Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering the combinatorial interaction landscape

From cellular activation to drug combinations, the control of biological systems involves multiple stimuli that can elicit complex nonlinear interactions. To elucidate the functions and logic of stimulus interactions, we developed SAIL (Synergistic/Antagonistic Interaction Learner). SAIL uses a machine learning classifier trained to categorize interactions across a complete taxonomy of possible combinatorial effects. The strategy resolves the most informative interactions, and helps infer their functions and regulatory mechanisms. SAIL-predicted interaction mechanisms controlling key immune functions were experimentally validated. SAIL can integrate results from multiple datasets to derive general properties of how cells respond to multiple stimuli. Using public immunological datasets, we assembled a fine-grained landscape of ∼30000 interactions. Analysis of the landscape shows the context-dependent functions of individual modulators, and reveals a probabilistic algebra that links the separate and combined stimulus effects. SAIL is available through a user friendly interface to resolve the effect of stimulus and drug combinations.
Cryptococcus neoformans Chitin Synthase 3 (Chs3) Plays a Critical Role in Dampening Host Inflammatory Responses

Cryptococcus neoformans infections are significant causes of morbidity and mortality among AIDS patients and the third most common invasive fungal infection in organ transplant recipients. One of the main interfaces between the fungus and the host is the fungal cell wall. The cryptococcal cell wall is unusual among human pathogenic fungi in that the chitin is predominantly deacetylated to chitosan. Chitosan deficient strains of C. neoformans were found to be avirulent and rapidly cleared from the murine lung. Moreover, infection with a chitosan deficient C. neoformans lacking three chitin deacetylases (cda1Δ2Δ3Δ) was found to confer protective immunity to a subsequent challenge with a virulent wild type counterpart. In addition to the chitin deacetylases, it was previously shown that chitin synthase 3 (Chs3) is also essential for chitin deacetylase mediated formation of chitosan. Mice inoculated with chs3Δ at a dose previously shown to induce protection with cda1Δ2Δ3Δ die within 36 hours after installation of the organism. Mortality was not dependent on viable fungi as mice inoculated with heat-killed preparation of chs3Δ died at the same rate as mice inoculated with live chs3Δ, suggesting the rapid onset of death was host mediated likely caused by an over exuberant immune response. Histology, cytokine profiling, and flow cytometry indicates a massive neutrophil influx in the mice inoculated with chs3Δ. Mice depleted of neutrophils survived chs3Δ inoculation indicating that death was neutrophil mediated. Altogether, these studies lead us to conclude that Chs3, along with chitosan, plays critical roles in dampening cryptococcal induced host inflammatory responses. IMPORTANCE Cryptococcus neoformans is the most common disseminated fungal pathogen in AIDS patients, resulting in ∼200,000 deaths each year. There is a pressing need for new treatments for this infection, as current antifungal therapy is hampered by toxicity and/or the inability of the host’s immune system to aid in resolution of the disease. An ideal target for new therapies is the fungal cell wall. The cryptococcal cell wall is different than many other pathogenic fungi in that it contains chitosan. Strains that have decreased chitosan are less pathogenic and strains that are deficient in chitosan are avirulent and can induce protective responses. In this study we investigated the host responses to chs3Δ, a chitosan-deficient strain, and found mice inoculated with chs3Δ all died within 36 hours and death was associated with an aberrant hyperinflammatory immune response driven by neutrophils, indicating that chitosan is critical in modulating the immune response to Cryptococcus.
Leaf Abundance Affects Tree Height Estimation Derived from UAV Images

Tree height is an important vegetative structural parameter, and its accurate estimation is of significant ecological and commercial value. We collected UAV images of six tree species distributed throughout a subtropical campus during three periods from March to late May, during which some deciduous trees shed all of their leaves and then regrew, while other evergreen trees kept some of their leaves. The UAV imagery was processed by computer vision and photogrammetric software to generate a three-dimensional dense point cloud. Individual tree height information extracted from the dense photogrammetric point cloud was validated against the manually measured reference data. We found that the number of leaves in the canopy affected tree height estimation, especially for deciduous trees. During leaf-off conditions or the early season, when leaves were absent or sparse, it was difficult to reconstruct the 3D canopy structure fully from the UAV images, thus resulting in the underestimation of tree height; the accuracy improved considerably when there were more leaves. For Terminalia mantaly and Ficus virens, the root mean square errors (RMSEs) of tree height estimation reduced from 2.894 and 1.433 m (leaf-off) to 0.729 and 0.597 m (leaf-on), respectively. We provide direct evidence that leaf-on conditions have a positive effect on tree height measurements derived from UAV photogrammetric point clouds. This finding has important implications for forest monitoring, management, and change detection analysis.
Complete genome sequence of Gordonia sp. MMS17-SY073, a soil actinobacterium

*For correspondence. E-mail: sbk01@cnu.ac. kr; Tel. : +82-42-821-6412; Fax: +82-42-822-7367 An actinobacterial strain designated Gordonia sp. MMS17SY073 (=KCTC 49257) was isolated from a coastal soil of an island, and its complete genome was analyzed. A single contig consisting of 5,962,176 bp with the G + C content of 67.4% was obtained, and the annotation resulted in 5,201 protein-coding genes, 6 rRNA genes and 45 tRNA genes. Strain MMS17SY073 was closest to the type strain of Gordonia soli based on the 16S rRNA gene sequence comparison, sharing 98.5% sequence similarity. A number of biosynthetic gene clusters for secondary metabolites, non-ribosomal peptide synthetase types in particular, could be identified from the genome.
Fish densities associated with structural elements of oil and gas platforms in southern California

There are thousands of offshore oil and gas platforms worldwide that will eventually become obsolete, and one popular decommissioning alternative is the "rigs to reefs" conversion that designates all or a portion of the underwater infrastructure as an artificial reef, thereby reducing the burden of infrastructure removal. The unique architecture of each platform may influence the size and structure of the associated fish assemblage if different structural elements form distinct habitats for fishes. Using scuba survey data from 11 southern California platforms from 1995 to 2000, we examined fish assemblages associated with structural elements of the structure, including the major horizontal crossbeams outside of the jacket, vertical jacket legs, and horizontal crossbeams that span the jacket interior. Patterns of habitat association were examined among three depth zones: shallow (<16.8 m), midwater (16.8–26 m), and deep (>26 m); and between two life stages: young- of-the-year and non-young-of-the-year. Fish densities tended to be greatest along horizontal beams spanning the jacket interior, relative to either horizontal or vertical beams along the jacket exterior, indicating that the position of the habitat within the overall structure is an important characteristic affecting fish habitat use. Fish densities were also higher in transects centered directly over a vertical or horizontal beam relative to transects that did not contain a structural element. These results contribute to the understanding of fish habitat use on existing artificial reefs, and can inform platform decommissioning decisions as well as the design of new offshore structures intended to increase fish production.
Temporal contiguity training does not affect size-tolerant representations in object-selective cortex

The human visual system has a remarkable ability to reliably identify objects across variations in appearance, such as variations in viewpoint, lighting and size. Here we used fMRI in humans to test whether temporal contiguity training with natural and altered image dynamics can respectively build and break neural size tolerance for objects. Participants (N = 23) were presented with sequences of images of “growing” and “shrinking” objects. In half of the trials, the object also changed identity when the size change happened. According to the temporal contiguity hypothesis, and studies with a similar paradigm in monkeys, this training process should alter size tolerance. After the training phase, BOLD responses to each of the object images were measured in the scanner. Neural patterns in LOC and V1 contained information on size, similarity and identity. In LOC, the representation of object identity was partially invariant to changes in size. However, temporal contiguity training did not affect size tolerance in LOC. Size tolerance in human object-selective cortex is more robust to variations in input statistics than expected based on prior work in monkeys supporting the temporal contiguity hypothesis.
Lymph node follicle formation and vaccination responses reconstituted in vitro in a human Organ Chip

Candidate vaccines and immunotherapeutic drugs often fail in clinical trials as human lymph node (LN) physiology is not faithfully modeled in animal models or immune cell cultures. Here we describe a microfluidic Organ Chip culture device that supports self-assembly of human blood-derived B and T lymphocytes into three-dimensional (3D), germinal center-like lymphoid follicles (LFs) containing Activation-Induced Cytidine Deaminase (AID) expressing lymphocytes. These microengineered LFs support plasma cell differentiation upon activation with IL-4 and CD40 agonistic antibody (AB) or inactivated S. aureus Cowan I (SAC). Immunization of the human LN chip with a quadrivalent split virion influenza vaccine resulted in plasma cell formation, viral strain-specific anti-hemagglutinin immunoglobulin G (IgG) production, and a secreted cytokine profile that recapitulates serum responses of vaccinated humans. Thus, the human LN chip may provide a new tool to study human immune reactions, evaluate vaccine responses, and validate the efficacies and toxicities of immunotherapies in vitro.
Analysis of mitochondrial transcription and replication on the single nucleoid level

Human mitochondrial DNA (mtDNA) is a circular molecule encoding for 13 subunits of the respiratory chain that are essential for its maintenance. Inside the mitochondria, mtDNA is associated with various proteins, forming a nucleoprotein complex termed a nucleoid. Mutations of the mtDNA as well as deviations in the composition of the associated proteins are implicated in a variety of diseases in humans. However, the regulation of the basic nucleoid functions, i.e. replication and transcription on the single nucleoid level is poorly understood. Human cells contain up to several hundreds of nucleoids, each with an average diameter of about 80 nm. Since nucleoids cluster together within mitochondria, the resolution and analysis of single nucleoids is impaired in diffraction-limited microscopy methods. In this work, nanoscopy is used to visualize single nucleoids and to address fundamental questions about the transcription and replication of mtDNA. For this purpose, a robust staining protocol to identify nucleoids engaged in replication or transcription, was established based on the incorporation of synthetic nucleosides. Three-color STED nanoscopy revealed the organization of nucleoids into at least two subpopulations within single cells. The results of this study indicate that nucleoids can either be active with a tendency to be engaged in both processes or seemingly totally inactive. This finding provides new explanations for the high copy number of the mitochondrial genome. In addition, the approach developed here was used to analyze knockdown cells of important key players of mitochondrial regulation, namely, the mitochondrial RNA Polymerase POLRMT and mitochondrial elongation factor TEFM. POLRMT is required for functional transcription and synthesis of the replication primer, while the switch between mitochondrial transcription and replication is mediated by TEFM. The present work demonstrates that POLRMT and TEFM together coordinate whether the mtDNA is used as a template for transcription or replication. Upon POLRMT reduction, transcription is favored over replication of mtDNA, whereas a decrease in the expression of TEFM leads to increased replication. This provides fundamental insights into the reciprocal regulation of mitochondrial transcription and replication.
Nasal and Indoors Fungal Contamination in Healthy Subjects

Background: Fungi are regarded as one of causal factors of respiratory allergies and are a serious threat to public health in indoor environments. Before conclusively identifying fungi as the major causative agent of all or some types of rhinitis, we should have a good knowledge of the fungal flora of the nasal cavity and indoor building environments of healthy subjects. Objectives: The aim of this study was to determine the presence and relative abundance of fungal flora in the nasal cavity and bedroom of healthy subjects in Mashhad city, north east of Iran. Patients and Methods: A group of fifty healthy volunteers without a history of respiratory system diseases were selected. Samples from the nasal cavity and different parts of the bedroom including indoor air, pillow, mattress, blanket, dust of the bed, dust of the shelf and dust of the air duct were collected and cultured. The fungi were identified by standard mycological techniques. Results: The most common fungi isolated from all samples were Aspergillus, Penicillium, Yeast, Alternaria and Cladosporium. Stemphylium, Ulocladium, Stachybotrys, Basidiobolus and Exophiala showed the least frequencies among the isolated fungi. Conclusions: The presence of fungi in the nasal cavity and indoors of healthy subjects in this study suggests that fungi should be considered as health hazards. Furthermore, it is important and seems necessary to monitor indoor air quality and raise awareness of existing threats due to microorganisms, including fungi.
Studies on Genetic Divergence and Canonical Analysis in Slender Grain Rice (Oryza sativa L.)

Rice, the most widely grown and consumed cereal crop, is the lifeline for more than half of the world’s population. It is the staple food for more than 65% of Indian population contributing approximately 40% to the total food grain production, occupying a pivotal role in the food, nutrition and livelihood security of the people. The country has the world’s largest area under rice i.e., about 44 Mha and the second highest production i.e., about 165Mt at productivity of 3.65 t/ha. Production of rice has increased more than five times since 1950-51. The source of growth is mostly increase in yield, which has increased by 3.6 times and marginally area which has increased by 1.4 times during the period (Pathak et al., 2018). Rice is the only cereal that is consumed as whole grain; its quality preferences too are diverse. Global demand of rice is likely to increase from the current 740 Mt to about 825 Mt in 2030. To meet this demand we need another quantum jump in rice production keeping in mind the quality preferences of this generation. The International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 8 Number 08 (2019) Journal homepage: http://www.ijcmas. com
Cortical contraction drives the 3D patterning of epithelial cell surfaces

Cellular protrusions create complex cell surface topographies, but biomechanical mechanisms regulating their formation and arrangement are largely unknown. To study how protrusions form, we focused on the morphogenesis of microridges, elongated actin-based structures projecting from the apical surfaces of zebrafish skin cells that are arranged in labyrinthine patterns. Microridges form by accreting simple finger-like precursors. Live imaging demonstrated that microridge morphogenesis is linked to apical constriction. A non-muscle myosin II (NMII) reporter revealed pulsatile contractions of the actomyosin cortex; inhibiting NMII demonstrated that contractions are required for apical constriction and microridge formation. A biomechanical model suggested that contraction reduces surface tension to permit the fusion of precursors into microridges. Indeed, reducing surface tension with hyperosmolar media promoted microridge formation. In anisotropically stretched cells, microridges formed by precursor fusion along the stretch axis, which computational modeling explained as a consequence of stretch-induced cortical flow. Collectively, our results demonstrate how contraction within the 2D plane of the cortex patterns 3D cell surfaces. SUMMARY Microridges, elongated 3D protrusions arranged in maze-like patterns on zebrafish skin cells, form by the accretion of simple precursor projections. Modeling and in vivo experiments showed that cortical contractions promote the coalescence of precursors into microridges by reducing membrane tension.
Biocontrol of sheep blowfly: is there a role for pathogen-based biopesticides?

ABSTRACT Blowflies cause a serious and debilitating disease of sheep in many countries. Reliance on the prophylactic use of chemicals for sheep protection is threatened by resistance and increasing awareness of the non-target and environmental consequences of their use. Further, consumer awareness of animal welfare issues is highlighting both the disease itself and some of the practices used to prevent it. Alternative approaches to fly control will likely be needed in future to maintain production and welfare levels. A range of fungal and bacterial pathogens are known to attack blowflies with some previously being investigated as potential biopesticides, however, to date none have been commercialised. Although much still remains to be discovered, the host–pathogen interaction appears complicated with the pathogen producing a range of compounds to facilitate invasion of the host and evasion of host defence mechanisms. While bacteria need to be ingested to infect a host, fungi appear to primarily invade through the cuticle. Fungal infection of adult flies can occur rapidly through the tarsi suggesting that only limited tactile contact is required. Many pathogens are intolerant of high temperatures such that their utility as prophylactic treatments, applied to sheep, may be limited. Also, while infected flies may not die rapidly, infection may result in behavioural changes and reduced fecundity, factors which need to be considered when evaluating the impact of pathogens. The use of pathogens in lure-and-kill strategies against adult flies or applied to pastures targeting pupal stages warrants further investigation.
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation

The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, we characterize the arrangement of cones in individual Y-Junction cores as well as the spatial distribution of Y-junctions across entire retinae. We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals. In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery. In physical crystals, regardless of the initial distribution of defects, grain boundaries can form via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion. Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries. In contrast to paradigmatic models of fate specification in mostly motionless cell packings, this study emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries. AUTHOR SUMMARY From hair cells in the mammalian inner ear to the bristles on a fly’s back, sensory cells often form precise arrays, ensuring that these cells are evenly spread out on the tissue’s surface. Here we consider the zebrafish cone mosaic, a crystal of cone photoreceptors in the outer retinal layer. Because the cone mosaic grows from the rim of the curved retinal surface, new rows of cones (i.e., defects) are inserted to maintain constant spacing between sensory cells. We study the spatial distribution of these defects to gain insight into how the cone pattern forms. By imaging retinae in live fish, we find that as differentiating cones are incorporated into the mosaic, defects form lines (grain boundaries) that separate mostly defect-free domains. Then, we show that a computational model based on repulsion between mobile cells during their incorporation into the mosaic generates similar grain boundaries. This study thus suggests that cell motion governed by repulsive cell-cell interactions can play an important role in establishing regular patterns in living systems.
The complete chloroplast genome sequence of Ludisia discolor from Hainan of China

Abstract Ludisia discolor is one of the most important ornamental and medicinal orchids. To improve our understanding of the evolution of chloroplast, we resequenced complete chloroplast (cp) genome of L. discolor from Hainan, China. The cp genome sequence of L. discolor of Hainan was 153,324 bp in length, with a large single-copy (LSC) region of 82,922 bp, a small single-copy (SSC) region of 17,258 bp, and a pair of inverted repeats (IR) regions of 26,572 bp. Complete chloroplast genome contain 132 genes, there were 86 protein-coding genes, 38 tRNA genes and eight rRNA genes. The phylogenetic tree showed that L. discolor of Hainan is sister to L. discolor (unknown distributed region). Their cp genomes have same gene number but different in length of genome, indicating high conserved among them.