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81.
Jelena uklina Chloe H Lee Evan G Williams Tatjana Sajic Ben C Collins María Rodríguez Martínez Varun S Sharma Fabian Wendt Sandra Goetze Gregory R Keele Bernd Wollscheid Ruedi Aebersold Patrick G A Pedrioli 《Molecular systems biology》2021,17(8)
Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step‐by‐step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology. 相似文献
82.
The effect of the glass industry on soil metal characterization was assessed at five test sites at five successive distances in a semi-arid area. A comprehensive profile of Zn, Cd, Pb, Ni, Cu, and As levels in soils was obtained. The spatial distribution patterns of integrated contamination indices for these metals show a similar decreasing trend in distribution as we move further from the industrial cluster. There was significant correlation among individual heavy metal concentrations in the soil samples. Integrated contamination indices indicate that 64% of the sites were in the high contamination range and 28% were in the moderate contamination range. A statistically significant difference (P ≤ 0.001) was obtained for each metal on comparing mean metal content among soil samples. Phytoremedial potential of 12 native plant species was also evaluated. Individual elements displayed remarkably different patterns of accumulation in soils as well as plants. Plants established limited capabilities in mobilizing Zn, Pb, Ni, and Cu in the root zone. While Cd, Cu, As, Zn and Pb were predominantly partitioned in shoots, Ni was equally partitioned between shoots and roots. Interestingly, some plants showed a different partitioning trend at higher concentrations of different metals compared to lower concentrations. Potential species for phytoremediation include Calotropis procera (Milk weed), Chenopodium murale (Goosefoot),Poa annua (Annual bluegrass) and Datura stramonium (Thorn apple). None of the species showed phytoremedial potential for Ni and Cu. 相似文献
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85.
Pallara Janardhanan Wills Mohan Anjana Mohan Nitin Raghuveeran Varun Parayil Sachidanandan Tharaniyil Mani Jacob Madhavan Lilly Raghava Varman Thampan Koyikkal Karthikeya Varma 《PloS one》2016,11(4)
Lepidopterism is a disease caused by the urticating scales and toxic fluids of adult moths, butterflies or its caterpillars. The resulting cutaneous eruptions and systemic problems progress to clinical complications sometimes leading to death. High incidence of fever epidemics were associated with massive outbreaks of tiger moth Asota caricae adult populations during monsoon in Kerala, India. A significant number of monsoon related fever characteristic to lepidopterism was erroneously treated as infectious fevers due to lookalike symptoms. To diagnose tiger moth lepidopterism, we conducted immunoblots for tiger moth specific IgE in fever patients’ sera. We selected a cohort of patients (n = 155) with hallmark symptoms of infectious fevers but were tested negative to infectious fevers. In these cases, the total IgE was elevated and was detected positive (78.6%) for tiger moth specific IgE allergens. Chemical characterization of caterpillar and adult moth fluids was performed by HPLC and GC-MS analysis and structural identification of moth scales was performed by SEM analysis. The body fluids and chitinous scales were found to be highly toxic and inflammatory in nature. To replicate the disease in experimental model, wistar rats were exposed to live tiger moths in a dose dependant manner and observed similar clinico-pathological complications reported during the fever epidemics. Further, to link larval abundance and fever epidemics we conducted cointegration test for the period 2009 to 2012 and physical presence of the tiger moths were found to be cointegrated with fever epidemics. In conclusion, our experiments demonstrate that inhalation of aerosols containing tiger moth fluids, scales and hairs cause systemic reactions that can be fatal to human. All these evidences points to the possible involvement of tiger moth disease as a major cause to the massive and fatal fever epidemics observed in Kerala. 相似文献
86.
Fangming Xiu Varun C. Anipindi Philip V. Nguyen Jeanette Boudreau Hong Liang Yonghong Wan Denis P. Snider Charu Kaushic 《PloS one》2016,11(4)
Female sex steroids, estradiol (E2) and progesterone (P4), play a key role in regulating immune responses in women, including dendritic cell (DC) development, and functions. Although the two hormones co-occur in the body of women throughout the reproductive years, no studies have explored their complex combinatorial effects on DCs, given their ability to regulate each other’s actions. We examined murine bone marrow derived dendritic cells (BMDC) differentiation and functions, in the presence of a wide range of physiological concentrations of each hormone, as well as the combination of the two hormones. E2 (10−12 to 10-8M) enhanced the differentiation of CD11b+CD11c+ DCs from BM precursor cells, and promoted the expression of CD40 and MHC Class-II, in a dose-dependent manner. In contrast, P4 (10−9 to 10-5M) inhibited DC differentiation, but only at the highest concentrations. These effects on BMDCs were observed both in the presence or absence of LPS. When both hormones were combined, higher concentrations of P4, at levels seen in pregnancy (10-6M) reversed the E2 effects, regardless of the concentration of E2, especially in the absence of LPS. Functionally, antigen uptake was decreased and pro-inflammatory cytokines, IL-12, IL-1 and IL-6 production by CD11b+CD11c+ DCs, was increased in the presence of E2 and these effects were reversed by high concentrations of P4. Our results demonstrate the distinct effects of E2 and P4 on differentiation and functions of bone marrow myeloid DCs. The dominating effect of higher physiological concentrations of P4 provides insight into how DC functions could be modulated during pregnancy. 相似文献
87.
Bone strains resulting from physical activity are thought to be a primary driver of bone adaptation, but cannot be directly noninvasively measured. Because bone adapts nonuniformly, physical activity may make an important independent structural contribution to bone strength that is independent of bone mass and density. Our objective was to create and validate methods for subject-specific finite element (FE) model generation that would accurately predict the surface strains experienced by the distal radius during an in vivo loading task, and to apply these methods to a group of 23 women aged 23–35 to examine variations in strain, bone mass and density, and physical activity. Four cadaveric specimens were experimentally tested and specimen-specific FE models were developed to accurately predict periosteal surface strains (root mean square error=16.3%). In the living subjects, when 300 N load was simulated, mean strains were significantly inversely correlated with BMC (r=−0.893), BMD (r=−0.892) and physical activity level (r=−0.470). Although the group of subjects was relatively homogenous, BMD varied by two-fold (range: 0.19–0.40 g/cm3) and mean energy-equivalent strain varied by almost six-fold (range: 226.79–1328.41 με) with a simulated 300 N load. In summary, we have validated methods for estimating surface strains in the distal radius that occur while leaning onto the palm of the hand. In our subjects, strain varied widely across individuals, and was inversely related to bone parameters that can be measured using clinical CT, and inversely related to physical activity history. 相似文献
88.
Guntupalli V.R. Prasad Omkar Verma Emmanuel Gheerbrant Anjali Goswami Ashu Khosla Varun Parmar Ashok Sahni 《Comptes Rendus Palevol》2010,9(1-2):63-71
The Late Cretaceous record of mammals from India assumes great significance in view of the fact that it is the only Gondwanan landmass that has yielded definitive eutherian mammals. These mammals have variously been assigned to palaeoryctids, archontans or Eutheria incertae sedis. Well preserved lower molars recovered from a new mammal-yielding Deccan intertrappean site near Kisalpuri village, Dindori District, Madhya Pradesh (state), India, are described here under a new species Deccanolestes narmadensis sp. nov. The new fossil material indicates close phylogenetic relationship between Deccanolestes from India and Afrodon (Adapisoriculidae) from the Late Palaeocene of Africa and Europe. In view of older age and more primitive state of Deccanolestes teeth, it is inferred that Deccanolestes represents an ancestral morphotype from which the African/European adapisoriculid Afrodon may have been derived. This is the first compelling terrestrial fossil evidence for an early dispersal between India and Africa. Such a dispersal possibly involved an East African contact with India at the KT transition. 相似文献
89.
Varun Ullal 《Molecular simulation》2014,40(12):976-986
Molecular dynamics simulations are used to compute diffusion coefficients for O2 molecules in polydimethylsiloxane (PDMS) and end-linked PDMS networks. The PDMS chains and penetrants are modelled using a hybrid interatomic potential which treats the Si and O atoms along the chain backbone explicitly while coarse-graining the methyl side groups and penetrants. In PDMS models with different molecular weights, diffusivity of the O2 penetrants is found to modestly decrease with an increase in chain length. To match typical experimental conditions, the end-linked PDMS networks are constructed with a PDMS to crosslinking (CL) molecule mass ratio of 5:1 or 10:1, demanding that the number of CL molecules exceeds the number of PDMS chains in each model. Despite end-linking, the presence of non-bonded CL molecules promotes increased O2 diffusivity in comparison with uncrosslinked PDMS. Temperature dependence is captured using the Williams–Landel–Ferry equation. 相似文献
90.
The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that mainly affect children and are grouped together by similar clinical features and the accumulation of autofluorescent storage material. More than a dozen genes containing nearly 400 mutations underlying human NCLs have been identified. Most of the mutations in these genes are associated with a typical disease phenotype, but some result in variable disease onset, severity and progression. There are still disease subgroups with unknown molecular genetic backgrounds. This article is part of a Special Issue entitled: The Neuronal Ceroid Lipofuscinoses or Batten Disease. 相似文献