Scaling of joint mass and metabolism fluctuations in in silico cell-laden spheroids.

Variations and fluctuations are characteristic features of biological systems and are also manifested in cell cultures. Here, we describe a computational pipeline for identifying the range of three-dimensional (3D) cell-aggregate sizes in which nonisometric scaling emerges in the presence of joint mass and metabolic rate fluctuations. The 3D cell-laden spheroids with size and single-cell metabolic rates described by probability density functions were randomly generated in silico. The distributions of the resulting metabolic rates of the spheroids were computed by modeling oxygen diffusion and reaction. Then, a method for estimating scaling exponents of correlated variables through statistically significant data collapse of joint probability distributions was developed. The method was used to identify a physiologically relevant range of spheroid sizes, where both nonisometric scaling and a minimum oxygen concentration (0.04 mol⋅m-3) is maintained. The in silico pipeline described enables the prediction of the number of experiments needed for an acceptable collapse and, thus, a consistent estimate of scaling parameters. Using the pipeline, we also show that scaling exponents may be significantly different in the presence of joint mass and metabolic-rate variations typically found in cells. Our study highlights the importance of incorporating fluctuations and variability in size and metabolic rates when estimating scaling exponents. It also suggests the need for taking into account their covariations for better understanding and interpreting experimental observations both in vitro and in vivo and brings insights for the design of more predictive and physiologically relevant in vitro models.

Using Support Vector Machines for Facet Partitioning in Multidimensional Scaling.

In this article we focus on interpreting multidimensional scaling (MDS) configurations using facet theory. The facet theory approach is attempting to partition a representational space, facet by facet, into regions with certain simplifying constraints on the regions' boundaries (e.g., concentric circular sub-spaces). A long-standing problem has been the lack of computational methods for optimal facet-based partitioning. We propose using support vector machines (SVM) to perform this task. SVM is highly attractive for this purpose as they allow for linear as well as nonlinear classification boundaries in any dimensionality. Using various classical examples from the facet theory literature we elaborate on the combined use of MDS and SVM for facet-based partitioning. Different types of MDS are discussed, and options for SVM kernel specification, tuning, and performance evaluation are illustrated.

Coevolutionary and Phylogenetic Analysis of Mimiviral Replication Machinery Suggest the Cellular Origin of Mimiviruses.

Mimivirus is one of the most complex and largest viruses known. The origin and evolution of Mimivirus and other giant viruses have been a subject of intense study in the last two decades. The two prevailing hypotheses on the origin of Mimivirus and other viruses are the reduction hypothesis, which posits that viruses emerged from modern unicellular organisms; whereas the virus-first hypothesis proposes viruses as relics of precellular forms of life. In this study, to gain insights into the origin of Mimivirus, we have carried out extensive phylogenetic, correlation, and multidimensional scaling analyses of the putative proteins involved in the replication of its 1.2-Mb large genome. Correlation analysis and multidimensional scaling methods were validated using bacteriophage, bacteria, archaea, and eukaryotic replication proteins before applying to Mimivirus. We show that a large fraction of mimiviral replication proteins, including polymerase B, clamp, and clamp loaders are of eukaryotic origin and are coevolving. Although phylogenetic analysis places some components along the lineages of phage and bacteria, we show that all the replication-related genes have been homogenized and are under purifying selection. Collectively our analysis supports the idea that Mimivirus originated from a complex cellular ancestor. We hypothesize that Mimivirus has largely retained complex replication machinery reminiscent of its progenitor while losing most of the other genes related to processes such as metabolism and translation.

Visualization of cross-resistance between antimicrobial agents by asymmetric multidimensional scaling.

WHAT IS KNOWN AND OBJECTIVE: In our previous studies, we developed a cross-resistance rate (CRR) correlation diagram (CRR diagram) that visually captures the magnitude of CRRs between antimicrobials using scatter plots. We used asymmetric multidimensional scaling (MDS) to transform cross-resistance similarities between antimicrobials into a 2-dimensional map and attempted to visually express them. We also explored the antibiograms of Pseudomonas aeruginosa before and after the transfer to newly built hospitals, and we determined by the CRR diagram that the CRRs among ß-lactam antimicrobials other than carbapenems decreased substantially with the facility transfer. The present study tests whether the analysis of CRRs by asymmetric MDS can be used as new visual information that is easy for healthcare professionals to understand. METHOD: We tested the impact of changes in the nosocomial environment due to institutional transfers on CRRs among antimicrobials in asymmetric MDS, as well as contrasted the asymmetric MDS map and CRR diagram. RESULTS AND DISCUSSION: In the asymmetric MDS map, antimicrobial groups with the same mechanism of action were displayed close together, and antimicrobial groups with different mechanisms of action were displayed separately. The asymmetric MDS map drawn solely for antimicrobials belonging to the group with the same mechanism of action showed similarities to the CRR diagram. Also, the distance of each antimicrobial to other antimicrobials shown in the asymmetric MDS map was negatively correlated with the CRRs for them against that antimicrobial. WHAT IS NEW AND CONCLUSION: The asymmetric MDS map expresses the dissimilarity as distances between agents, and there are no meanings or units on the ordinate and abscissa axes of the output map. In contrast, the CRR diagram expresses the antimicrobials' resistance status as values, such as resistance rate and CRR. By analysing the CRRs in the asymmetric MDS, it is feasible to visually recognize cross-resistance similarities between antimicrobial groups as distances. The use of the asymmetric MDS combined with the CRR diagram allows us to visually understand the resistance and cross-resistance status of each antimicrobial agent as a 2-dimensional map, as well as to understand the trends and characteristics of the data by means of quantitative values.

A map of desire: multidimensional scaling of men's sexual interest in male and female children and adults.

BACKGROUND: Men sexually interested in children of a specific combination of maturity and sex tend to show some lesser interest in other categories of persons. Patterns of men's sexual interest across erotic targets' categories of maturity and sex have both clinical and basic scientific implications. METHOD: We examined the structure of men's sexual interest in adult, pubescent, and prepubescent males and females using multidimensional scaling (MDS) across four datasets, using three large samples and three indicators of sexual interest: phallometric response to erotic stimuli, sexual offense history, and self-reported sexual attraction. The samples were highly enriched for men sexually interested in children and men accused of sexual offenses. RESULTS: Results supported a two-dimensional MDS solution, with one dimension representing erotic targets' biological sex and the other dimension representing their sexual maturity. The dimension of sexual maturity placed adults and prepubescent children on opposite ends, and pubescent children intermediate. Differences between men's sexual interest in adults and prepubescent children of the same sex were similar in magnitude to the differences between their sexual interest in adult men and women. Sexual interest in adult men was no more associated with sexual interest in boys than sexual interest in adult women was associated with sexual interest in girls. CONCLUSIONS: Erotic targets' sexual maturity and biological sex play important roles in men's preferences, which are predictive of sexual offending. The magnitude of men's preferences for prepubescent children v. adults of their preferred sex is large.

Close genetic relationship between central Thai and Mon people in Thailand revealed by autosomal microsatellites.

Central Thailand is home to diverse populations with the central Thai constituting the major group, while the Mon, who migrated from southern Myanmar, are sparsely distributed within the region. A total of 338 individuals of eight central Thai (246 samples) and three Mon populations (92 samples) were newly genotyped. When combined with our previously published Mon data, this provides a total of 139 Mon samples. We found genetic similarity between the central Thai and Mon and weak sub-structuring among Thais from central, northern, and northeastern Thailand. The forensic parameter results show high discrimination values which are appropriate for forensic personal identification and paternity testing in both the central Thai and Mon; the probabilities of excluding paternity are 0.999999112 and 0.999999031, respectively, and the combined discrimination power is 0.9999999999999999999999 in both groups. This regional allelic frequency on forensic microsatellites may serve as a useful reference for further forensic investigations in both Thailand and Myanmar.

Genetic polymorphism analysis of 23 STR loci in the Tujia population from Chongqing, Southwest China.

To evaluate the applicability of 23 autosomal STR loci (D10S1248, D11S4463, D12ATA63, D14S1434, D17S1301, D18S853, D1GATA113, D1S1627, D6S1017, D20S1082, D20S482, D17S974, D22S1045, D1S1677, D2S1776, D2S441, D3S4529, D4S2408, D9S1122D5S2500, D6S474, D18S51, D9S2157) included in DNA Typer™ 25 Kit for individual identification and parentage testing, allele frequencies and forensic efficiency parameters were first obtained from healthy, unrelated 506 Chongqing Tujia individuals. A total of 1012 alleles were identified in 23 STR loci, and allele frequencies ranged from 0.001 to 0.5761. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci were 0.999999999999999999999753 and 0.99999967, respectively. These results suggested that 23 autosomal STR loci could be used as an effective tool for forensic application in Chongqing Tujia population. Comprehensive comparisons were conducted based on the analysis of genetic distance, principal component analysis (PCA), multidimensional scaling plot (MDS), and phylogenetic tree to explore the interpopulation genetic relationship. Our results revealed that Chongqing Tujia keeps the more relatively genetic similarity with Hunan Han, Hubei Tujia, and Sichuan Han, which could be interpreted by that those populations were originated from the same ethnic ancestor or genetic communication were happened in adjacent areas.

Associating Psychotic Symptoms with Altered Brain Anatomy in Psychotic Disorders Using Multidimensional Item Response Theory Models.

Reduced cortical thickness has been demonstrated in psychotic disorders, but its relationship to clinical symptoms has not been established. We aimed to identify the regions throughout neocortex where clinical psychosis manifestations correlate with cortical thickness. Rather than perform a traditional correlation analysis using total scores on psychiatric rating scales, we applied multidimensional item response theory to identify a profile of psychotic symptoms that was related to a region where cortical thickness was reduced. This analysis was performed using a large population of probands with psychotic disorders (N = 865), their family members (N = 678) and healthy volunteers (N = 347), from the 5-site Bipolar-Schizophrenia Network for Intermediate Phenotypes. Regional cortical thickness from structural magnetic resonance scans was measured using FreeSurfer; individual symptoms were rated using the Positive and Negative Syndrome Scale, Montgomery-Asberg Depression Rating Scale, and Young Mania Rating Scale. A cluster of cortical regions whose thickness was inversely related to severity of psychosis symptoms was identified. The regions turned out to be located contiguously in a large region of heteromodal association cortex including temporal, parietal and frontal lobe regions, suggesting a cluster of contiguous neocortical regions important to psychosis expression. When we tested the relationship between reduced cortical surface area and high psychotic symptoms we found no linked regions describing a related cortical set.

Diagnostic performance of classification trees and hematological functions in hematologic disorders: an application of multidimensional scaling and cluster analysis.

BACKGROUND: Several hematological indices have been already proposed to discriminate between iron deficiency anemia (IDA) and ß-thalassemia trait (ßTT). This study compared the diagnostic performance of different hematological discrimination indices with decision trees and support vector machines, so as to discriminate IDA from ßTT using multidimensional scaling and cluster analysis. In addition, decision trees were used to determine the diagnostic classification scheme of patients. METHODS: Consisting of 1178 patients with hypochromic microcytic anemia (708 patients with ßTT and 470 patients with IDA), this cross-sectional study compared the diagnostic performance of 43 hematological discrimination indices with classification tree algorithms and support vector machines in order to discriminate IDA from ßTT. Moreover, multidimensional scaling and cluster analysis were used to identify the homogeneous subgroups of discrimination methods with similar performance. RESULTS: All the classification tree algorithms except the LOTUS tree algorithm showed acceptable accuracy measures for discrimination between IDA and ßTT in comparison with other hematological discrimination indices. The results indicated that the CRUISE and C5.0 tree algorithms had better diagnostic performance and efficiency among other discrimination methods. Moreover, the AUC of CRUISE and C5.0 tree algorithms indicated more precise classification with values of 0.940 and 0.999, indicating excellent diagnostic accuracy of such models. Moreover, the CRUISE and C5.0 tree algorithms showed that mean corpuscular volume can be considered as the main variable in discrimination between IDA and ßTT. CONCLUSIONS: CRUISE and C5.0 tree algorithms as powerful methods in data mining techniques can be used to develop accurate differential methods along with other laboratory parameters for the discrimination of IDA and ßTT. In addition, the multidimensional scaling method and cluster analysis can be considered as the most appropriate techniques to determine the discrimination indices with similar performance for future hematological studies.

Object Positioning Algorithm Based on Multidimensional Scaling and Optimization for Synthetic Gesture Data Generation.

This work studies the feasibility of a novel two-step algorithm for infrastructure and object positioning, using pairwise distances. The proposal is based on the optimization algorithms, Scaling-by-Majorizing-a-Complicated-Function and the Limited-Memory-Broyden-Fletcher-Goldfarb-Shannon. A qualitative evaluation of these algorithms is performed for 3D positioning. As the final stage, smoothing filtering techniques are applied to estimate the trajectory, from the previously obtained positions. This approach can also be used as a synthetic gesture data generator framework. This framework is independent from the hardware and can be used to simulate the estimation of trajectories from noisy distances gathered with a large range of sensors by modifying the noise properties of the initial distances. The framework is validated, using a system of ultrasound transceivers. The results show this framework to be an efficient and simple positioning and filtering approach, accurately reconstructing the real path followed by the mobile object while maintaining low latency. Furthermore, these capabilities can be exploited by using the proposed algorithms for synthetic data generation, as demonstrated in this work, where synthetic ultrasound gesture data are generated.

Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana.

In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.

Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia.

Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.

Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.

Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.

Regularized Estimation of the Nominal Response Model.

The nominal response model is an item response theory model that does not require the ordering of the response options. However, while providing a very flexible modeling approach of polytomous responses, it involves the estimation of many parameters at the risk of numerical instability and overfitting. The lasso is a technique widely used to achieve model selection and regularization. In this paper, we propose the use of a fused lasso penalty to group response categories and perform regularization of the unidimensional and multidimensional nominal response models. The good performance of the method is illustrated through real-data applications and simulation studies.

Minimum Distance Estimation of Multidimensional Diffusion-Based Item Response Theory Models.

Diffusion-based item response theory models are models for responses and response times on psychological tests, which can be used as measurement models in the same way as standard item response theory models (Tuerlinckx, Molenaar, & van der Maas, 2016). Their range of application, however, is narrowed by the fact that multidimensional versions of the model are not easy to fit. Marginal maximum likelihood estimation (e.g., Molenaar, Tuerlinckx, & van der Maas, 2015a) is computationally intensive and infeasible for multidimensional versions. The weighted least squares estimator of Ranger, Kuhn, and Szardenings (2016) is inefficient. Here, we propose an alternative estimator that is more efficient than the least squares estimator and less demanding than the maximum likelihood estimator. The estimator is based on minimum distance estimation and consists in modeling the sample quantiles and sample covariances. The performance of the estimator is investigated in a simulation study. The simulation study corroborates that the estimator performs well. The application of the estimator is demonstrated with real data.

The Multidimensional Scale of Perceived Social Support (MSPSS): Reliability and Validity of Russian Version.

Objective: To assess factorial and construct validity along with reliability of the Russian version of the Multidimensional Scale of Perceived Social Support (MSPSS) in cardiac patients.Methods: The study included 1018 patients with coronary artery disease. All patients were offered the opportunity to complete a questionnaire to detect psychosocial risk and protective factors, including the MSPSS.Results: Internal consistency of the Russian version of the MSPSS was high: Cronbach's alpha coefficient in the group of patients with stable angina was .91 vs. .90 in the group with acute coronary syndrome. The three-factor structure of the MSPSS was proved with exploratory and confirmatory factor analyses. As expected, the Russian version of the MSPSS was negatively correlated with measures of anxiety and depression, and positively correlated with curiosity.Conclusions: The Russian version of MSPSS corresponds closely with the English version in reliability, consistency, and internal structure. Test-retest reliability was satisfactorally high and construct validity was supported with the results of the correlation analysis.Clinical Implications: Our study confirms that MSPSS questionnaire is a high valid tool to estimate social support and it can be successfully applied to define social support in patients with cardiac pathology.

Can we spot fake public comments generated by ChatGPT(-3.5, -4)?: Japanese stylometric analysis expose emulation created by one-shot learning.

Public comments are an important opinion for civic when the government establishes rules. However, recent AI can easily generate large quantities of disinformation, including fake public comments. We attempted to distinguish between human public comments and ChatGPT-generated public comments (including ChatGPT emulated that of humans) using Japanese stylometric analysis. Study 1 conducted multidimensional scaling (MDS) to compare 500 texts of five classes: Human public comments, GPT-3.5 and GPT-4 generated public comments only by presenting the titles of human public comments (i.e., zero-shot learning, GPTzero), GPT-3.5 and GPT-4 emulated by presenting sentences of human public comments and instructing to emulate that (i.e., one-shot learning, GPTone). The MDS results showed that the Japanese stylometric features of the public comments were completely different from those of the GPTzero-generated texts. Moreover, GPTone-generated public comments were closer to those of humans than those generated by GPTzero. In Study 2, the performance levels of the random forest (RF) classifier for distinguishing three classes (human, GPTzero, and GPTone texts). RF classifiers showed the best precision for the human public comments of approximately 90%, and the best precision for the fake public comments generated by GPT (GPTzero and GPTone) was 99.5% by focusing on integrated next writing style features: phrase patterns, parts-of-speech (POS) bigram and trigram, and function words. Therefore, the current study concluded that we could discriminate between GPT-generated fake public comments and those written by humans at the present time.

Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis.

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis, principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization, to a microbiome dataset from 186 subjects with symptoms of  allergic rhinitis (AR) and 106 controls. All the dimension reduction methods supported that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed depending on the distance matrices and the dimension reduction methods. The first composite variables calculated from PCoA and NMDS with the UniFrac distance were strongly associated with AR (FDR adjusted P = 2.4 × 10-4 for PCoA and P = 2.8 × 10-4 for NMDS), and also with the relative abundance of Bifidobacterium and Prevotella. The abundance of Bifidobacterium was also linked to intake of several nutrients, including carbohydrate, saturated fat, and alcohol via composite variables. Notably, the association between the composite variables and AR was much stronger than the association between the relative abundance of individual genera and AR. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

Heterogeneity and overlap in the continuum of linguistic profile of logopenic and semantic variants of primary progressive aphasia: a Profile Analysis based on Multidimensional Scaling study.

BACKGROUND: Primary progressive aphasia (PPA) diagnostic criteria underestimate the complex presentation of semantic (sv) and logopenic (lv) variants, in which symptoms partially overlap, and mixed clinical presentation (mixed-PPA) and heterogenous profile (lvPPA +) are frequent. Conceptualization of similarities and differences of these clinical conditions is still scarce. METHODS: Lexical, semantic, phonological, and working memory errors from nine language tasks of sixty-seven PPA were analyzed using Profile Analysis based on Multidimensional Scaling, which allowed us to create a distributed representation of patients' linguistic performance in a shared space. Patients had been studied with [18F] FDG-PET. Correlations were performed between metabolic and behavioral data. RESULTS: Patients' profiles were distributed across a continuum. All PPA, but two, presented a lexical retrieval impairment, in terms of reduced production of verbs and nouns. svPPA patients occupied a fairly clumped space along the continuum, showing a preponderant semantic deficit, which correlated to fusiform gyrus hypometabolism, while only few presented working memory deficits. Adjacently, lvPPA + presented a semantic impairment combined with phonological deficits, which correlated with metabolism in the anterior fusiform gyrus and posterior middle temporal gyrus. Starting from the shared phonological deficit side, a large portion of the space was occupied by all lvPPA, showing a combination of phonological, lexical, and working memory deficits, with the latter correlating with posterior temporo-parietal hypometabolism. Mixed PPA did not show unique profile, distributing across the space. DISCUSSION: Different clinical PPA entities exist but overlaps are frequent. Identifying shared and unique clinical markers is critical for research and clinical practice. Further research is needed to identify the role of genetic and pathological factors in such distribution, including also higher sample size of less represented groups.

A unified approach based on multidimensional scaling for calibration estimation in survey sampling with qualitative auxiliary information.

Survey calibration is a widely used method to estimate the population mean or total score of a target variable, particularly in medical research. In this procedure, auxiliary information related to the variable of interest is used to recalibrate the estimation weights. However, when the auxiliary information includes qualitative variables, traditional calibration techniques may be not feasible or the optimisation procedure may fail. In this article, we propose the use of linear calibration in conjunction with a multidimensional scaling-based set of continuous, uncorrelated auxiliary variables along with a suitable metric in a distance-based regression framework. The calibration weights are estimated using a projection of the auxiliary information on a low-dimensional Euclidean space. The approach becomes one of the linear calibration with quantitative variables avoiding the usual computational problems in the presence of qualitative auxiliary information. The new variables preserve the underlying assumption in linear calibration of a linear relationship between the auxiliary and target variables, and therefore the optimal properties of the linear calibration method remain true. The behaviour of this approach is examined using a Monte Carlo procedure and its value is illustrated by analysing real data sets and by comparing its performance with that of traditional calibration procedures.