC) value of drug sensitivity (p > 0.05). The infection control rate of the experimental group was 60%, and that of the control group was 25%. The difference between the two groups was statistically significant (χ2 = 5.013, p = 0.025). The median wound healing rate of the experimental group was 34.4% and that of the control group was 33.3%. There was no significant difference between the two groups (p > 0.05). During the follow-up 1 month later, the wound healing rate in the experimental group was higher, and the difference was statistically significant (p = 0.047). Pharmacoeconomic evaluations indicated that the experimental group had greater cost-effectiveness compared to the control group.Conclusion: In the preliminary study, FFHB demonstrated comparable pathogenic and clinical efficacy to ACAWD in the treatment of mild DF infection, and exhibited superior pharmacoeconomic advantages. With the aid of infection control, the wound healing rate in the FFHB group showed notable improvement. Nevertheless, due to the limited sample size, larger-scale studies are warranted to further validate these findings.Clinical Trial Registration: (https://www.chictr.org.cn/showproj.aspx?proj=66175), identifier (ChiCTR2000041443)