Supervised diagnostic classification of cognitive attributes using data augmentation.

Over recent decades, machine learning, an integral subfield of artificial intelligence, has revolutionized diverse sectors, enabling data-driven decisions with minimal human intervention. In particular, the field of educational assessment emerges as a promising area for machine learning applications, where students can be classified and diagnosed using their performance data. The objectives of Diagnostic Classification Models (DCMs), which provide a suite of methods for diagnosing students' cognitive states in relation to the mastery of necessary cognitive attributes for solving problems in a test, can be effectively addressed through machine learning techniques.

Enhancement of the Anticancer Ability of Natural Killer Cells through Allogeneic Mitochondrial Transfer.

An in vitro culture period of at least 2 weeks is required to produce sufficient natural killer (NK) cells for immunotherapy, which are the key effectors in hematological malignancy treatment. Mitochondrial damage and fragmentation reduce the NK cell immune surveillance capacity. Thus, we hypothesized that the transfer of healthy mitochondria to NK cells could enhance their anticancer effects.

gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.

Summary: For the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image.

Fusion of a highly N-glycosylated polypeptide increases the expression of ER-localized proteins in plants.

Plants represent promising systems for producing various recombinant proteins. One key area of focus for improving this technology is developing methods for producing recombinant proteins at high levels. Many methods have been developed to increase the transcript levels of recombinant genes.

Prolines in Transit Peptides Are Crucial for Efficient Preprotein Translocation into Chloroplasts.

Chloroplasts import many preproteins that can be classified based on their physicochemical properties. The cleavable N-terminal transit peptide (TP) of chloroplast preproteins contains all the information required for import into chloroplasts through Toc/Tic translocons. The question of whether and how the physicochemical properties of preproteins affect TP-mediated import into chloroplasts has not been elucidated.

A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs.

Motivation: Linkage disequilibrium (LD) block construction is required for research in population genetics and genetic epidemiology, including specification of sets of single nucleotide polymorphisms (SNPs) for analysis of multi-SNP based association and identification of haplotype blocks in high density sequencing data. Existing methods based on a narrow sense definition do not allow intermediate regions of low LD between strongly associated SNP pairs and tend to split high density SNP data into small blocks having high between-block correlation.

Results: We present Big-LD, a block partition method based on interval graph modeling of LD bins which are clusters of strong pairwise LD SNPs, not necessarily physically consecutive.

Evolution of rubisco complex small subunit transit peptides from algae to plants.

Chloroplasts evolved from a free-living cyanobacterium acquired by the ancestor of all photosynthetic eukaryotes, including algae and plants, through a single endosymbiotic event. During endosymbiotic conversion, the majority of genes in the endosymbiont were transferred to the host nucleus and many of the proteins encoded by these genes must therefore be transported into the chloroplast after translation in the cytosol. Chloroplast-targeted proteins contain a targeting signal, named the transit peptide (TP), at the N-terminus.

The Prenylated Rab GTPase Receptor PRA1.F4 Contributes to Protein Exit from the Golgi Apparatus.

Prenylated Rab acceptor1 (PRA1) functions in the recruitment of prenylated Rab proteins to their cognate organelles. Arabidopsis () contains a large number of proteins belonging to the AtPRA1 family. However, their physiological roles remain largely unknown.

Effects of Single Nucleotide Polymorphism Marker Density on Haplotype Block Partition.

Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1.

Multiple linear combination (MLC) regression tests for common variants adapted to linkage disequilibrium structure.

By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive.

Interactions between Transmembrane Helices within Monomers of the Aquaporin AtPIP2;1 Play a Crucial Role in Tetramer Formation.

Aquaporin (AQP) is a water channel protein found in various subcellular membranes of both prokaryotic and eukaryotic cells. The physiological functions of AQPs have been elucidated in many organisms. However, understanding their biogenesis remains elusive, particularly regarding how they assemble into tetramers.

Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test.

Gene-based analysis of multiple single nucleotide polymorphisms (SNPs) in a gene region is an alternative to single SNP analysis. The multi-bin linear combination test (MLC) proposed in previous studies utilizes the correlation among SNPs within a gene to construct a gene-based global test. SNPs are partitioned into clusters of highly correlated SNPs, and the MLC test statistic quadratically combines linear combination statistics constructed for each cluster.

Gene-based multiple regression association testing for combined examination of common and low frequency variants in quantitative trait analysis.

Multi-marker methods for genetic association analysis can be performed for common and low frequency SNPs to improve power. Regression models are an intuitive way to formulate multi-marker tests. In previous studies we evaluated regression-based multi-marker tests for common SNPs, and through identification of bins consisting of correlated SNPs, developed a multi-bin linear combination (MLC) test that is a compromise between a 1 df linear combination test and a multi-df global test.

Combined linkage and association analyses identify a novel locus for obesity near PROX1 in Asians.

Objective: Although genome-wide association studies (GWAS) have substantially contributed to understanding the genetic architecture, unidentified variants for complex traits remain an issue. One of the efficient approaches is the improvement of the power of GWAS scan by weighting P values with prior linkage signals. Our objective was to identify the novel candidates for obesity in Asian populations by using genemapping strategies that combine linkage and association analyses.

A family-based association study after genome-wide linkage analysis identified two genetic loci for renal function in a Mongolian population.

The estimated glomerular filtration rate is a well-known measure of renal function and is widely used to follow the course of disease. Although there have been several investigations establishing the genetic background contributing to renal function, Asian populations have rarely been used in these genome-wide studies. Here, we aimed to find candidate genetic determinants of renal function in 1007 individuals from 73 extended families of Mongolian origin.

Mitochondrial targeting of the Arabidopsis F1-ATPase γ-subunit via multiple compensatory and synergistic presequence motifs.

The majority of mitochondrial proteins are encoded in the nuclear genome and imported into mitochondria posttranslationally from the cytosol. An N-terminal presequence functions as the signal for the import of mitochondrial proteins. However, the functional information in the presequence remains elusive.

Comprehensive genomic analyses associate UGT8 variants with musical ability in a Mongolian population.

Background: Musical abilities such as recognising music and singing performance serve as means for communication and are instruments in sexual selection. Specific regions of the brain have been found to be activated by musical stimuli, but these have rarely been extended to the discovery of genes and molecules associated with musical ability.

Methods: A total of 1008 individuals from 73 families were enrolled and a pitch-production accuracy test was applied to determine musical ability.

Real data examples in statistical methods papers: Tremendously valuable, and also tremendously misvalued.

When a statistical methods paper is submitted to a journal for publication, examples in which the method is applied to real data are highly encouraged by many journals and in some cases are explicitly demanded. In this commentary, we argue that real data examples serve several useful purposes. However, we also argue that in many cases, particularly in the fields of genetics and genomics, there is an implicit or explicit expectation for examples to support purposes for which they are ill-suited and furthermore that these inappropriate expectations have negative consequences for the field.

Small heat shock protein Hsp17.8 functions as an AKR2A cofactor in the targeting of chloroplast outer membrane proteins in Arabidopsis.

Plastid proteins that are encoded by the nuclear genome and synthesized in the cytosol undergo posttranslational targeting to plastids. Ankyrin repeat protein 2A (AKR2A) and AKR2B were recently shown to be involved in the targeting of proteins to the plastid outer envelope. However, it remains unknown whether other factors are involved in this process.

The first Irish genome and ways of improving sequence accuracy.

Whole-genome sequencing of an Irish person reveals hundreds of thousands of novel genomic variants. Imputation using previous known information improves the accuracy of low-read-depth sequencing.

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.

Copy number variants (CNVs) account for the majority of human genomic diversity in terms of base coverage. Here, we have developed and applied a new method to combine high-resolution array comparative genomic hybridization (CGH) data with whole-genome DNA sequencing data to obtain a comprehensive catalog of common CNVs in Asian individuals. The genomes of 30 individuals from three Asian populations (Korean, Chinese and Japanese) were interrogated with an ultra-high-resolution array CGH platform containing 24 million probes.

Transmission-ratio distortion in the Framingham Heart Study.

Transmission-ratio distortion (TRD) is a phenomenon in which the segregation of alleles does not obey Mendel's laws. As a simple example, a recessive locus that results in fetal lethality will result in live-born individuals sharing more alleles at this locus than expected under Mendel's laws. This could result in apparent linkage of the phenotype of 'being alive' to such a chromosomal regions.

Region-based analysis in genome-wide association study of Framingham Heart Study blood lipid phenotypes.

Due to the high-dimensionality of single-nucleotide polymorphism (SNP) data, region-based methods are an attractive approach to the identification of genetic variation associated with a certain phenotype. A common approach to defining regions is to identify the most significant SNPs from a single-SNP association analysis, and then use a gene database to obtain a list of genes proximal to the identified SNPs. Alternatively, regions may be defined statistically, via a scan statistic.

Genome-wide association analyses of North American Rheumatoid Arthritis Consortium and Framingham Heart Study data utilizing genome-wide linkage results.

The power of genome-wide association studies can be improved by incorporating information from previous study findings, for example, results of genome-wide linkage analyses. Weighted false-discovery rate (FDR) control can incorporate genome-wide linkage scan results into the analysis of genome-wide association data by assigning single-nucleotide polymorphism (SNP) specific weights. Stratified FDR control can also be applied by stratifying the SNPs into high and low linkage strata.

Human leukocyte antigen class I genotypes in relation to heterosexual HIV type 1 transmission within discordant couples.

Differences in immune control of HIV-1 infection are often attributable to the highly variable HLA class I molecules that present viral epitopes to CTL. In our immunogenetic analyses of 429 HIV-1 discordant Zambian couples (infected index partners paired with cohabiting seronegative partners), several HLA class I variants in index partners were associated with contrasting rates and incidence of HIV-1 transmission within a 12-year study period. In particular, A*3601 on the A*36-Cw*04-B*53 haplotype was the most unfavorable marker of HIV-1 transmission by index partners, while Cw*1801 (primarily on the A*30-Cw*18-B*57 haplotype) was the most favorable, irrespective of the direction of transmission (male to female or female to male) and other commonly recognized cofactors of infection, including age and GUI.