Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Spatial-Resolution Multi-Omics Atlas Sequencing of Mouse Embryos via Deterministic Barcoding in Tissue

Spatial gene expression heterogeneity plays an essential role in a range of biological, physiological and pathological processes but it remains a scientific challenge to conduct high-spatial-resolution, genome-wide, unbiased biomolecular profiling over a large tissue area. Herein, we present a fundamentally new approach – microfluidic Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq). Parallel microfluidic channels (10μm, 25μm, or 50μm in width) are used to deliver molecular barcodes to the surface of a formaldehyde fixed tissue slide in a spatially confined manner. Crossflow of two sets of barcodes A1-A50 and B1-B50 followed by ligation in situ yields a 2D mosaic of tissue pixels, each containing a unique combination of full barcode AiBj (i=1-50, j=1-50). It permits simultaneous barcoding of mRNAs, proteins, or even other omics on a fixed tissue slide, enabling the construction of a high-spatial-resolution multi-omics atlas by NGS sequencing. Applying it to mouse embryo tissues revealed all major tissue types in early organogenesis, distinguished brain microvascular networks, discovered new developmental patterning in forebrain, and demonstrated the ability to detect a single-cell-layer of melanocytes lining an optical vesicle and asymmetric expression of Rorb and Aldh1a1 within it, presumably associated with the onset of retina and lens, respectively. Automated feature identification using spatial differential expression further identified dozens of developmental features. DBiT-seq is a highly versatile technology that may become a universal method for spatial barcoding and sequencing of a range of molecular information at a high resolution and the genome scale. It can be readily adopted by biologists with no experience in microfluidics or advanced imaging, and could be quickly disseminated for broader impacts in a variety of fields including developmental biology, cancer biology, neuroscience, and clinical pathology.
Characterisation of the complete mitochondrial genome of Bactrocera ruiliensis (Diptera: Tephritidae), with its phylogenetic analysis

Abstract The complete mitochondrial genome (mitogenome) of the Bactrocera ruiliensis (Diptera: Tephritidae: Dacinae) is sequenced and annotated. The mitochondrial genome is 15,870 bp (GenBank No. MN477221) and has an A + T content of 73.3% (A 39.2%; C 16.2%; G 10.3%, and T 34.4%), which is the classical structure for insect mitogenome. All PCGs started with ATN, except ATP8, which is started with TTG; 12 PCGs use TAR (TAA/TAG) as the stop codon, except COX1, which ends with single T––. The phylogenetic tree confirms that B. ruiliensis clustered with other Bactrocera species. This study enriches the mitogenomes of the fruit flies.
The complete plastome of Peucedanum praeruptorum (Apiaceae)

Abstract Peucedanum praeruptorum is an important traditional herbal medicine unique to China. The complete chloroplast genome of P. praeruptorum was generated here using high-throughput sequencing. The plastome was 147,197 bp in size, which consisted of a pair of inverted repeats (IRs; 18,713 bp), a large single copy (LSC; 92,161 bp) and a small single copy (SSC; 17,610 bp). The GC content of the plastome was 37.6%, with 44.5%, 36.0%, and 31.1% in IRs, LSC, and SSC, respectively. A total of 128 genes were annotated, including 84 protein-coding genes, 35 tRNAs, eight rRNAs, and one pseudogene (Ψycf1). The phylogenomic analysis indicated that P. praeruptorum formed a monophyletic clade with Peucedanum japonicum.
Deep analytics for workplace risk and disaster management

We discuss dynamic real-time analysis from multimodal data fusion for contextual risk identification to generate “risk maps” for the workplace, resulting in timely identification of hazards and associated risk mitigation. It includes new machine/deep learning, analytics, methods, and its applications that deal with the unconventional data collected from pictures, videos, documents, mobile apps, sensors/Internet of Things, Occupational Safety and Health Administration (OSHA) rules, and Building Information Model (BIM) Models. Specifically, we describe a number of advances and challenges in this field with applications of computer vision, natural language processing, and sensor data analysis. Applications include automated cause identification, damage prevention, and disaster recovery using current and historical claims data and other public data. The methods developed can be applied to any given situation with different groups of people, including first responders. Finally, we discuss some of the important nontechnical challenges related to business practicality, privacy, and industry regulations.
Natural Selection For Disease Resistance In Hybrid Poplars Targets Stomatal Patterning Traits And Regulatory Genes.

The evolution of disease resistance in plants occurs within a framework of interacting phenotypes, balancing natural selection for life-history traits along a continuum of fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant populations connected by gene flow are physiologically limited to evolving along a single axis of the spectrum of the growth-defense trade-o , and strong local selection can purge phenotypic variance from a population or species, making it di cult to detect variation linked to the trade-o . Hybridization between two species that have evolved di erent growth-defense trade-o optima can reveal trade-o s hidden in either species by introducing phenotypic and genetic variance. Here, I investigated the phenotypic and genetic basis for variation of disease resistance in a set of naturally formed hybrid poplars. The focal species of this dissertation were the balsam poplar (Populus balsamifera), black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from natural populations and clonally replicated in a common garden. Ecophysiology and stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae) were collected. To overcome the methodological bottleneck of manually phenotyping stomata density for thousands of cuticle micrographs, I developed a publicly available tool to automatically identify and count stomata. To identify stomata, a deep convolutional neural network was trained on over 4,000 cuticle images of over 700 plant species. The neural network had an accuracy of 94.2% when applied to new cuticle images and phenotyped hundreds of micrographs in a matter of minutes. To understand how disease severity, stomata, and ecophysiology traits changed as a result of hybridization, statistical models were fit that included the expected proportion of the genome from either parental species in a hybrid. These models indicated that the ratio of stomata on the upper surface of the leaf to the total number of stomata was strongly linked to disease, was highly heritable, and wass sensitive to hybridization. I further investigated the genomic basis of stomata-linked disease variation by performing an association genetic analysis that explicitly incorporated admixture. Positive selection in genes involved in guard cell regulation, immune system negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis were identified. Together, my dissertation incorporated advances in image-based phenotyping with evolutionary theory, directed at understanding how disease frequency changes when hybridization alters the genomes of a population.
FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these phylogenomic challenges. For evolutionary studies in frogs, we introduce the new publicly available FrogCap suite of genomic resources, which is a large and flexible collection of probes corresponding to ∼15,000 markers that unifies previous frog sequencing work. FrogCap is designed to be modular, such that subsets of markers can be selected based on the phylogenetic scale of the intended study. FrogCap uses a variety of molecular marker types that include newly obtained exons and introns, previously sequenced UCEs, and Sanger-sequencing markers, which span a range of alignment lengths (100–12,000 base pairs). We tested three probe sets from FrogCap using 105 samples across five phylogenetic scales, comparing probes designed using a consensus- or genome-based approach. We also tested the effects of using different bait kit sizes on depth of coverage and missing data. We found that larger bait kits did not result in lowered depth of coverage or increased missing data. We also found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We observed sequence capture success (in terms of missing data, quantity of sequence data, recovered marker length, and number of informative sites) and compared them at all phylogenetic scales. The incorporation of different molecular marker types allowed recovery of the variation required for resolving difficult phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for performing high-throughput sequencing projects across variable timescales.
Domestication in Real Time: The Curious Case of a Trigenomic Sunflower Population

This study chronicles the ongoing process to domesticate an interspecific trigenomic tetraploid hybrid sunflower derived from a series of interspecific crosses between Helianthus annuus and Helianthus tuberosus. The goal of this process is to develop a perennial oilseed crop that can produce both high value vegetable oil and continuous ground-cover. Selection has focused on developing an ideotype with the domesticated morphology of H. annuus and the below-ground perennial features of H. tuberosus. The overarching challenge in the process of breeding and domesticating this interspecific perennial sunflower is overcoming obstacles associated with interploid meiosis in order to resolve a chromosomally stable hybrid population. As selection progresses through generations of intermating, there are improvements toward the desired ideotype, but selection efficiency is slowed by apparent antagonisms between annual- and perennial morphological targets and irregular meiosis which is especially problematic in a trigenomic tetraploid. This shows that keys toward perennial crop development through interspecific hybridization will be to capitalize on the abundant phenotypic variation within our population, achieve meiotic stability in order to maximize selection efficiency, and to break genetic correlations between annual and perennial traits.
The influence of Mothers’ Socioeconomic status on Pneumonia in Childhood (Case study in Khartoum State-Sudan)

Children in developing countries suffer the highest burden of pneumonia. However, few studies have evaluated associations between socioeconomic status of mothers and prevalence of pneumonia among their children. A prospective population-based study on pneumonia was carried in Khartoum State. Sample size was 400 families, the main respondents were mothers. Different quantitative and qualitative methods of data collection were used (questionnaires, interviews, focus groups, and observations). The prevalence of pneumonia and anthropometric measurement were performed for children under ten years old. The study found that income was the strongest influencing factor (P=0.000) affecting negatively the prevalence of pneumonia among children through affecting many standards of living. Also there is strong relation between mothers’ education and children pneumonia (P=0.05). Therefore, the government must give more attention to mother's education, and adopt more effective policies to improve the standards of living in general.
Expression of Secondary Metabolite Gene Clusters and Production of Secondary Metabolites in Three Nostoc strains Subjected to Deprivation on Nutrients and Competition

II TABLE OF CONTENT . III ABBREVIATIONS . V INTRODUCTION . 1 A prokaryote with photosynthesis – The cyanobacteria . 1 Morphology . 2 Nutrition . 3 Habitats . 3 Nostocales . 4 Production of secondary metabolites . 5 Biosynthesis of secondary metabolites . 6 Non-ribosomal peptide synthases . 7 Hybrid pathways (NRPS/PKS) . 8 Anabaenopeptins . 8 Aeruginosins . 9 Nostopeptolides & Nostocyclopeptides . 11 Polyketide Synthases . 12 Ribosomal peptide synthesis of complex peptides (RiPP) . 12 Bioinformatics as a tool for finding novel nature products . 15 Subject of study; Nostoc spp. KVJ20, KVJ10 & KVJ2 . 16 AIM . 17 METHODS AND EQUIPMENT . 18 Workflow . 18 Cultivation conditions. 20 Experimental setup . 20 Bioinformatics . 22 Primer design . 22 Primer test . 23 RNA extraction . 24 cDNA synthesis . 24 Reverse transcription quantitative PCR . 25 Extraction of secondary metabolites . 26 Medium extraction. 26 Cell extraction. 27 Mass Spectrometry . 27 RESULTS . 28 Bioinformatics . 28 Homologous gene clusters . 28 Nostoc KVJ20 . 29 Nostoc KVJ2 . 30 Nostoc KVJ10 . 31 Observed changes associated with different cultivation conditions. 31 Allelopathic experiment . 33 Gene expression patterns . 34 Analysis of gene expression patterns in KVJ20 . 35 Fold changes against respective controls for KVJ20 . 35
Supply-side readiness for universal health coverage : assessing the depth of coverage for non-communicable diseases in Indonesia

Non-communicable diseases (NCDs) account for the largest share of the overall burden of disease in Indonesia. There are several challenges facing effective implementation of universal health coverage (UHC) in Indonesia, both from a health financing and a service delivery perspective. Some key issues from a health financing perspective are the collection of contributions from the non-poor in the informal sector, ensuring adequate fiscal space for financing coverage for the poor and near-poor, managing an effective transition from supply-side to demand-side financing of the health system, reducing out-of-pocket (OOP) payments, and ensuring cost containment and financial sustainability of UHC. This policy paper focuses on the issue of supply-side readiness from the perspective of assessing the effective depth of UHC in Indonesia, especially in rural and remote areas of the country where a large proportion of the poor and near-poor populations reside. It assesses the ability of Indonesia's public primary care health facilities to provide preventive, diagnostic, and curative care for selected tracer NCD conditions: diabetes mellitus (DM), cardiovascular conditions, and chronic respiratory diseases. The paper compares supply-side implications of UHC benefit entitlements as derived from national health facility and program-specific guidelines with the World Health Organization's (WHO's) recommendations for service availability and readiness assessment (SARA) for these same tracer NCD conditions. The focus in the paper is on highlighting gaps in benefit entitlements and service readiness to stimulate policy dialogue on ways to enhance UHC implementation in the country. The policy note is structured as follows: section one gives introduction. Section two provides some background and context related both to NCDs and to UHC in Indonesia. Section three analyzes the benefit package for key tracer NCD conditions, derives the supply-side implications of the benefit package, and compares these implications to the WHO's SARA-recommended indicators. Section four presents results from analysis of data related to the effective depth and distribution of coverage for key NCD conditions in Indonesia. Section five concludes with a summary and some policy implications.
Information processing in the “not-in-my-backyard” strategy: An empirical study of anti-nuclear behavioral responses

Abstract Nuclear power has become an effective way of addressing environmental challenges such as resources depletion and climate change and is consistent with a strategy of sustainable development. However, popular resistance has increased significantly because the potential accident risk poses a tremendous threat to people, property and ecosystems. This study explored the key determinants of the behavioral response to nuclear power plants. The protective action decision model and the heuristic-systematic information processing model were integrated and adapted to construct a hypothetical model emphasizing the important role of information processing strategies in the “not-in-my-backyard” phenomenon. The research verified the arguments by randomly conducting 405 questionnaires. The empirical results show that risk perception and information need are both important in predicting information seeking and behavioral response. Additionally, the results suggest a mediating role of information processing in the relationship between information seeking and behavioral response. Moreover, the results show that systematic processing is different from heuristic processing. Specifically, systematic processing is positively influenced by information seeking and has a negative influence on anti-nuclear behavioral response, but heuristic processing is negatively correlated with information need and positively correlated with behavioral response. Theoretical contributions, policy implications and further research are also discussed.
Not All Molossus are Created Equal: Genetic Variation in the Mastiff Bat Reveals Diversity Masked by Conservative Morphology

The genus Molossus of the free-tailed bat family Molossidae is morphologically conservative and the level of genetic divergence is also low among many species, which has masked the actual species diversity in the genus. We analyzed the evolutionary relationships among species within Molossus using three mitochondrial (COI, Cytb, and 16S RNA), and two nuclear genes (RAG2 and β-fib) from more than 400 specimens across the Neotropics. We also investigated the genetic integrity of currently recognized species, especially those with broad geographic distributions and controversial taxonomic arrangements. Maximum likelihood and Bayesian phylogenetic reconstructions show that some recognized species are not monophyletic. The use of combined mitochondrial and nuclear genes as well as the use of only mitochondrial markers revealed more robust phylogenies than those for individual data sets and those restricted to the two nuclear genes. We recovered the recently described M. fentoni and M. alvarezi, validated M. milleri and M. verrilli as distinct species relative to M. molossus, and confirmed that the name M. barnesi should be considered as a junior synonym of M. coibensis. Additionally, M. rufus appears to be a complex of cryptic species, showing that the broadly distributed genus Molossus is more diverse than previously reported.
Intercropping the Sharp-Leaf Galangal with the Rubber Tree Exhibits Weak Belowground Competition

Intercropping the sharp-leaf galangal with the rubber tree could help to improve the sustainability of the rubber tree planting industry. However, our understanding of belowground competition in such agroforestry systems is still limited. Therefore, we used stable isotope methods (i.e., water δ2H and δ18O and leaf δ13C) to investigate plant water-absorbing patterns and water use efficiency (WUE) in a monocultural rubber plantation and in an agroforestry system of rubber trees and sharp-leaf galangal. We also measured leaf carbon (C), nitrogen (N), and phosphorus (P) to evaluate the belowground competition effects on plant nutrient absorption status. Through a Bayesian mixing model, we found that the monocultural rubber trees and the intercropped sharp-leaf galangal absorbed much more surface soil water at a depth of 0–5 cm, while the rubber trees in the agroforestry system absorbed more water from the shallow and middle soil layers at a depth of 5–30 cm. This phenomenon verified the occurrence of plant hydrologic niche segregation, whereas the WUE of rubber trees in this agroforestry system suggested that the competition for water was weak. In addition, the negative correlation between the leaf P concentration of the rubber trees and that of the sharp-leaf galangal demonstrated their competition for soil P resources, but this competition had no obvious effects on the leaf nutrient status of the rubber trees. Therefore, this study verified that the belowground competition between rubber trees and sharp-leaf galangal is weak, and this weak competition may benefit their long-term intercropping.
Mc1r Genotype and Plumage Colouration in Highly Polymorphic Jackal Buzzards, Buteo rufofuscus

Evolution is driven by natural selection acting on variable phenotypic traits. Understanding the molecular basis of those traits is crucial for elucidating the mechanisms of natural selection. The southern African jackal buzzard (Buteo rufofuscus) displays extreme plumage colour polymorphism, with colouration on the chest varying from dark black to pale white. In a number of birds and other vertebrates, genetic variation at the melanocortin-1 receptor (Mc1r) gene is associated with melanin-based colour variation. Here, the Mc1r gene was sequenced from 12 jackal buzzard individuals displaying three distinct colour morphs (dark, intermediate and pale). A single nucleotide change was found, which although it resulted in an amino acid change, was shared by all jackal buzzards irrespective of colour morph. Although the Mc1r has played an important role in colour polymorphism in other species, in this study no association between Mc1r genotype and plumage polymorphism in jackal buzzards was found.
Characterization of Microbial Communities Populating the Inflorescences of Humulus lupulus L.

Abstract The aerial portion of plants (phyllosphere) harbors complex and diverse microbial communities that have been shown to influence host growth and fitness, tolerance to environmental stressors, disease susceptibility, and the productivity of economically significant crops. However, despite its reproductive importance to the host and economic value, the microbial ecology of anatomical flowers (anthosphere) remains largely uninvestigated. Here a culture-independent assessment of bacterial communities on freshly harvested and dried inflorescences of eight hop varieties (Humulus lupulus L.), using Illumina MiSeq 16S platform-based rRNA gene sequence analysis, is reported. The results reveal the hops anthosphere is dominated by a single taxonomic phylum, the Proteobacteria, where at least 60% of the sequences are attributed across two genera, Pseudomonas (Gammaproteobacteria) and Sphingomonas (Alphaproteobacteria). Chao1 diversity analysis indicated the presence of many very rare taxa across all varieties. Beta-diversity analysis resolved, from the comparison of unweighted and weighted UniFrac distances, the absence of distinct clustering between freshly harvested and dried hops or between hop varieties. The prevalence of Proteobacteria associated with hop inflorescences is consistent with other anthosphere microbiomes; however, presently the predominance of Gammaproteobacteria in the phyllosphere appears to be a distinct characteristic of the hops microbiome.