text stringlengths 4 179k | predicted_class stringclasses 5
values | confidence float64 0 100 |
|---|---|---|
text | predicted_class | 0 |
text | predicted_class | 0 |
text | predicted_class | 0 |
The original disease list of neurodegenerative disease from MeSH database contains 55 subdivisions. Several diseases are counted more than once since they are in different classifications, such as, ‘Gerstmann-Straussler-Scheinker Disease’ existed in both ‘Heredodegenerative Disorders, Nervous System’ and ‘Prion Disease... | study | 28.73 |
Totally, 5680 amino acid variations were collected and 2839 of them are substitutions without duplicates. Among these variations, the arginine (R) residue is the most common one (both in mutated residues and mutants), which is in agreement with the previous study (12). Top row of Figure 1 shows the amino acid distribut... | other | 35.44 |
Neurodegenerative diseases (NDDs), caused by the progressive dysfunction of neurons, are very common worldwide, affecting people of all ages but especially the aged ones. Since the first patient was diagnosed with Alzheimer’s disease a century ago (2), millions have been found suffering from the neurodegenerative disor... | other | 30.86 |
An integrated literature-based variation database for a series of related diseases can serve as a research platform for further discovering of relationships between diseases and genetic variations. The variation data of NDDs can be compared with that of other diseases, e.g. immunodeficiencies (5), to find their similar... | study | 28.88 |
Most of diseases are associated with genetic variations including point substitutions, copy number alterations, insertions and deletions. The genetic variations in DNA sequences may lead to abnormal messenger RNA splicing or coding and produce pathogenic proteins. It is well-known that the relationship between genes an... | other | 35.8 |
In LOVD3.0 view, the information is shown in eight different tags: genes, transcripts, variants, individuals, diseases, screenings, submit and documentation. It is a LOVD standard structure, which provides series useful information through a user-friendly interface by clicking each hyperlink. Users can also register as... | other | 29.05 |
The disease list of NDDs was obtained from the category of ‘neurodegenerative disease’ in MeSH database (http://www.ncbi.nlm.nih.gov/mesh). Each disease associated gene and variation was collected by the following method, i.e. the disease name or aliases plus ‘variation’ or ‘mutation’ was used as the keyword for queryi... | other | 35.3 |
LOVD (Leiden Open Variation Database) platform, supplied by Leiden University Medical Center, provides a flexible, freely available tool for gene-centered collection and display of DNA variations. The current version LOVD 3.0 extends this idea to provide storage for patient-centered data, NGS data and even variants out... | other | 28.2 |
To study the biological functions of the variations, especially the amino acid substitutions, a number of models and tools were developed to characterize their effects to protein’s sequence conservation, structural stability, aggregation, disorder, etc.(14–17). We developed a SVM classifier for predicting the effects o... | other | 35.12 |
We still chose the previous three diseases, MC, DMD and FTLD for the analysing. For MC there are 83 amino acid substitutions collected from 2 genes, SCN4 and CLCN1, corresponding to protein sodium channel protein type 4 subunit alpha and chloride channel protein 1, respectively. The results are shown in Supplementary T... | other | 31.81 |
Amino Acid distribution and variation profiles. Top row, amino acid distribution (left), overall mutability of mutated (middle) and mutant residues (right) for all the NDDs related proteins. The same information for Myotonia Congenita (MC), Dystonia Musculorum Deformans (DMD) and Hereditary Sensory and Frontotemporal L... | other | 31.12 |
Variation distribution according to physiochemical properties. Left top: mutability distribution for all NDDs in 36 variation situations: number 1–6 denotes to 6 groups of amino acids according to their physiochemical properties: (1) hydrophobic (V, I, L, F, M, W, Y, C), (2) negatively charged (D, E), (3) positively ch... | other | 31.16 |
We chose three diseases abundant with variations, i.e. Myotonia Congenita (MC), Dystonia Musculorum Deformans (DMD) as well as Frontotemporal Lobar Degeneration (FTLD) to study their mutation profiles (lower three rows in Figure 1). Arginine (R) is the most common variant residues for all the NDD diseases, the same as ... | other | 35.75 |
To investigate the functional effects of these variations, we grouped the 20 amino acids into six groups based on their physicochemical properties as, hydrophobic (V, I, L, F, M, W, Y, C), negatively charged (D and E), positively charged (R, K, H), conformational (G and P), polar (N, Q, S) and (A and T) (14). Therefore... | other | 35.53 |
In total 101 variations from 10 different proteins are found for DMD, the analysis result is shown in Supplementary Table S4. Most residues are high conserved predicted by SIFT. Three proteins, solute carrier family 2 and facilitated glucose transporter member 1 (gene: SLC2A1), interferon-inducible double-stranded RNA-... | other | 29.78 |
In total 142 variations from 20 different proteins related to FTLD are analysed (Supplementary Table S5). Some variations are in low conservation position predicted by SIFT and most of these variations are considered not pathogenic by PON-P2 (unknown or neutral). Variations from 15 proteins can be analysed by PPSC sinc... | study | 29.52 |
Variations found in more than one disease were also collected and analysed. There are 67 such variations found in 25 proteins (Supplementary Table S6). Majority of variations are happened at the conserved sites, only a few exceptions, e.g. p.Ile723Val, p.Val380Leu and p.Ala53Thr are predicted very low conserved (Supple... | other | 31.5 |
The primary objective of this work is to design a disease-centric resource for further data analysis and clinical research. We will make the database open to data submission and expert checking, and try to develop data mining tools to collect and update data from existing database automatically. In addition, more tools... | other | 33.16 |
With the paradigm shifting toward personalized medicine and precision medicine, the personal phenotyping data will be collected for the precision mapping to the genotyping information (21, 22). The NDDVD database will be updated with more personalized and paired genotyping-phenotyping data for systems or network level ... | other | 31.61 |
This work is supported by the National Key Research and Development Program of China (No. 2016YFC1306605), the National Nature Science Foundation of China (Grant No. 31670851, 31470821, 91530320, 61602332, 31600671) and the University Science Research Project of Jiangsu Province (No.14KJB520035). | clinical case | 26.78 |
Respiratory syncytial virus (RSV) is a leading viral cause of acute respiratory illnesses (ARI) worldwide (Haynes et al. 2013), with the virus infecting 5–10% of the world population annually (Falsey et al. 2005) resulting in an estimated 3 million hospitalizations of children aged under 5 years (Nair et al. 2010) and ... | study | 28.39 |
RSV belongs to family Paramyxoviridae and its genome is a non-segmented single-stranded negative-sense RNA molecule (∼15,200 nucleotides long) that encodes eleven viral proteins (in the order NS1-NS2-N-P-M-SH-G-F-M2 (1 and 2)-L). Two genetically and antigenically distinct RSV groups are recognized (A and B) whose local... | other | 32.44 |
Improved understanding of RSV epidemiological patterns, transmission chains, and mechanism of persistence in host populations can help with infection control (Munywoki et al. 2014; Agoti et al. 2015a). Information on the origins of RSV seed strains for local epidemics, hubs of virus transmission, and spread patterns du... | other | 32.97 |
RSV surveillance in Kilifi County, located in coastal Kenya, has been ongoing since 2002 with a continuous hospital-based arm and intermittent community-based arm (Nokes et al. 2004, 2008, 2009; Munywoki et al. 2014; Agoti et al. 2015a]. Recently, we reported the RSV infection epidemiological findings from a cohort of ... | other | 30.56 |
The intensive sampling regime during the household study provides an opportunity to uncover RSV transmission and evolution patterns in community epidemics. We recently showed that analysis of the relatedness of G gene sequences identified within and between epidemics can distinguish virus strains newly introduced into ... | other | 34.8 |
The analysis reported here investigated RSV A transmission in a community setting, the source of seed viruses and genomic diversification in a subset of samples collected during the household cohort study (Munywoki et al. 2014). We assessed the strength of the phylogenetic signal provided by analyzing the individual RS... | other | 34.03 |
The samples analyzed in this study were collected following an informed written consent from each individual participant if aged ≥18 years or through a guardian or parent if aged <18 years and all children assented to participate. The study protocol was reviewed and approved by both the Scientific and Ethics Review Uni... | other | 39.28 |
RNAs were extracted from raw nasal specimens using the QIAamp viral RNA extraction Kit following the manufacturer’s instructions (QIAGEN Ltd, London, UK). Complementary DNA (cDNA), PCR amplification and nucleotide sequencing of RSV genomes were performed as previously described (Agoti et al. 2015b). Briefly, the RSV ge... | other | 35.5 |
Raw sequence data from MiSeq were de-multiplexed into sample specific readsets and processed in QUASR (Watson et al. 2013) to remove low quality reads (median Phred score of <35) and primer and adapter sequences at the end of the individual reads. The resulting reads were de novo assembled using the SPades Program v3.5... | other | 33.88 |
Nucleotides at polymorphic positions on the genomes were checked as follows: A sequence alignment for each household was generated (all sequenced viruses) and any nucleotides showing variation from the group were directly examined. For each observed variant site, a 21-nucleotide (nt) motif spanning the variant nucleoti... | other | 37.34 |
The household study was undertaken within Kilifi County of Coastal Kenya in two local administrative units located to the north of the Kilifi Health and Demographic Surveillance System (KHDSS) (Scott et al. 2012). A household (HH) was defined as group of people living in the same compound and eating from the same kitch... | other | 31.89 |
A detailed description of the household study design was provided in previous publications (Munywoki et al. 2014, 2015a, 2015b). Briefly, 47 households were recruited and closely followed up over a 6-month period between December 2009 and June 2010 to document all respiratory virus infection episodes. Twice weekly thro... | other | 28.72 |
A total of 131 virus genomes for which the assembly yielded contigs >5000 nucleotides long were included in the analyses (i.e. gene-by-gene and whole genome analysis). These genomes were derived from 9 households. Of the 131 genomes, 103 were > 14000 nt in length with fewer than 500 ambiguous nucleotides (henceforth re... | other | 35.5 |
Three data sets were prepared for comparison with the household study viruses. First, 11 G gene reference sequences, one for each of the known RSV A genotypes (GA1-7, SAA1-3 and ON1) were prepared and used for genotyping the household viruses on the basis of phylogenetic clustering. Second, 275 RSV A G sequences collat... | other | 36.22 |
Phylogenies were generated from the nucleotide alignment of both whole genomes and from the excised individual genes. The trees were reconstructed using Maximum Likelihood (ML) method in either MEGA v5.22 (Tamura et al. 2011) or PhyML v3.1 program (Guindon et al. 2010). The best-fitted models of nucleotide substitution... | other | 40.66 |
The household viruses were genotyped by phylogenetic clustering pattern of their G ORF region with reference G sequences. Representative sequences of all known RSV A genotypes (GA1-7 & ON1) were included. A genome was assigned to a particular genotype if its G sequence clustered with the genotype reference sequence wit... | other | 39.66 |
The baseline characteristics of the households yielding RSV A positive samples and details on the number of genomes obtained per household are given in Table 1. Nucleotide changes were observed across the entire RSV genome (Fig. 2) in the 8 households with more than one genome sequenced. Within individual households, t... | other | 29.1 |
Nucleotide differences between viruses (total = 130) detected within the individual households. Each panel is a single household. The viruses were compared to the earliest virus genome sequenced from the same household. Vertical colored bars show the nucleotide differences. Red is a change to T, orange is a change to A... | other | 32.84 |
The temporal signal in nucleotide divergence of the household viruses was estimated in TempEst v1.4 (Rambaut et al. 2016) using a ML whole genome tree as input. The evolutionary pattern and time to the Most Recent Common Ancestor (tMRCA) of the obtained whole genome sequences were determined in BEAST v1.8.2 under HKY85... | other | 37.56 |
The sequence nomenclature on the phylogenetic trees is country of origin (_sample source for Kilifi indicating if sampled from inpatient (IP) or household (HH))/Unique identifier/Date of specimen collection. The unique identifier for household samples includes the household identifier (first two digits) and subject ide... | other | 30.94 |
A ML inferred phylogenetic tree showing the global phylogenetic context of the RSV A household study genomes. The taxa of the household study viruses (n= 103) are in red while viruses from the rest of Kenya (inpatient) are colored blue. The taxa of RSV A viruses from around the globe are colored by continent of origin.... | other | 30 |
A time-resolved phylogenetic clustering of the 103 household study genomes (Fig. 4, panel A) revealed that all viruses clustered by household of origin, except for those from households 26, 38 and 57. This pattern was also observed with a ML phylogeny (Supplementary Fig. S2) and MJT network that showed household-specif... | other | 33.7 |
The sequence relatedness of the household study RSV A viruses. (a) A time-scaled phylogenetic tree of the 103 genome sequenced household study viruses inferred in BEAST program. The genomes are represented by a filled circle colored differently for each household (color scheme similar to Fig. 1). (b) A median-joining (... | other | 34.4 |
In contrast to the genome-based phylogeny, when considering individual gene ORFs, the resolution was reduced and fewer household-specific distinct clusters were identified compared to the full genome analysis. ML phylogenetic clustering of the sequenced viruses by ORF is shown in Supplementary Fig. S3 (whole genome phy... | other | 30.55 |
The spatial distribution of the nine households is shown in Fig. 1. The geographical distance between the study households ranged from 302 to 3925 meters. There were a variable number of nucleotide differences across the genomes distinguishing clusters of viruses found in one household from the next (range 2-16), Fig. ... | other | 33.88 |
Inferred virus transmission patterns within household 14. (a) Temporal infection patterns. Every rectangular box represent a sample collected from members of the household 14, if there is a circle inside implies the sample was RSV A positive. Unfilled circle implies specimen was not sequenced while filled colored circl... | other | 33.2 |
We reconstructed a plausible virus transmission chain between the household members by combining the genetic data with sampling dates. As examples we show analysis for HH 14, a six-member household (Fig. 5) and household 38, a 23-member household (Supplementary Fig. S4). In household 14, of the 18 RSV positive samples ... | other | 30.72 |
Individual 1402 was virus positive for the longest period (39 days) compared to other members in this household, Fig. 5, Panel A. Interestingly, the positive sample collected on the 15th April came after several samples collected between 20th March and 13th April had tested RSV negative. The virus from 1402 on 15th Apr... | other | 34.34 |
TempEst analysis estimated that the MRCA for the household viruses occurred in December 2009 and their evolutionary rate was 4.948 ×10 − 3 sub/site/year. Notably, the R squared value for the linear model was 0.29 indicating the stochastic nature of variation observable in this limited time period. Different households ... | clinical case | 25.66 |
Our knowledge of RSV transmission in the community, evolutionary patterns and ‘who acquires infection from whom’ (WAIFW) is incomplete (Agoti et al. 2015a; Munywoki et al. 2014). Close contacts within households, workplaces, worship places, market places and other social gathering avenues may provide opportunities for ... | other | 32.06 |
Our findings support the hypothesis that RSV transmission within households is common as members belonging to the same household were infected with closely related strains, in terms of genomic sequence than viruses found in members from different households. Specifically, household-specific genomic variation was observ... | other | 34.28 |
The genomes of all the household study viruses fell within a single branch on the global phylogeny and G gene analysis suggested that all the nine households were infected by a single virus variant that had entered into this community. Due to limited contemporary sequences from other parts of Kenya or Africa, it was no... | other | 32.34 |
Within two individual households (HH 38 and 57), we observed higher genomic variation. We hypothesize three possible sources for this variation: (1) multiple virus introductions into these households, (2) co-infection of the index case with multiple genetic variants, and (3) diversification of a single virus in the pro... | other | 30.81 |
The variation of genomes within households aided in identifying members who are likely to have shared an infection source or sequentially transmitted the infection from one to the other (e.g. the chains inferred for household fourteen and thirty-eight). However, it was not possible to elaborate in complete detail the t... | other | 33.8 |
The evolutionary rates calculated at genome level from the household outbreak were significantly higher than rates derived from long-term data (Tan et al. 2012, 2013; Agoti et al. 2015b;). Our findings support the notion that evolutionary rates for viruses are highly context-specific and decrease when calculated from l... | other | 32.28 |
Among respiratory viruses, viral genetic data have been previously utilized for influenza A viruses to define within and between household virus spread. Sequencing of hemagglutinin and neuramidase genes of 2009 pandemic H1N1 viruses found occurrence of only limited genetic diversity for viruses derived from different h... | other | 34.8 |
For RSV, our study is the first of its kind using full genomic data to define patterns of its transmission in a community setting. Using temporal infection data alone, it has been previously concluded that young children are most likely to introduce RSV infection into households (Hall et al. 1976; Munywoki et al. 2014;... | other | 30.55 |
We are aware of limitations in this study. First, sampling in the households only reached ∼85.6% of the planned level with gaps mostly occurring in adults (Munywoki et al. 2014). Thus, it is possible that we missed important samples in inferring the transmission chains. Second, a significant proportion (34.2%) of the s... | other | 30.42 |
In conclusion, our study has shown that the analysis of genome sequences provides better phylogenetic resolution in tracking RSV spread compared to analysis of small partial sequences including the highly variable G gene. Although whole genome analysis alone could not resolve every step in the transmission chains withi... | other | 28.9 |
One of the main research areas in metabolomics is to study the metabolic response to one or a few factors of interest in a given biological system. Design of experiment (DOE) has been widely employed to determine such cause-and-effect relationships. There are many statistical tests to analyse these data generated by d... | other | 29.9 |
Historically, the design of output Y is usually categorised into two types: regression and classification. If the coded output is a series of continuous numbers (e.g., different concentrations of a specific metabolite, time points, temperatures, and so on), these numbers can be directly used as Y and the corresponding ... | other | 35.78 |
However, there are cases when neither regression nor classification would be able to present the information in a DOE well. For example, if one conducted an experiment in which two different extraction methods (denoted as E1 and E2) were applied to extract metabolites from three different bacterial cells (denoted as B1... | other | 35.06 |
It has been recognised that not all problems can be explained well in real numbers (regression) or discrete coding (classification) schemes and, sometimes, more general, structured outputs are needed to cope with these data, which cannot be formulated as simple regression or binary classification problems . The key dif... | other | 29.69 |
In this study, we explored such a possibility of using a structured output, designed according to the DOE, for PLS modelling and compared the results with classic binary coding. Two recently published real metabolomics datasets were employed which used two different DOEs with different complexity and characteristics. | other | 33.66 |
One dataset (denoted as riboswitch in this paper), was obtained from an experiment to investigate the metabolic effects of producing enhanced green fluorescent protein (eGFP) as a recombinant protein in Escherichia coli (E. coli) cells . A two-factor, full-factorial experimental design was employed and the metabolic pr... | other | 34.1 |
The other dataset, denoted as propranolol, was the results of an experiment investigating the role of efflux pumps in stress tolerance Pseudomonas putida exposed to toxic hydrocarbons. In this experiment three different strains of P. putida (denoted as DOT-T1E, DOT-T1E-PS28, and DOT-T1E-18) were exposed to four differe... | other | 33.7 |
Since the results from the PLS modelling were in agreement with our previous reports, the detailed biological interpretations and significance of the results of the two datasets can be found in our previous publications (riboswitch and propanolol ) and will not be repeated again in this paper. | other | 34.53 |
The structured output of this data set is illustrated in Figure 1 and a detailed description is given in Section 4.3.1. The PLS models were validated using a double cross-validation procedure and the reported results were the average of 1000 random splits of training and test sets as described in Section 4.3.2. | other | 34.1 |
The confusion matrix of strain predictions are given in Table 1, while that of inducer condition predictions are shown in Table 2. The overall correct classification rate (CCR) for strain prediction was 80.21%, while that of the inducer condition was 58.20%, suggesting that the strain difference was a more dominating f... | other | 31.22 |
For reasons of brevity we denote the three P. putida strains: DOT-T1E, DOT-T1E-PS28, and DOT-T1E-18 as S1, S2, and S3, respectively; the four propranolol dosages: control, 0.2, 0.4, and 0.6 mg/mL are denoted as D0, D1, D2, and D3; the three monitored time points: 0, 10, and 60 min after exposure are denoted as T0, T1, ... | other | 34.38 |
The confusion matrices of strain predictions, dosages, and time point predictions are given in Table 5, Table 6 and Table 7. The confusion matrix of strain classification suggested that S3 (DOT-T1E-18) was most different to the other two strains. The predictive accuracy in dosages prediction showed a gradient from cont... | other | 31.95 |
We also performed a PLS-DA using binary coding and treated each unique combination of strain, dosage, and time as a distinct class. The results did not show any sensible pattern and the predictive accuracies were no better than a pure random classifier (data not shown). This could be caused by a large number of classes... | other | 35.2 |
Identifying significant metabolites is also an important aspect in metabolomics studies and PLS models can provide many statistics which can aid in the discovery of important (input) variables which have contributed to the separation between classes. In this study we employed variable importance in projection (VIP) sco... | other | 36.22 |
The VIP score plots of the riboswitch dataset are provided in Figure 3. The top 10 most significant metabolites that could be definitive identified according to MSI (variable 21 and 53, although significant, could not be confidently identified through mass spectra matching) across two blocks in the plot were identifie... | other | 31.9 |
The VIP scores plots from PLS-DA analysis on the propranolol dataset are shown in Figure 4. The top 10 most significant and identified metabolites are: alanine (14), butanoic acid (26), leucine (37), serine (54), silanamine (86), phenylalanine (95), ornithine (100), trehalose (188), metoprolol (189), and 5′-adenylic ac... | other | 29.6 |
In this paper we have demonstrated that PLS can also be used to model structured outputs and provide improved results over classical binary output coding for modelling data from complex DOEs. It is also easy to implement this methodology, as one only needs to design a structured output Y based on the experimental desig... | other | 28.61 |
The results from the riboswitch data suggested that when there is a mixture of strong and weak factors, using binary output coding may result in a model which is focused on separating the classes of the weak factor and compromise its capability in predicting strong factors. Using a structured output coding has resulted... | other | 32.88 |
It is also important to note that compared to those methods which have dedicated structural data modelling, such as S-SVM, PLS has a major limitation in that the model has no flexibility in choosing how to represent the errors, i.e., the difference between coded and predicted outputs. The solution found by PLS models i... | other | 31.03 |
Since these two datasets had already been published elsewhere, only brief descriptions are provided here, and more detailed information about the motivation of the experimental design, bacterial characteristics, sample analysis, and biological interpretations can be found in . | other | 34.56 |
Five E. coli strains were used in this study, coded as wild, PET, EGFP, iL3PET, and iL3EGFP, a detailed description of these strains can be found in . All strains were streak plated three times on LB agar prior to every experiment to ensure the purity of the stocks. One-hundred milligrams per litre of ampicillin and/or... | other | 33.97 |
Fifty millilitres of LB broth, three biological replicates per condition, was inoculated with the appropriate strains using the overnight grown cells to a final OD600nm = 0.1, followed by incubation at 37 °C at 200 rpm shaking for 3 h. Upon reaching the OD600nm = 0.5 the samples were exposed to one of the inducing cond... | other | 32.1 |
The derivatized samples were randomised and analysed using a Gerstel MPS-2 autosampler (Gerstel, Baltimore, MD, USA) used in conjunction with an Agilent 6890N GC oven (Wokingham, UK) coupled to a Leco Pegasus III mass spectrometer (St. Joseph, MI, USA) following previously published methods . Collected data were deconv... | other | 33.47 |
Three bacterial strains of P. putida DOT-T1E were used in this study, denoted as DOT-T1E, DOT-T1E-PS28, and DOT-T1E-18; their relevant characteristics, and references for further information on each strain can be found in . All strains were sub-cultured in triplicate to obtain axenic cultures. Individual colonies were ... | other | 37.7 |
Cells were grown in 50 mL of LyB medium for 5 h at 30 °C and 200 rpm. Once cell cultures reached the mid-exponential phase, samples were divided into two groups. One group was kept as a control and to the second group propranolol was added at three different concentrations (0.2, 0.4, and 0.6 mg/mL). These cultures were... | other | 39.66 |
The samples (15 mL) were plunged into a double volume of 60% cold methanol (−50 °C) in a 50 mL tube. The quenched culture mixture was centrifuged (3000× g, 10 min, 1 °C), and then the supernatant was discarded, while the cell pellets were stored at −80 °C until required for metabolite extraction. | other | 36.44 |
The biomass pellets were resuspended in 750 μL of freshly prepared cold methanol (80%). The solution was then transferred to a 2 mL Eppendorf microcentrifuge tube. This was followed by a freeze-thaw cycle in order to extract the intracellular polar metabolites from the cells. Samples were centrifuged at (13,500× g, 3 m... | other | 32.22 |
Prior to GC-MS analysis the samples were derivatized using the same method used in riboswitch experiment. These samples were then randomised and analysed by using gas chromatography electron ionisation time-of-flight mass spectrometry (GC-TOF-MS) using an Agilent 6890 GC instrument coupled to a LECO Pegasus III TOF mas... | other | 34.72 |
All of the data analysis were performed using in-house scripts written in MATLAB 2014a (Mathworks, MA, USA) environment and these scripts are freely available online at . Both datasets were firstly aligned using QCs , and the missing values were imputed by using KNN-imputation method and then subjected to PLS analysis... | other | 35.72 |
The structured coding for this dataset is relatively straightforward. It can be considered as a classification model that will be calibrated to predict two class membership simultaneously. Therefore, the structure coded output is a combination of two binary matrices, one for bacterial strains and another for inducer co... | other | 34.03 |
The structured coding for propranolol dataset was more complicated as it consisted of three blocks: one classification block (strains) and two ordinal blocks (dosage and time). These three blocks were also at different scales in which the strain block could be presented by a dummy binary matrix in any scale, the dosage... | other | 37.78 |
This coding method ensured that the “worst” predictions in different blocks would result in similar errors, e.g., a “complete” misclassification error in strain prediction, D0 had been predicted as D3 or T2 had been predicted as T0. The coded values in the dosage column were evenly spaced as in the experiment the dosag... | other | 35.53 |
The interpretation of the predicted outputs was also performed on three blocks separately, and the classification block was interpreted in the same way as what had been done for the riboswitch dataset. The interpretations on the two ordinal blocks also followed a similar “crisping” of the output. For each sample, the p... | other | 36.25 |
For PLS with multiple columns of outputs, there is a VIP score vector for each column in Y. To simplify the task of inspection the VIP scores were summarised according to the blocks. This is done by taking the maximum of the VIP scores of the Y variables within the group. For the riboswitch dataset, the VIP scores for ... | other | 35.44 |
In conclusion, we have demonstrated that it is possible to implement a structured output for modelling metabolomics data when multiple interacting factors are present in the experimental design. We believe that this approach would have general utility in metabolomics data analysis as well as in other areas where the an... | other | 31.38 |
A double cross-validation (CV) procedure was employed to train and validate the PLS models. The split of training and test set was based on biological replicates. For example, in the riboswitch experiment, there were three biological replicates for each of the 5 × 4 = 20 different combinations of the two factors (five... | other | 39.4 |
Mean centre pre-processing was applied for the PLS modelling . On the training set, the means of both X and Y matrices (denoted as x¯ and y¯, respectively) were calculated, recorded, and subtracted from X and Y, respectively. The PLS model was then built between the mean centred X and Y. Then, in the validation or blin... | other | 35.8 |
An important property of the cochlea is the ability to “amplify” the mechanical vibrations at the basilar membrane (Dallos, 2008). This process is under the control of the medial olivocochlear (MOC) system via efferent fibers that innervate the outer hair cells. Activation of these efferents, called the MOC reflex (MOC... | study | 28.6 |
End of preview. Expand in Data Studio
README.md exists but content is empty.
- Downloads last month
- 4