Read Mapping Research Articles

Single-Cell Profiling Uncovers the Roles of Endometrial Fibrosis and Microenvironmental Changes in Adenomyosis.

Adenomyosis (AM) is a common benign uterine disorder that has deleterious effects on women's health. However, the pathogenesis of AM is not clearly understood. We aimed to investigate the pathophysiological changes and molecular mechanism in AM. Single-cell RNA sequencing (scRNA-seq) was employed to construct a transcriptomic atlas of various cell subsets from the ectopic endometrium (EC) and eutopic endometrium (EM) of one AM patient and evaluate differential expression. The Cell Ranger software pipeline (version 4.0.0) was applied to conduct sample demultiplexing, barcode processing and mapping reads to the reference genome (human GRCh38). Different cell types were classified with markers with the "FindAllMarkers" function, and differential gene expression analysis was performed with Seurat software in R. The findings were confirmed by Reverse Transcription Real-Time PCR using samples from three AM patients. We identified nine cell types: endothelial cells, epithelial cells, myoepithelial cells, smooth muscle cells, fibroblasts, lymphocytes, mast cells, macrophages and unknown cells. A number of differentially expressed genes, including CLO4A1, MMP1, TPM2 and CXCL8, were identified from all cell types. Functional enrichment showed that aberrant gene expression in fibroblasts and immune cells was related to fibrosis-associated terms, such as extracellular matrix dysregulation, focal adhesion and the PI3K-Akt signaling pathway. We also identified fibroblast subtypes and determined a potential developmental trajectory related to AM. In addition, we identified increased cell-cell communication patterns in EC, highlighting the imbalanced microenvironment in AM progression. Our results support the theory of endometrial-myometrial interface disruption for AM, and repeated tissue injury and repair could lead to increased fibrosis in the endometrium. Therefore, the present study reveals the association between fibrosis, the microenvironment, and AM pathogenesis. This study provides insight into the molecular mechanisms regulating AM progression.

Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota

Rhodopsin photosystems convert light energy into electrochemical gradients used by the cell to produce ATP, or for other energy-demanding processes. While these photosystems are widespread in the ocean and have been identified in diverse microbial taxonomic groups, their physiological role in vivo has only been studied in few marine bacterial strains. Recent metagenomic studies revealed the presence of rhodopsin genes in the understudied Verrucomicrobiota phylum, yet their distribution within different Verrucomicrobiota lineages, their diversity, and function remain unknown. In this study, we show that more than 7% of Verrucomicrobiota genomes (n = 2916) harbor rhodopsins of different types. Furthermore, we describe the first two cultivated rhodopsin-containing strains, one harboring a proteorhodopsin gene and the other a xanthorhodopsin gene, allowing us to characterize their physiology under laboratory-controlled conditions. The strains were isolated in a previous study from the Eastern Mediterranean Sea and read mapping of 16S rRNA gene amplicons showed the highest abundances of these strains at the deep chlorophyll maximum (source of their inoculum) in winter and spring, with a substantial decrease in summer. Genomic analysis of the isolates suggests that motility and degradation of organic material, both energy demanding functions, may be supported by rhodopsin phototrophy in Verrucomicrobiota. Under culture conditions, we show that rhodopsin phototrophy occurs under carbon starvation, with light-mediated energy generation supporting sugar transport into the cells. Overall, this study suggests that photoheterotrophic Verrucomicrobiota may occupy an ecological niche where energy harvested from light enables bacterial motility toward organic matter and supports nutrient uptake.

Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman.

The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning >130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data.

Abstract 2055: Prevalent focal amplification of oncogene in lung adenocarcinomas without canonical driver alterations

Abstract Lung adenocarcinoma (LADC) is the most common type of lung cancer and a leading cause of death worldwide. Typical oncogenes that drive LADCs when mutated (referred to as canonical drivers) include EGFR (30-60%), KRAS (10-30%), and fusion oncogenes (~10%) involving ALK, RET, and ROS1. However, approximately 30% of lung adenocarcinomas lack canonical drivers, implying unseen kinds of genomic alterations. Here, we explore alterations beyond the scope of canonical drivers in LADCs (referred to as non-canonical drivers) using large-scale whole-genome sequencing (WGS) of LADCs. We gathered total 183 WGS of LADCs, 138 of which were from our previous study (Lee et al. Cell. 2019) and 45 were newly sequenced from surgically resected LADCs. For raw data processing, we used a standard WGS analysis pipeline from read mapping to variant calling. Variant filtering and downstream analyses were performed using in-house scripts. Genomic variants analyzed in this study include single-base substitution (SBS), indel, structural variation (SV), and copy number variation (CNV). As a result, we found that 53 cases (29%) had no canonical drivers (ND group). Intriguingly, LADCs without canonical drivers had a contrasting genomic landscape compared to LADCs with canonical drivers (CD group). First, the point-mutation burden was ~3-fold higher in the ND group than in the CD group (52,500 vs. 17,900 for SNVs, p<0.001). Mutational signature analysis revealed that these additional mutations are attributable mainly to tobacco smoking (by mutational signature SBS4) and APOBEC-mediated mutagenesis (SBS12 and SBS13) and that they are more enriched in the ND group (4,800 vs 2,600, p=0.03). Second, the ND group harbored more frequent focal amplifications. Recurrently amplified genes include TERT, IL7R, NKX2-1, CCND1, CCND3, CCNE1, and EGFR. The pattern of SVs suggest that the amplifications occurred through the formation of extra-chromosomal DNA involving multiple chromosomes or following chromothripsis. Overall, this study broadens our understanding of non-canonical drivers of LADCs. Similar analyses of thousands of cancers with clinical information of the patient will likely yield the functional impact of these driver mutations and may offer more opportunities for LADC treatment in the future. Citation Format: Seongyeol Park, Joonoh Lim, Kijong Yi, Boram Yi, Ryul Kim, Jaemo Koo, Kwon Joong Na, Samina Park, In Kyu Park, Chang Hyun Kang, Jeong Seok Lee, Young Seok Ju, Young Tae Kim. Prevalent focal amplification of oncogene in lung adenocarcinomas without canonical driver alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2055.

Abstract 2056: Large-scale whole genome sequencing of hepatocellular carcinoma reveals stepwise cancer evolution

Abstract Liver cancer is a leading cause of death worldwide where somatic mutation plays a key role in tumorigenesis. As such, many recent researches have been conducted using DNA sequencing methods to study somatic mutations in liver cancer, such as whole-exome sequencing (WES), panel sequencing, and whole-genome sequencing (WGS). However, our understanding of genomic landscape of liver tumorigenesis has been limited by a low number of quality samples from diverse clinical contexts. Here, we explore comprehensive genomic landscape of liver cancer throughout its tumorigenesis using large-scale whole-genome sequencing of hepatocellular carcinoma (HCC) in various cancer stages and liver conditions. Total 500 patients of HCCs were enrolled in this study and whole-genome sequenced. 462 samples that passed quality control were included for final analysis. Most of the samples (427; 92%) were obtained from surgical resection and the rest (35; 8%) from liver transplantation. We used a standard WGS analysis pipeline from read mapping to variant calling of single-base substitution (SBS), indel, structural variation (SV), and copy number variation (CNV). Downstream data analyses were performed using in-house scripts with a particular focus on mutational signatures. To study how genome changes as HCC progresses, we classified samples into three groups by T stage: T1, T2, and T3/4. The number of samples for each group was 205 (44%), 222 (48%), and 35 (8%), respectively. There was no significant difference in the number of SBSs and indels, but the number of SVs was significantly higher in T3/4 (the mean of T1/2 vs. T3/4 = 51 vs. 93; p=0.001). Major mutational signatures were SBS5, 40 (both clock-like), 12 (unknown), and 22 (aristolochic acid) for SBSs and ID1, 2, 5 (all clock-like), and 3 (tobacco smoking) for indels. The proportion of ID2, characterized by 1bp deletion at homopolymer site, was increased in the samples of higher T stage (the mean proportion of T1/2 vs. T3/4=11% vs. 16%; p=0.01). The higher-stage samples also harbored more frequent whole-genome duplication (WGD) and loss of heterozygosity (LOH) (the frequency of WGD in T1/2 vs. T3/4=42% vs. 68%, p<0.001; the mean LOH fraction of T1/2 vs. T3/4=0.12 vs. 0.19, p<0.001). There was a significant enrichment of driver mutations of multiple genes (e.g., TP53, MTCP1, CCND3, etc.) in T3/4 group. Interestingly, in surgically resected T1 samples, ID2 proportion was the only significant contributor to early recurrence over tumor size, N stage, mean ploidy, and LOH fraction (n=199, p=0.05; Cox regression). Overall, we found that HCCs at different T stages exhibit some common and yet apparently distinguishing genomic features. We believe that the comprehensive genomic profile of HCC across cancer stages will provide deep insights into the genomic evolution of HCC and one day lend itself to clinicogenomic bases for better HCC management in the future. Citation Format: Seongyeol Park, Suk Kyun Hong, Joonoh Lim, YoungRok Choi, Boram Yi, Jaemo Koo, June-Young Koh, Ryul Kim, Nam-Joon Yi, Jeong Seok Lee, Kyung-Suk Suh, Kwang-Woong Lee, Young Seok Ju. Large-scale whole genome sequencing of hepatocellular carcinoma reveals stepwise cancer evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2056.

Impact of Long-term Soil and Water Conservation Training for Effective Implementation of Watershed Programmes in India

Responses received from fi eld functionaries who had completed fi ve and a half months of long-term soil and water conservation training at the Indian Institute of Soil and Water Conservation during 2003–2009 were analyzed to determine training impact as well as training needs for eff ective implementation of watershed management Programmes in India. The majority of trainees (81%) had total service experience ranging from 10 to 20 years. Major responsibilities of trainees mainly involved in planning and execution of watershed and soil conservation projects. The topic of structural measures for soil and water conservation in non-arable lands received the highest mean score from trainees (2.57), followed by the application of RS and GIS, map reading, delineation, characterization of watersheds (2.38),water harvesting, storage, and recycling for irrigation planning (2.33). This study further indicates that capacity-building programmes improve not only individual knowledge but also the productivity of their working areas. This fi ndings also identifi ed that lack of appropriate literature on SWC technologies is found as a major technological constraint in order to implement watershed project more eff ectively.

Revisiting and corrections to the annotated SRSF3 (SRp20) gene structure and RefSeq sequences from the human and mouse genomes.

SRSF3 (SRp20) is the smallest member of the serine/arginine (SR)-rich protein family. We found the annotated human SRSF3 and mouse Srsf3 RefSeq sequences are much larger than the detected SRSF3/Srsf3 RNA size by Northern blot. Mapping of RNA-seq reads from various human and mouse cell lines to the annotated SRSF3/Srsf3 gene illustrated only a partial coverage of its terminal exon 7. By 5' RACE and 3' RACE, we determined that SRSF3 gene spanning over 8422 bases and Srsf3 gene spanning over 9423 bases. SRSF3/Srsf3 gene has seven exons with exon 7 bearing two alternative polyadenylation signals (PAS). Through alternative PAS selection and exon 4 exclusion/inclusion by alternative RNA splicing, SRSF3/Srsf3 gene expresses four RNA isoforms. The major SRSF3 mRNA isoform with exon 4 exclusion by using a favorable distal PAS to encode a full-length protein is 1411nt long (not annotated 4228nt) and the same major mouse Srsf3 mRNA isoform is only 1295nt (not annotated 2585nt). The difference from the redefined RNA size of SRSF3/Srsf3 to the corresponding RefSeq sequence is at the 3' UTR region. Collectively, the redefined SRSF3/Srsf3 gene structure and expression will allow better understanding of SRSF3 functions and its regulations in health and diseases.

HERV-K (HML-2) insertion polymorphisms in the 8q24.13 region and their potential etiological associations with acute myeloid leukemia.

Human endogenous retroviruses (HERVs) are LTR retrotransposons that are present in the human genome. Among them, members of the HERV-K (HML-2) group are suspected to play a role in the development of different types of cancer, including lung, ovarian, and prostate cancer, as well as leukemia. Acute myeloid leukemia (AML) is an important disease that causes 1% of cancer deaths in the United States and has a survival rate of 28.7%. Here, we describe a method for assessing the statistical association between HERV-K (HML-2) transposable element insertion polymorphisms (or TIPs) and AML, using whole-genome sequencing and read mapping using TIP_finder software. Our results suggest that 101 polymorphisms involving HERV-K (HML-2) elements were correlated with AML, with a percentage between 44.4 to 56.6%, most of which (70) were located in the region from 8q24.13 to 8q24.21. Moreover, it was found that the TRIB1, LRATD2, POU5F1B, MYC, PCAT1, PVT1, and CCDC26 genes could be displaced or fragmented by TIPs. Furthermore, a general method was devised to facilitate analysis of the correlation between transposable element insertions and specific diseases. Finally, although the relationship between HERV-K (HML-2) TIPs and AML remains unclear, the data reported in this study indicate a statistical correlation, as supported by the χ2 test with p-values < 0.05.

Preschoolers' Perceptual Analogical Reasoning and Map Reading: A Preliminary Study on the Mediating Effect of Spatial Language.

Reading and interpreting a map represents an essential part of daily life, enabling appropriate orientation and navigation through space. Based on the idea that perceptual analogical reasoning is critical in aligning the spatial structure of the map with the spatial structure of the space and given the critical role of language, especially spatial language, in encoding and establishing spatial relations among elements in the environment, the present study investigated the joint contribution of perceptual analogical reasoning and spatial language in map reading. The study was conducted with 56 typically developing 4- to 6-year-old children, and the results indicated that perceptual abstract reasoning affected map reading through the mediating effect of spatial language. These findings yielded theoretical and practical implications regarding the role of perceptual abstract reasoning and spatial language in shaping map-reading abilities in the early stages of life, highlighting that domain-specific language competencies are necessary to improve the encoding of spatial relations, to establish object correspondences, and to ensure successful navigation. Limitations and future research directions were discussed.

Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam)

The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.

The Influence of Mobile Technology-Assisted Flipped Classroom Model on Student Learning Outcomes of Map Read Material

This study aims to determine the effect of using the flipped classroom learning model assisted by mobile technology on the learning outcomes of Infantry Officer School of Indonesia Marine Corps students about reading maps. Officer graduates are required to have a good understanding of the concepts in each topic related to assignments. The ability to read maps is a top priority that must be mastered by the marine corps in war military operations. Time allocation in class is not enough for mastering the concept of map reading. It takes more time to master the material for the soldiers. The use of mobile technology provides access for Marine Corps students to additional study time online. The research method used is quasi-experimental or quasi-experimental using t-test data analysis techniques. The research design used a static group comparison design. Comparing the two groups that were taught using the flipped classroom model assisted by mobile technology and the conventional model. The subjects of this research were 133 students of Marine Corps Officer Formation Education at the Advanced Stage (Sargolan) who were divided into two groups, namely the experimental group of 67 students and the control group of 66 students. The findings in this study indicate that students who are taught with the flipped classroom model assisted by mobile technology obtain a better average learning outcome score. The flipped classroom model with the help of mobile technology is very suitable for Marine Corps Officer Formation Education students at the Advanced Class Basic Stage (Sargolan).

Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates.

The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.

Assessing navigational map reading competencies with the location-based GeoGame “GeoGami”

School curricula as well as scientific literature emphasize the need of understanding how children navigate with maps. To date, however, there is no empirically validated assessment tool for analyzing navigational map reading competencies that can be used in map-based navigation tasks in the real-world. This paper fills this gap by presenting GeoGami NMR Assessment , a test for measuring children’s navigational map reading (NMR) competencies for educational purpose. Our target group are primary school children aged six to ten. The assessment uses configural and directional map information to assess the learning progress of individual children regarding their spatial navigational performance. While we evaluated our GeoGami NMR Assessment for two specific locations, our study design, our script scoring participants’ performances as well as the assessment can easily be adapted by researchers and teachers for their own locations. Our item analysis evaluates difficulties of individual tasks. We validate our assessment and demonstrate, that GeoGami NMR Assessment is suitable to distinguish strong and weak navigational map readers.

Verification of Cartographic Communication Models Using Detection of Map Reading Strategies Based on Eye Movement Recording

ABSTRACT The aim of this paper is to introduce a method that can be used for the verification of cartographic communication models. The authors of the maps were placed in the role of the users of their maps. Then, eye-tracking was utilized to reveal their map reading strategies and compare them with the strategies of other cartographers and cartographic novices. The crucial part of the data analysis was scanpath comparison using the sequence of visited Areas of Interest, which helped quantify map reading strategies’ similarity. The use of the same strategy as the map author used might be a prerequisite for users’ proper understanding of a map reflected by the overlap of the author’s and users’ realities in Koláčný’s model. The overlap was considerable in most cases; however, exceptions in which authors used a different map reading strategy were identified.

Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity

BackgroundIt is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome. Spurious SNPs may result from mapping of reads to unrecognized duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million (44%) heterozygous SNPs. Given that Arabidopsis thaliana (A. thaliana) is highly selfing, and that extensively heterozygous individuals have been removed, we hypothesize that these SNPs reflected cryptic copy number variation.ResultsThe heterozygosity we observe consists of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. Focusing on such pseudo-heterozygosity in annotated genes, we use genome-wide association to map the position of the duplicates. We identify 2500 putatively duplicated genes and validate them using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that transpose together. We also demonstrate that cryptic structural variation produces highly inaccurate estimates of DNA methylation polymorphism.ConclusionsOur study confirms that most heterozygous SNP calls in A. thaliana are artifacts and suggest that great caution is needed when analyzing SNP data from short-read sequencing. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggests that future analyses based on independently assembled genomes will be very informative.

Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

BackgroundThe Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics.ResultsThe performed comparison demonstrates that GeneMind Genolab M sequencing platform produces highly consistent with Illumina NextSeq 2000 sequencing results. Both platforms have similar performance in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. Raw read mapping and following read counting produced highly comparable results that is confirmed by quality control metrics and strong correlation between expression profiles in the same tissue spots. Downstream analysis including dimension reduction and clustering demonstrated similar results, and differential gene expression analysis predominantly detected the same genes for both platforms.ConclusionsGeneMind Genolab M instrument is similar to Illumina sequencing efficacy and is suitable for 10x Genomics Visium spatial transcriptomics.

Climate, cartography, and the life and death of the ‘natural region’ in British geography

During the first fifteen years of the twentieth century, Oxford-based Scottish geographer Andrew Herbertson constructed a framework for comprehending and categorising climate and its interrelations: natural regions. Along with a large circle of students and collaborators, Herbertson promoted natural regions as the conceptual keystone for geographical teaching and research. This article shows how natural regions theory conceived of climate as an object that was differently defined in different academic disciplines. Geography’s climate, according to Herbertson and his supporters, was defined by its relations with other spatially distributed phenomena rather than being the quantifiable and isolable entity of modern climatology. Building on recent work in the history of cartography foregrounding map use and reception, the article also argues that natural regions were products of particular modes of map reading, comparison, and synthesis. Although maps were arguably the most influential medium for communicating natural regions, they also proved limited as bearers of the multiscalar version of climate that Herbertson and his successors sought to convey. Finally, the article explains how natural regions and associated conceptions of climate came to be sidelined in the mid-twentieth century as geographers foregrounded human agency in region formation and adopted climatology’s definitions and analytical tools. Revisiting the life and death of theories of natural regions illuminates the contested significance of climate in the discipline of geography, and contributes to ongoing efforts to pluralise the history of climate sciences.

Kajian Kesiapan Pengguna Google Maps Sebagai Salah Satu Penerapan Sistem Transportasi Cerdas

Information technology in this era can help the users to get what is needed. Measurement of technolgy readiness is necessary with Technology Readiness Index (TRI) approach, to aims determine the readiness level of using technology. On of the technolofy uses in transportation field is application of intelligent transportation system like google maps. A general problem of google maps uses is error reading map or instructions, is cause the user is at in wrong way, like the case of motorcyclist enter the toll road. The author will measure the user's readiness to use a google maps, of academic civitas in Politeknik Rukun Abdi Luhur amounts of 65 peoples, with TRI method measurement. The result is, there are final respondents is 59 peoples. Where, 39 peoples using the method of viewing the display on google maps. The result of TRI measurement indicate that respondents is at medium level which a kumulative value is 3,284. Need an advice to google maps users in using the voice feature to avoid losing focus when driving. Besides that, google maps users also can explore and learn many feature of google maps, like choosing to avoid the toll road for motrocycle

Pitfalls of genotyping microbial communities with rapidly growing genome collections.

Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many tools that perform this metagenotyping rely on aligning reads of unknown origin to a database of sequences from many species before calling variants. In this synthesis, we investigate how databases of increasingly diverse and closely related species have pushed the limits of current alignment algorithms, thereby degrading the performance of metagenotyping tools. We identify multi-mapping reads as a prevalent source of errors and illustrate a trade-off between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we evaluate several actionable mitigation strategies and review emerging methods showing promise to further improve metagenotyping in response to the rapid growth in genome collections. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.

Effectiveness of Rectangular Cartogram for Conveying Quantitative Information: An Eye Tracking-Based Evaluation

A rectangular cartogram is a kind of graphical representation that uses a rectangular area to represent the attributes of geographical objects and is widely used in the representation of statistical data such as population, economic statistics, and epidemic distribution. However, there is currently little research on the effectiveness of rectangular cartograms for conveying quantitative data. In this paper, the rectangular cartogram and unclassed choropleth map are compared to evaluate the rectangular cartogram’s effectiveness in quantity representation through task-driven eye-tracking cognitive experiments. In addition, the accuracy and efficiency of information communication and the differences in the reading processes of map readers when using the two types of maps for different tasks have been analyzed to provide references for more effective use of rectangular cartograms in the future. The main contributions of this paper are: (1) it has been proven by experiments that when completing the four tasks of locate, compare, find extreme, and estimate, the participants have higher accuracy rates with the rectangular cartogram; (2) the reading process shown by the eye tracking experiment shows that the more complex the task is, the more patient the participants would be with the rectangular cartogram, and the more pronounced the advantages of the rectangular cartogram are.