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Pockle R, Masareddy R, Bambulkar V, Desai R, Kiran S. Exploring magnesium myristate for its dual functionality as a binder and lubricant in the formulation of tablet. Ther Deliv 2024; 15:253-266. [PMID: 38420754 DOI: 10.4155/tde-2023-0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Purpose: To explore 'magnesium myristate' for its dual functionality as a lubricant and binder in the formulation of tablets. Methods: Using (DoE), tablet formulations using magnesium myristate and conventional excipients (magnesium stearate and PVP K30) were developed by wet granulation technique. The prepared granules and formulated tablets were evaluated for pre- and post-compression parameters, respectively. Results: Magnesium myristate exhibited excellent flow properties. The optimized formulations containing magnesium myristate exhibited increased hardness and in vitro drug release in comparison to conventional excipients. f2 similarity index for in vitro drug release showed no significant variations with optimized formulations and with the marketed formulations. Conclusion: Magnesium myristate shows a promising replacement for conventional excipients as both a lubricant and binder in tablet formulation.
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Affiliation(s)
- Rachana Pockle
- Department of Pharmaceutics, KLE College of Pharmacy, KLE Academy of Higher Education & Research, Nehru Nagar, Belagavi - 590010, Karnataka, India
| | - Rajashree Masareddy
- Department of Pharmaceutics, KLE College of Pharmacy, KLE Academy of Higher Education & Research, Nehru Nagar, Belagavi - 590010, Karnataka, India
| | | | | | - Sai Kiran
- Department of Pharmaceutics, KLE College of Pharmacy, KLE Academy of Higher Education & Research, Nehru Nagar, Belagavi - 590010, Karnataka, India
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Lin YC, Guo XP, Li WY, Yang F, Luo C, Hao JH, Wu YX. [Effects of coal mine waste dump on soil seed bank and vegetation distribution pattern]. Ying Yong Sheng Tai Xue Bao 2024; 35:95-101. [PMID: 38511445 DOI: 10.13287/j.1001-9332.202401.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Long-term occupation of coal gangue dumping sites (CGDS) may destroy ecological environment of nearby area. However, how the CGDS affects the distribution pattern of soil seed banks and vegetation in the nearby area is not clear. In this study, we investigated soil seed bank and vegetation at different distances from the second CGDS of Yangchangwan in Ningdong mining area, Lingwu, Ningxia. The results showed that soil seed bank was mainly distributed in 0-10 cm layer and decreased with increasing soil depth. Species richness of soil seed bank and vegetation first increased and then tended to be stable with increasing distance to the CGDS. The influence range of CGDS on soil seed banks was 300-500 m and was 100-300 m on aboveground vegetation. The CGDS did not affect the vertical distribution pattern of soil seed bank, but significantly affected the horizontal distribution pattern of soil seed banks and aboveground vegetation. The key area of vegetation restoration around the CGDS was between 100 m and 300 m.
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Affiliation(s)
- Ya-Chao Lin
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
| | - Xiao-Ping Guo
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
| | - Wen-Ye Li
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
| | - Fan Yang
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
| | - Chao Luo
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jia-Hang Hao
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
| | - Yu-Xi Wu
- School of Soil and Water Conservation, Beijing Forestry University/Key Laboratory of State Forestry Administration on Soil and Water Conservation, Beijing 100083, China
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Tao Y, Zhou XB, Yin BF, Dimeyeva L, Zhang J, Zang YX, Zhang YM. Combining Multiple Plant Attributes to Reveal Differences in Community Structure in Two Distant Deserts in Central Asia. Plants (Basel) 2023; 12:3286. [PMID: 37765450 PMCID: PMC10537988 DOI: 10.3390/plants12183286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
International interest is growing in biodiversity conservation and sustainable use in drylands. Desert ecosystems across arid Central Asia are severely affected by global change. Understanding the changes in a plant community is an essential prerequisite to revealing the community assembly mechanism, vegetation conservation, and management. The knowledge of large-scale spatial variation in plant community structure in different Central Asian deserts is still limited. In this study, we selected the Taukum (TD, Kazakhstan) and the Gurbantunggut (GD, China) deserts as the research area, with similar latitudes despite being nearly 1000 km apart. Thirteen and 15 sampling plots were set up and thoroughly investigated. The differences in community structure depending on multiple plant attributes (individual level: plant height, canopy diameter, and plant volume, and community level: plant density, total cover, and total volume) were systematically studied. TD had a better overall environmental status than GD. A total of 113 species were found, with 68 and 74 in TD and GD, respectively. The number of species and plant attributes was unequally distributed across different families and functional groups between deserts. The values of several plant attributes, such as ephemerals, annuals, dicotyledons, and shrubs with assimilative branches in GD, were significantly lower than those in TD. The Motyka indices of six plant attributes (26.18-38.61%) were higher between the two deserts than the species similarity index (20.4%), indicating a more robust convergence for plant functional attributes. The community structures in the two deserts represented by different plant attribute matrices demonstrated irregular differentiation patterns in ordination diagrams. The most variance in community structure was attributed to soil and climatic factors, while geographic factors had the smallest proportion. Consequently, the community structures of the two distant deserts were both different and similar to an extent. This resulted from the long-term impacts of heterogeneous environments within the same region. Our knowledge is further deepened by understanding the variation in community structure in different deserts on a large spatial scale. This therefore provides valuable insights into conserving regional biodiversity in Central Asia.
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Affiliation(s)
- Ye Tao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Xiao-Bing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Ben-Feng Yin
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Liliya Dimeyeva
- Institute of Botany and Phytointroduction, Ministry of Ecology and Natural Resources of the Republic of Kazakhstan, Almaty 050040, Kazakhstan;
| | - Jing Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Yong-Xin Zang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
| | - Yuan-Ming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Security and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (Y.T.); (X.-B.Z.); (B.-F.Y.); (J.Z.); (Y.-X.Z.)
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Natsume H, Okamoto S, Nagano H. TDS Similarity: Outlier Analysis Using a Similarity Index to Compare Time-Series Responses of Temporal Dominance of Sensations Tasks. Foods 2023; 12:foods12102025. [PMID: 37238843 DOI: 10.3390/foods12102025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/22/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Temporal dominance of sensations (TDS) methods are used to record temporally developing sensations while eating food samples. Results of TDS tasks are typically discussed using averages across multiple trials and panels, and few methods have been developed to analyze differences between individual trials. We defined a similarity index between two time-series responses of TDS tasks. This index adopts a dynamic level to determine the importance of the timing of attribute selection. With a small dynamic level, the index focuses on the duration for attributes to be selected rather than on the timing of the attribute selection. With a large dynamic level, the index focuses on the temporal similarity between two TDS tasks. We performed an outlier analysis based on the developed similarity index using the results of TDS tasks performed in an earlier study. Certain samples were categorized as outliers irrespective of the dynamic level, whereas the categorization of a few samples depended on the level. The similarity index developed in this study achieved individual analyses of TDS tasks, including outlier detection, and adds new analysis techniques to TDS methods.
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Affiliation(s)
- Hiroharu Natsume
- Department of Computer Science, Tokyo Metropolitan University, Hino 191-0065, Japan
| | - Shogo Okamoto
- Department of Computer Science, Tokyo Metropolitan University, Hino 191-0065, Japan
| | - Hikaru Nagano
- Department of Mechanical Engineering, Kobe University, Kobe 657-8501, Japan
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Tuwo M, Kuswinanti T, Nasruddin A, Tambaru E. Diverse Morphology and Anatomy of <i>Citrus</i> Spp. (Orange) in South Sulawesi, Indonesia Plantations: A Comprehensive Study. Pak J Biol Sci 2023; 26:321-333. [PMID: 37902046 DOI: 10.3923/pjbs.2023.321.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
<b>Background and Objective:</b> South Sulawesi, one of the Indonesian provinces, is a producer of oranges with various varieties grown extensively for export and domestic use. Information about the diversity of oranges is crucial for plant breeding and germplasm conservation. This study aims to analyze the diversity of oranges from several plantation centers in South Sulawesi based on morphological and anatomical characteristics. <b>Materials and Methods:</b> Orange leaf samples were collected from five plantation locations in South Sulawesi, namely Pangkep, Sidrap, Bantaeng, North Luwu and Selayar Regencies. The morphological characteristics were identified using descriptors from the International Plant Genetic Resources Institute and Tjitrosoepomo. The anatomical characteristics were identified by preparing stomata slides observed under a microscope at a magnification of 200-400x. Similarity analysis between orange varieties was conducted using the NTSYS software and presented in the form of a dendrogram. <b>Results:</b> The results of the diversity analysis of 13 orange varieties showed morphological variability in tree form and leaf shape, while anatomical characteristics showed variability in stomata size and stomata index. The similarity analysis showed that morphological characteristics formed clusters consisting of seeded selayar (SB), kaffir lime (NN), JC-selayar (JS), selayar-selayar (SS), batu (B), japansche citroen (JC) and dekopon (D) varieties, which had a 75% similarity with siam (SI) and sweet santang (SM) varieties. Meanwhile, the anatomical cluster analysis showed that the JC and SM orange varieties had a 79% similarity with the D variety. <b>Conclusion:</b> The dendrogram diagram can serve as a basis for determining desired plant traits in plant breeding activities.
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Lin CY, Chiang CH, Te ALD, Lin YJ, Lo MT, Lin C, Chang SL, Lo LW, Hu YF, Chung FP, Tuan TC, Chao TF, Liao JN, Chen SA. Characterization and identification of atrial fibrillation drivers in patients with nonparoxysmal atrial fibrillation using simultaneous amplitude frequency electrogram transform. J Cardiovasc Electrophysiol 2023; 34:536-545. [PMID: 36598424 DOI: 10.1111/jce.15806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/08/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
INSTRUCTION We hypothesized that real-time simultaneous amplitude frequency electrogram transform (SAFE-T) during sinus rhythm (SR) is able to identify and characterize the drivers of atrial fibrillation (AF) in nonparoxysmal (NP) AF. METHODS Twenty-one NPAF patients (85.71% males, mean age 52 years old) underwent substrate mapping during SR (SAFE-T and voltage) and during AF (complex fractionated atrial electrograms [CFAE] and similarity index [SI]). After pulmonary veins isolation, extensive substrate ablation was performed with the endpoint of procedural termination or elimination of all SI sites (>63% similarities). Sites with procedural termination and non-termination sites were tagged for postablation SR analysis using SAFE-T. RESULTS In 74 CFAE sites identified (average of 3 ± 2 sites per person), 28 (37.84%) were identified as termination sites demonstrating a high SI compared with the non-termination sites (80.11 ± 9.57% vs. 45.96 ± 13.38%, p < .001) during AF. During SR, these termination sites have high SAFE-T values and harbor a highly resonant, localized, repetitive high frequency components superimposed in the low frequency components compared with non-termination sites (5.70 ± 3.04 vs. 1.49 ± 1.66 Hz·mV, p < .001). In the multivariate analysis, the termination sites have higher SAFE-T and SI value (p < .001). CONCLUSION AF procedural termination sites harbored signal characteristics of repetitive, high frequency component of individualized electrogram during SR, which can be masked by the low frequency fractionated electrogram and are difficult to see from the bipolar electrogram. Thus, SAFE-T mapping is feasible in identifying and characterizing sites of AF drivers.
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Affiliation(s)
- Chin-Yu Lin
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Hsin Chiang
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Research Center for Adaptive Analysis, Taoyuan City, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Chungli, Taiwan
| | - Abigail Louise D Te
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Heart Institute, St. Luke's Medical Center, Global City, Philippines
| | - Yenn-Jiang Lin
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Men-Tzung Lo
- Research Center for Adaptive Analysis, Taoyuan City, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Chungli, Taiwan
| | - Chen Lin
- Center for Dynamical Biomarkers and Translational Medicine, National Central University, Chungli, Taiwan.,Heart Institute, St. Luke's Medical Center, Global City, Philippines
| | - Shih-Lin Chang
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Wei Lo
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Feng Hu
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Fa-Po Chung
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ta-Chuan Tuan
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tze-Fan Chao
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jo-Nan Liao
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Ann Chen
- Department of Medicine, Division of Cardiology, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan.,Cardiovascular Research Center, Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Medicine, Division of Cardiology, Taichung Veterans General Hospital, Taichung, Taiwan
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Khandia R, Khan AA, Karuvantevida N, Gurjar P, Rzhepakovsky IV, Legaz I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts. Pathogens 2023; 12:pathogens12020325. [PMID: 36839597 PMCID: PMC9961758 DOI: 10.3390/pathogens12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
- Correspondence: (R.K.); (I.L.)
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
- Correspondence: (R.K.); (I.L.)
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Cozzolino D, Bureš D, Hoffman LC. Evaluating the Use of a Similarity Index (SI) Combined with near Infrared (NIR) Spectroscopy as Method in Meat Species Authenticity. Foods 2023; 12. [PMID: 36613404 DOI: 10.3390/foods12010182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023] Open
Abstract
A hand-held near infrared (NIR) spectrophotometer combined with a similarity index (SI) method was evaluated to identify meat samples sourced from exotic and traditional meat species. Fresh meat cuts of lamb (Ovis aries), emu (Dromaius novaehollandiae), camel (Camelus dromedarius), and beef (Bos taurus) sourced from a commercial abattoir were used and analyzed using a hand-held NIR spectrophotometer. The NIR spectra of the commercial and exotic meat samples were analyzed using principal component analysis (PCA), linear discriminant analysis (LDA), and a similarity index (SI). The overall accuracy of the LDA models was 87.8%. Generally, the results of this study indicated that SI combined with NIR spectroscopy can distinguish meat samples sourced from different animal species. In future, we can expect that methods such as SI will improve the implementation of NIR spectroscopy in the meat and food industries as this method can be rapid, handy, affordable, and easy to understand for users and customers.
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9
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Hokkanen S, Frey AD, Yang B, Linderborg KM. Similarity Index for the Fat Fraction between Breast Milk and Infant Formulas. J Agric Food Chem 2022; 70:6191-6201. [PMID: 35543583 PMCID: PMC9136929 DOI: 10.1021/acs.jafc.1c08029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
The similarity of the fat fraction in infant formulas rich in either bovine milk fat (MF) or vegetable oil (VO) to breast milk was evaluated by analyzing their lipid composition. Milk fat-rich formulas were highly similar (average similarity index 0.68) to breast milk compared to the VO-rich formulas (average similarity index 0.56). The highest difference in the indices was found in the contents of cholesterol (0.66 vs 0.28 in MF- and VO-rich formulas, respectively, on average) and polar lipids (0.84 vs 0.53), the positional distribution of fatty acids in the sn-2 position of triacylglycerols (0.53 vs 0.28), and fatty acid composition (0.72 vs 0.54). The VO-based formulas were superior in similarity in n - 6 PUFA. Thus, the addition of bovine MF fractions is an effective way to increase the similarity between the lipid composition of infant formulas and human milk.
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Affiliation(s)
- Sanna Hokkanen
- Molecular
Biotechnology, Department of Bioproducts and Biosystems, School of
Chemical Engineering, Aalto University, 02150 Espoo, Finland
| | - Alexander D. Frey
- Molecular
Biotechnology, Department of Bioproducts and Biosystems, School of
Chemical Engineering, Aalto University, 02150 Espoo, Finland
| | - Baoru Yang
- Food
Chemistry and Food Development, Department of Life Technologies, University of Turku, 20500 Turku, Finland
| | - Kaisa M. Linderborg
- Food
Chemistry and Food Development, Department of Life Technologies, University of Turku, 20500 Turku, Finland
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Lv Y, Shen M, Meng B, Zhang H, Sun Y, Zhang J, Chang L, Li J, Yi S. The Similarity between Species Composition of Vegetation and Soil Seed Bank of Grasslands in Inner Mongolia, China: Implications for the Asymmetric Response to Precipitation. Plants (Basel) 2021; 10:1890. [PMID: 34579423 DOI: 10.3390/plants10091890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022]
Abstract
The asymmetric response of productivity to precipitation was recently proposed as an early warning signal for the shifts in temperate grassland function in China. It was hypothesized that the asymmetry was influenced by the increased growth of the newly emerged seedlings from the soil seed bank. Therefore, the seed density in the soil seed bank and the similarity between species composition of the vegetation and the soil seed bank should be maximized where asymmetry was maximized. However, this knowledge was still limited and unconfirmed. In this study, the desert steppe, typical steppe and the transition zone between them (with the highest asymmetry) were selected for studying the similarity index in both 2018 (dry year) and 2019 (wet year). Plant species composition was monitored in situ using an unmanned aerial vehicle. Soil seed bank samples were collected, and the seed bank density and species composition were then examined and identified in the laboratory. Results showed that: (1) The variation in vegetation species richness between the two years was the highest (41%) in the transition zone (p < 0.05), while it was only 7% and 13% for the desert steppe and typical steppe, respectively. The presence of herbaceous species mainly caused the differences in variation among three grassland types. (2) Seed density was the highest in the transition zone (114 seeds/m2 and 68 seeds/m2 in the transient and persistent soil seed bank, respectively) (p < 0.05). Additionally, herbaceous species were the main components of the soil seed bank. (3) The similarity index was the highest in the transition zone (p < 0.05), with 38%/44% and 33%/44% for the transient/persistent soil seed bank in 2018 and 2019, respectively. Our study demonstrated that variation in vegetation species composition was very similar to the composition of the seeds accumulated in the soil seed bank. These results warrant further investigation for the mechanism of asymmetric response of productivity to precipitation.
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Hsieh YC, Lin YJ, Lo MT, Chen YY, Lin CY, Lin C, Chung FP, Lo LW, Chang SL, Chao TF, Hu YF, Tuan TC, Liao JN, Wu CI, Liu CM, Vicera JJB, Chen CC, Chin CG, Lugtu IC, Chen SA. Optimal substrate modification strategies using catheter ablation in patients with persistent atrial fibrillation: 3-year follow-up outcomes. J Cardiovasc Electrophysiol 2021; 32:1561-1571. [PMID: 33825268 PMCID: PMC8252615 DOI: 10.1111/jce.15033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 03/11/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
Objectives This study aimed to assess the comparative efficacy of four ablation strategies on the incidence rates of freedom from atrial fibrillation (AF) or atrial tachycardia (AT) through a 3‐year follow‐up in patients with persistent AF. Background The optimal substrate modification strategies using catheter ablation for patients with persistent AF remain unclear. Methods Patients with persistent AF were enrolled consecutively to undergo each of four ablation strategies: (a) Group 1 (Gp 1, n = 69), pulmonary vein isolation (PVI) plus rotor ablation assisted by similarity index and phase mapping; (b) Gp 2 (n = 75), PVI plus linear ablations at the left atrium; (c) Gp 3 (n = 42), PVI plus the elimination of complex fractionated atrial electrograms; (d) Gp 4 (n = 67), PVI only. Potential confounders were adjusted via a multivariate survival parametric model. Results Baseline characteristics were similar across the four groups. At a follow‐up period of 34.9 ± 38.6 months, patients in Gp 1 showed the highest rate of freedom from AF compared with the other three groups (p = .002), while patients in Gp 3 and 4 showed lower rates of freedom from AT than those of the other two groups (p = .006). Independent predictors of recurrence of AF were the ablation strategy (p = .002) and left atrial diameter (LAD) (p = .01). Conclusion In patients with persistent AF, a substrate modification strategy using rotor ablation assisted by similarity index and phase mapping provided a benefit for maintaining sinus rhythm compared with the other strategies. Both ablation strategy and baseline LAD predicted the 3‐year outcomes of freedom from AT/AF
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Affiliation(s)
- Yu-Cheng Hsieh
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yenn-Jiang Lin
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Men-Tzung Lo
- Department of Biomedical Sciences and Engineering, National Central University, Chungli, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Chungli, Taiwan
| | - Yun-Yu Chen
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin-Yu Lin
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chen Lin
- Department of Biomedical Sciences and Engineering, National Central University, Chungli, Taiwan.,Center for Dynamical Biomarkers and Translational Medicine, National Central University, Chungli, Taiwan
| | - Fa-Po Chung
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Li-Wei Lo
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shih-Lin Chang
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tze-Fan Chao
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Feng Hu
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ta-Chuan Tuan
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jo-Nan Liao
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Cheng-I Wu
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Min Liu
- Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jennifer-Jeanne B Vicera
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Chao Chen
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chye-Gen Chin
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Isaiah C Lugtu
- Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shih-Ann Chen
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung, Taiwan.,Department of Internal Medicine, Faculty of Medicine, Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Division of Cardiology, Department of Medicine, Heart Rhythm Center, Taipei Veterans General Hospital, Taipei, Taiwan
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12
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Szabó D, Schlosser G, Vékey K, Drahos L, Révész Á. Collision energies on QTof and Orbitrap instruments: How to make proteomics measurements comparable? J Mass Spectrom 2021; 56:e4693. [PMID: 33277714 DOI: 10.1002/jms.4693] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
Quadrupole time-of-flight (QTof) collision-induced dissociation (CID) and Orbitrap higher-energy collisional dissociation (HCD) are the most commonly used fragmentation techniques in mass spectrometry-based proteomics workflows. The information content of the MS/MS spectra is first and foremost determined by the applied collision energy. How can we set up the two instrument types to achieve maximum transferability? To answer this question, we compared MS/MS spectra obtained on a Bruker QTof CID and a Thermo Q-Exactive Focus Orbitrap HCD instrument as a function of collision energy using the similarity index. Results show that with a few eV lower collision energy setting on HCD (Orbitrap-specific CID) than on QTof CID, nearly identical MS/MS spectra can be obtained for leucine enkephalin pentapeptide standard, for selected +2 and +3 enolase tryptic peptides and for a large number of peptides in a HeLa protein digest. The Bruker QTof was able to produce colder ions, which may be significant to study inherently labile compounds. Further, we examined energy dependence of peptide identification confidence, as characterized by Mascot scores, on the HeLa peptides. In line with earlier QTof results, this dependence shows one or two maxima (unimodal or bimodal behavior) on Orbitrap. The fraction of bimodal peptides is lower on Orbitrap. Optimal energies as a function of m/z show a similar linear trend on both instruments, which suggests that with appropriate collision energy adjustment, matching conditions for proteomics can be achieved. Data have been deposited in the MassIVE repository (MSV000086434).
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Affiliation(s)
- Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Faculty of Science, Institute of Chemistry, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, H-1117, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, H-1117, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest, H-1117, Hungary
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13
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Kuperman VY, Figueiredo G. Technical Note: New similarity index for radiotherapy and medical imaging. Med Phys 2020; 47:4325-4331. [PMID: 32406538 DOI: 10.1002/mp.14234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 11/06/2022] Open
Abstract
PURPOSE To describe a new similarity index and consider its biomedical applications. METHODS Similarity index for a pair of objects is defined by the number of shared features and total number of features in these objects. Similarity measure for more than two objects is commonly defined by using pairwise similarity indices. In the current study we suggest a novel similarity index which depends on the number of features shared between multiple objects and does not have the limitations of the recently described similarity measures. In order to introduce the new index, we consider a concept of "commonality." For a collection of sets A 1 , A 2 … , A N , commonality of a given element equals the number of sets this element belongs to. The similarity index for the compared sets is then defined by a weighted sum of normalized commonalities. RESULTS The considered biomedical applications of the proposed index include comparison of independent delineations of critical cranial structures in MR images and comparison of isodose distributions from different radiotherapy plans. CONCLUSIONS This study describes a novel similarity index which can be used to assess the similarity of multiple independent delineations of the anatomical structure or similarity of multiple dose distributions. Unlike the commonly used pairwise similarity indices, the new index is defined by the number of elements shared between multiple sets. Potential applications of the suggested similarity index for radiotherapy and medical imaging have been described.
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14
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Fellows AP, Casford MTL, Davies PB. Spectral Analysis and Deconvolution of the Amide I Band of Proteins Presenting with High-Frequency Noise and Baseline Shifts. Appl Spectrosc 2020; 74:597-615. [PMID: 31868519 DOI: 10.1177/0003702819898536] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The challenge of deriving quantitative information from the infrared spectra of proteins arises from the large number of secondary structures and amino acid side-chain functional groups that all contribute to the spectral intensity, such as within the amide I band (1600-1700 cm-1). The band is invariably heavily convoluted from overlapping spectral features, thereby making interpretation difficult such that deconvolution is usually required. This work critically examines the methods available to deconvolute the spectra and assesses the commonly used methods and algorithms applied to vibrational spectra for smoothing and peak identification. We show that unless their spectra have very high signal-to-noise ratios, quantitative analysis to decipher protein constituents is not feasible. The advantages and disadvantages of spectral smoothing using adjacent averaging, the Savitzky-Golay filter and the fast Fourier transform filter are examined in detail. The use of derivative spectra to identify peaks is described with particular reference to the influence and reduction of interfering water bands in the amide I region. The reliability of band narrowing techniques such as second-derivative analysis or Fourier deconvolution that lead to the identification of the contributing protein peaks is investigated. Both methods are shown to be limited in their capacity to resolve features with very similar frequencies. Additionally, the presence of narrow bands arising from high-frequency noise whether from atmospheric water vapor, acoustic vibrations, or electrical interference results in both methods becoming increasingly unusable as narrow bands are preferentially enhanced at the expense of broad ones such as the amide I bands. An optimal strategy is critically developed to allow accurate determination and quantification of protein constituents and their conformations. Additionally, quantitative methods are proposed to account for baseline shifts, which would otherwise introduce significant errors in similarity indices.
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Affiliation(s)
| | | | - Paul B Davies
- Department of Chemistry, University of Cambridge, Cambridge, UK
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15
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Fordham G, Shanee S, Peck M. Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments. Am J Primatol 2020; 82:e23136. [PMID: 32323350 DOI: 10.1002/ajp.23136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 11/05/2022]
Abstract
The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.
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Affiliation(s)
- Gail Fordham
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Sam Shanee
- Neotropical Primate Conservation, Torpoint, Cornwall, UK
| | - Mika Peck
- School of Life Sciences, University of Sussex, Brighton, UK.,Neotropical Primate Conservation, Torpoint, Cornwall, UK
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16
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Baskaran S, Agarwal A, Panner Selvam MK, Henkel R, Durairajanayagam D, Leisegang K, Majzoub A, Singh D, Khalafalla K. Is there plagiarism in the most influential publications in the field of andrology? Andrologia 2019; 51:e13405. [PMID: 31489696 DOI: 10.1111/and.13405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/22/2019] [Accepted: 08/03/2019] [Indexed: 11/28/2022] Open
Abstract
Plagiarism is a common form of academic misconduct that extensively jeopardises the quality of scientific publication. The purpose of this study is to determine the extent of plagiarism in the most influential andrology articles. A total of 77 highly cited andrology articles were analysed for their similarity index using iThenticate and Turnitin. The articles were categorised based on the year (before and on/after 2000) and type of publication (review and research articles), and the similarity indices were compared. Furthermore, the analysed articles were categorised based on the level of similarity using an arbitrary similarity index range (low: ≤10, moderate: 11-20, high: 21-50 and very high: >50) and average incidence rate (%) was determined. Our analysis revealed a higher percentage of the similarity indices for reviews than research articles. We noticed a higher similarity index for articles published on/after 2000 than those published before. The majority of the influential articles in the field of andrology showed a low similarity index, while some articles exhibited moderate to high levels of similarity. These findings support the need for the development of similarity index guidelines as a major pre-requisite for establishing a more transparent and efficient system to address plagiarism in scientific publications.
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Affiliation(s)
- Saradha Baskaran
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Ralf Henkel
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.,Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa
| | | | - Kristian Leisegang
- School of Natural Medicine, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Ahmad Majzoub
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.,Urology Department, Hamad Medical Corporation, Doha, Qatar.,Urology Department, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Dipty Singh
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.,Neuroendocrinology Department, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
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17
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Khandia R, Singhal S, Kumar U, Ansari A, Tiwari R, Dhama K, Das J, Munjal A, Singh RK. Analysis of Nipah Virus Codon Usage and Adaptation to Hosts. Front Microbiol 2019; 10:886. [PMID: 31156564 PMCID: PMC6530375 DOI: 10.3389/fmicb.2019.00886] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/05/2019] [Indexed: 12/19/2022] Open
Abstract
A recent outbreak of Nipah virus (NiV) in India has caused 17 deaths in people living in districts of Kerala state. Its zoonotic nature, as well as high rate of human-to-human transmission, has led researchers worldwide to work toward understanding the different aspects of the NiV. We performed a codon usage analysis, based on publicly available nucleotide sequences of NiV and its host adaptation, along with other members of the Henipavirus genus in ten hosts. NiV genome encodes nine open reading frames; and overall, no significant bias in codon usage was observed. Aromaticity of proteins had no impact on codon usage. An analysis of preferred codons used by NiV and the tRNA pool in human cells indicated that NiV prefers codons from a suboptimal anticodon tRNA pool. We observed that codon usage by NiV is mainly constrained by compositional and selection pressures, not by mutational forces. Parameters that define NiV and host relatedness in terms of codon usage were analyzed, with a codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index calculations; which indicated that, of all hosts analyzed, NiV was best adapted to African green monkeys. A comparative analysis based on the relative codon deoptimization index (RCDI) for host adaptation of NiV, Hendra virus (HeV), Cedar virus (CedV), and Hendra like Mojiang virus (MojV) revealed that except for dogs and ferrets, all evaluated hosts were more susceptible to HeV than NiV.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Shailja Singhal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Utsang Kumar
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Afzal Ansari
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Uttar Pradesh Pandit Deen Dayal Upadhyaya Pashu Chikitsa Vigyan Vishwavidyalaya Evam Go Anusandhan Sansthan (DUVASU), Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Jayashankar Das
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ashok Munjal
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
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Abstract
The institutional integrity constitutes the bases of scientific activity. The frequent incidences of similarity, plagiarism, and retraction cases created the space for frequent use of similarity and plagiarism detecting tools. Turnitin is software that identifies the matched material by checking the electronically submitted documents against its database of academic publications, internet, and previously submitted documents. Turnitin provides a “similarity index,” which does not mean plagiarism. The prevalence of plagiarism could not reduce tremendously in the presence of many paid and un-paid plagiarism detecting tools because of the assortment of reasons such as poor research and citation skills, language problems, underdeveloped academic skills, etc., This paper may provide an adequate feedback to the students, researchers, and faculty members in understanding the difference between similarity index and plagiarism.
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Affiliation(s)
- Sultan A Meo
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Talha
- Deanship of Scientific Research, King Saud University, Riyadh, Saudi Arabia
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Abstract
Background: The overall similarity index (OSI) and highest similarity scores (HSSs) from a single source might help to predict the potential reasons for the retraction from the anesthesia journals. Methods: Retracted publications, from five highest impact anesthesia journals, were retrieved from the MEDLINE and journal archives and analyzed using a plagiarism detection software (iThenticate) and manually verified for citation characteristics, OSI, HSS, and the presence, extent, and location of the duplicate text. The validity of the OSI including and excluding quotations and references and the HSS in predicting the potential reasons for retraction were tested using the receiver operating characteristic curves. Results: Of the total 138 retracted original and corresponding articles identified, 131 articles were analyzed. Most of them had the HSS more than 40% arising from a single source. Extensive degree of plagiarism (OSI score >35%) was identified through the main text of all analyzed retracted articles. The areas under the curves indicate that the OSI including and excluding quotations and bibliography and the HSS had reasonable ability to predict plagiarism and fabrication with a perfect sensitivity rate and low specificity but were weaker at distinguishing ethical misconduct or inconsistent or erroneous contents. Conclusions: The study highlights the presence of significant plagiarism in the retracted anesthesia publications irrespective to the reasons for retraction. The high OSI and the HSS could be useful tools to identify the potential manuscripts with high risks for plagiarism and fabrication.
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Affiliation(s)
- Mohamed R El-Tahan
- Anaesthesiology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Al Khubar, Saudi Arabia
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20
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Figueroa-Castro DM, González-Tochihuitl G, Rivas-Arancibia SP, Castaño-Meneses G. Floral Visitors of Three Asteraceae Species in a Xeric Environment in Central Mexico. Environ Entomol 2016; 45:1404-1414. [PMID: 28028087 DOI: 10.1093/ee/nvw132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
We describe the spatial variation in the structure and composition of the communities of insects visiting the inflorescences of Flaveria ramosissima Klatt, Florestina pedata (Cav.) Cass., and Parthenium bipinnatifidum (Ort.) Rollins (Asteraceae) in a xeric environment in Central Mexico. Inflorescences of the three Asteraceae were visited by a total of 96 species of Hymenoptera, Diptera, Lepidoptera, Coleoptera, and Hemiptera. Total species richness of floral visitors to the three Asteraceae and total abundance of insects of Fl. pedata and P. bipinnatifidum did not differ between low and high vegetation cover sites. Total abundance of insects visiting the inflorescences of F. ramosissima and abundance of Hymenoptera in all three Asteraceae were higher at the low vegetation coverage (LVC) site than at the high vegetation coverage (HVC) one. Diversity of insects of Fl. pedata and P. bipinnatifidum was higher at the HVC site. However, in F. ramosissima diversity was higher at the LVC site. The communities of insects of each Asteraceae were dissimilar between sites. These differences can be attributed to variation in the abundance of Lepidophora (Diptera: Bombyliidae), Miridae (Hemiptera), Melyridae (Coleoptera), Tiphiidae (Hymenoptera), Myrmecocystus mexicanus Wesmael, and Dorymyrmex grandulus (Forel) (Hymenoptera: Formicidae). The first three insect groups were sensitive to LVC, high temperature, and low humidity, whereas the last three tolerated those same environmental conditions. Changes in temperature, humidity, and resources associated with vegetation coverage seem to differentially affect each species of floral visitors of the three Asteraceae species studied.
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Affiliation(s)
- Dulce María Figueroa-Castro
- Escuela de Biología, Benemérita Universidad Autónoma de Puebla. Boulevard Valsequillo y Av. San Claudio s/n, Edif. 112 A, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, Puebla, México (; ;)
| | - Guadalupe González-Tochihuitl
- Escuela de Biología, Benemérita Universidad Autónoma de Puebla. Boulevard Valsequillo y Av. San Claudio s/n, Edif. 112 A, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, Puebla, México (; ;)
| | - Sombra Patricia Rivas-Arancibia
- Escuela de Biología, Benemérita Universidad Autónoma de Puebla. Boulevard Valsequillo y Av. San Claudio s/n, Edif. 112 A, Ciudad Universitaria, Col. Jardines de San Manuel, C.P. 72570, Puebla, Puebla, México (; ;)
| | - Gabriela Castaño-Meneses
- Ecología de Artrópodos en Ambientes Extremos, Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Campus Juriquilla, Universidad Nacional Autónoma de México. Juriquilla, Querétaro, 76230, México
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21
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Polavarapu PL, Covington CL. Comparison of experimental and calculated chiroptical spectra for chiral molecular structure determination. Chirality 2014; 26:539-52. [PMID: 24644231 DOI: 10.1002/chir.22316] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/26/2014] [Accepted: 02/07/2014] [Indexed: 01/30/2023]
Abstract
For three different chiroptical spectroscopic methods, namely, vibrational circular dichroism (VCD), electronic circular dichroism (ECD), and Raman optical activity (ROA), the measures of similarity of the experimental spectra to the corresponding spectra predicted using quantum chemical theories are summarized. In determining the absolute configuration and/or predominant conformations of chiral molecules, these similarity measures provide numerical estimates of agreement between experimental observations and theoretical predictions. Selected applications illustrating the similarity measures for absorption, circular dichroism, and corresponding dissymmetry factor (DF) spectra, in the case of VCD and ECD, and for Raman, ROA, and circular intensity differential (CID) spectra in the case of ROA, are presented. The analysis of similarity in DF or CID spectra is considered to be much more discerning and accurate than that in absorption (or Raman) and circular dichroism (or ROA) spectra, undertaken individually.
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Bhattacharya J, Petsche H, Pereda E. Long-range synchrony in the gamma band: role in music perception. J Neurosci 2001; 21:6329-37. [PMID: 11487656 PMCID: PMC6763152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023] Open
Abstract
Synchronization seems to be a central mechanism for neuronal information processing within and between multiple brain areas. Furthermore, synchronization in the gamma band has been shown to play an important role in higher cognitive functions, especially by binding the necessary spatial and temporal information in different cortical areas to build a coherent perception. Specific task-induced (evoked) gamma oscillations have often been taken as an indication of synchrony, but the presence of long-range synchrony cannot be inferred from spectral power in the gamma range. We studied the usefulness of a relatively new measure, called similarity index to detect asymmetric interdependency between two brain regions. Spontaneous EEG from two groups-musicians and non-musicians-were recorded during several states: listening to music, listening to text, and at rest (eyes closed and eyes open). While listening to music, degrees of the gamma band synchrony over distributed cortical areas were found to be significantly higher in musicians than non-musicians. Yet no differences between these two groups were found at resting conditions and while listening to a neutral text. In contrast to the degree of long-range synchrony, spectral power in the gamma band was higher in non-musicians. The degree of spatial synchrony, a measure of signal complexity based on eigen-decomposition method, was also significantly increased in musicians while listening to music. As compared with non-musicians, the finding of increased long-range synchrony in musicians independent of spectral power is interpreted as a manifestation of a more advanced musical memory of musicians in binding together several features of the intrinsic complexity of music in a dynamical way.
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Affiliation(s)
- J Bhattacharya
- Commission for Scientific Visualization Austrian Academy of Sciences, A-1010 Vienna, Austria.
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Chen S, Dickson DW, Kimbrough JW, McSorley R, Mitchell DJ. Fungi Associated with Females and Cysts of Heterodera glycines in a Florida Soybean Field. J Nematol 1994; 26:296-303. [PMID: 19279895 PMCID: PMC2619503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Fungal colonization was determined for females and cysts of Heterodera glycines on soybean roots or in rhizosphere soil from a Florida soybean field. A total of 1,620 females and cysts were examined in 1991, and 1,303 were examined in 1992. More than 35 species of fungi were isolated from females and cysts. The frequency of fungi colonizing white and yellow females was low, but a high frequency of fungi was encountered in brown cysts, which increased with time of exposure of the cysts to the soil. No single fungal species predominated in the nematode females or cysts in this field. Rarely was a female or cyst colonized by more than one fungus. The common fungi isolated from the females and cysts were Neocosmospora vasinfecta, Fusarium solani, Fusarium oxysporum, Dictyochaeta coffeae, Dictyochaeta heteroderae, Pyrenochaeta terrestris, Exophiala pisciphila, Gliocladium catenulatum, Stagonospora heteroderae, and a black yeast-like fungus. The communities of common fungal species isolated from cysts in several regions in the southeastern United States appear to be similar.
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