Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Illustrates That Genomic Selection Provides New Opportunities for Intercrop Breeding

Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pests and diseases. Especially in subsistence agriculture, intercropping has great potential to optimize farming and increase profitability. However, breeding for intercrop varieties is complex as it requires simultaneous improvement of two or more component crops that combine well in the field. We hypothesize that genomic selection can significantly simplify and accelerate the process of breeding crops for intercropping. Therefore, we used stochastic simulation to compare four different intercrop breeding programs implementing genomic selection and an intercrop breeding program entirely based on phenotypic selection. We assumed three different levels of genetic correlation between monocrop grain yield and intercrop grain yield to investigate how the different breeding strategies are impacted by this factor. We found that all four simulated breeding programs using genomic selection produced significantly more intercrop genetic gain than the phenotypic selection program regardless of the genetic correlation with monocrop yield. We suggest a genomic selection strategy which combines monocrop and intercrop trait information to predict general intercropping ability to increase selection accuracy in the early stages of a breeding program and to minimize the generation interval.
Canonical goal-selective representations are absent from prefrontal cortex in a spatial working memory task requiring behavioral flexibility

The prefrontal cortex (PFC)’s functions are thought to include working memory, as its activity can reflect information that must be temporarily maintained to realize the current goal. We designed a flexible spatial working memory task that required rats to navigate - after distractions and a delay - to multiple possible goal locations from different starting points and via multiple routes. This made the current goal location the key variable to remember, instead of a particular direction or route to the goal. However, across a broad population of PFC neurons, we found no evidence of current-goal-specific memory in any previously reported form - i.e. differences in the rate, sequence, phase or covariance of firing. This suggests such patterns do not hold working memory in the PFC when information must be employed flexibly. Instead, the PFC grouped locations representing behaviorally equivalent task features together, consistent with a role in encoding long-term knowledge of task structure.
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations

The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. ABSTRACT Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or “species”). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.
Interannual differences in growth and hatch‐date distributions of early juvenile European anchovy in the Bay of Biscay: implications for recruitment

In order to understand better the recruitment variability in European anchovy in the Bay of Biscay, it is important to investigate the processes that affect survival during the early life stages. Anchovy juvenile growth trajectories and hatch-date distributions were inferred over a 3-year period based on otolith microstructure analysis. Otolith growth trajectories showed a characteristic shape depending on their hatch-date timing. Earlier-born juveniles had notably broader maximum increments than later born conspecifics, resulting in higher growth rates. This observation suggests that early hatching would be beneficial for larval and juvenile growth, and, therefore, survival. The estimated juvenile hatch-date distributions were relatively narrow compared with the extended anchovy spawning season (March–August) in the Bay of Biscay and indicated that only individuals originated mainly from the summer months (June–August) survived until autumn. Hatch-date distributions were markedly different among years and seemed to influence the interannual recruitment strength of anchovy. We conclude that years characterized by juvenile survivors originating from the peak spawning period (May and June) would lead to considerable recruitment success. Downwelling events during the peak spawning period seem to affect larval survival. Furthermore, size-dependent overwinter mortality would be an additional process that regulates recruitment strength in the anchovy population in the Bay of Biscay.
Transcriptional Up-Regulation of Grapevine MLO Genes in Response to Powdery Mildew Infection

Mildew resistance locus o (MLO) proteins are plant-specific seven-transmembrane (7TM) proteins that are thought to play a role in vesicle trafficking to the plasma membrane. Certain members of the MLO gene family are required for powdery mildew (PM) fungi (Erysiphales) to establish a pathogenic interaction with their plant hosts. Such MLO genes increase in transcription in response to PM infection, and the loss of their function confers broad-spectrum resistance to PM pathogens in barley, tomato, and Arabidopsis thaliana. In this study, a 17-member MLO gene family has been identified in the genome sequence of Vitis vinifera. Fourteen genes of the VvMLO family have been shown to be transcribed at various levels in shoot tips, flower buds, flowers, and leaves. Two VvMLOs increased in transcription in response to the grapevine-adapted PM fungus Erysiphe necator. The predicted polypeptides encoded by these two PM-responsive VvMLOs clustered in the same phylogenetic clade as AtMLO2, AtMLO6, and AtMLO12, proteins that are required by the PM fungus Golovinomyces orontii for causing disease on A. thaliana. The PM-responsiveness of these grapevine genes and their relatedness to AtMLOs suggest that a grapevine MLO gene (or genes) may also be involved in the pathogenesis of E. necator.
Potential Vorticity Mixing and Rapid Intensification in the Numerically Simulated Supertyphoon Haiyan (2013)

The inner-core dynamics of Supertyphoon Haiyan (2013) undergoing rapid intensification (RI) are studied with a 2-km-resolution cloud-resolving model simulation. The potential vorticity (PV) field in the simulated storm reveals an elliptical and polygonal-shaped eyewall at the low and middle levels during RI onset. The PV budget analysis confirms the importance of PV mixing at this stage, that is, the asymmetric transport of diabatically generated PV to the storm center from the eyewall and the ejection of PVfilaments outside the eyewall. We employ a piecewise PV inversion (PPVI) and an omega equation to interpret the model results in balanced dynamics. The omega equation diagnosis suggests eye dynamical warming is associated with the PVmixing. The PPVI indicates that PVmixing accounts for about 50%of the central pressure fall duringRI onset. The decrease of central pressure enhances the boundary layer (BL) inflow. The BL inflow leads to contraction of the radius of the maximum tangential wind (RMW) and the formation of a symmetric convective PV tower inside the RMW. The eye in the later stage of the RI is warmed by the subsidence associated with the convective PV towers. The results suggest that the pressure change associated with PV mixing, the increase of the symmetric BL radial inflow, and the development of a symmetric convective PV tower are the essential collaborating dynamics for RI. An experiment with 500-m resolution shows that the convergence of BL inflow can lead to an updraft magnitude of 20 m s and to a convective PV tower with a peak value of 200 PVU (1 PVU 5 10 K kg m s).
Nanomotors Sense Local Physicochemical Heterogeneities in Tumor Microenvironments**

Abstract The invasion of cancer is brought about by continuous interaction of malignant cells with their surrounding tissue microenvironment. Investigating the remodeling of local extracellular matrix (ECM) by invading cells can thus provide fundamental insights into the dynamics of cancer progression. In this paper, we use an active untethered nanomechanical tool, realized as magnetically driven nanomotors, to locally probe a 3D tissue culture environment. We observed that nanomotors preferentially adhere to the cancer‐proximal ECM and magnitude of the adhesive force increased with cell lines of higher metastatic ability. We experimentally confirmed that sialic acid linkage specific to cancer‐secreted ECM makes it differently charged, which causes this adhesion. In an assay consisting of both cancerous and non‐cancerous epithelia, that mimics the in vivo histopathological milieu of a malignant breast tumor, we find that nanomotors preferentially decorate the region around the cancer cells.
SARS‐CoV‐2 multifaceted interaction with human host. Part I: What we have learnt and done so far, and the still unknown realities

SARS‐CoV‐2, the causing agent of the ongoing COVID‐19 pandemic, is a beta‐coronavirus which has 80% genetic homology with SARS‐CoV, but displays increased virulence and transmissibility. Initially, SARS‐CoV‐2 was considered a respiratory virus generally causing a mild disease, only severe and fatal in the elderly and individuals with underlying conditions. Severe illnesses and fatalities were attributed to a cytokine storm, an excessive response from the host immune system. However, with the number of infections over 10 millions and still soaring, the insidious and stealthy nature of the virus has emerged, as it causes a vast array of diverse unexpected symptoms among infected individuals, including the young and healthy. It has become evident that besides infecting the respiratory tract, SARS‐CoV‐2 can affect many organs, possibly through the infection of the endothelium. This review presents an overview of our learning curve with the novel virus emergence, transmission, pathology, biological properties and host‐interactions. It also briefly describes remedial measures taken until an effective vaccine is available, that is non‐pharmaceutical interventions to reduce the viral spread and the repurposing of existing drugs, approved or in development for other conditions to eliminate the virus or mitigate the cytokine storm.
Teaching virtual protein‐centric CUREs and UREs using computational tools

Readily available, free, computational approaches, adaptable for topics accessible for first to senior year classes and individual research projects, emphasizing contributions of noncovalent interactions to structure, binding and catalysis were used to teach Course‐based Undergraduate Research Experiences that fulfil generally accepted main CURE components: Scientific Background, Hypothesis Development, Proposal, Experiments, Teamwork, Data Analysis of quantitative data, Conclusions, and Presentation.
Rapid Isolation of High-quality RNA from High Phenol-,Polysaccharide Plants

High-quality biologically active RNA isolation is crucialin plant molecular biological experiment.Many plants have high levels of endogenous phenolics,polysaccharides,and secondary metabolityes,so isolating high-quality biologically active RNA from these plants is very difficult.In this paper,a modified LiCl RNA preparation method was developed to isolate RNA from cotton young plant,to yields high-quality total RNA.Then the high-quality RNAs were successfully isolated under this method from banana leaf,cassava leaf and banana root.All these results showed that the modified LiCl RNA preparation method is universal to isolate high-quality RNA from those plants that have high levels of endogenous phenolics and polysaccharides.
APPLICATION OF MONOCLONAL ANTIBODIES TO IMMUNOHISTOCHEMISTRY

Since Kohler and Milstein (9) developed a method to prepare the monoclonal antibody (McAb), the antibody has widely used in every field of biological science. As is well known, the McAb recognizes only one determinant of the antigen with high specificity and contains antibody class or subclass in the uniform pattern. Moreover, the hybridoma, once established, produces the homogeneous antibody molecule in the culture media continuously. On the other hand, McAb does not precipitate the antigen in the form of the immune complex of the large molecule, and shows cross-reactivity (11). In the application of McAb to immunohistochemical studies, it is necessary to
Altered skeletal maturation in moderate to severe cerebral palsy

Abnormalities of growth and development are prevalent in children with cerebral palsy (CP). The purpose of this study was to assess skeletal maturation (‘bone age’) in this population and to identify those factors related to alterations in this aspect of development. The study group was a convenience sample of 80 participants (47 males, 33 females; age range 2y 6mo to 21y 1mo; mean age 10y 10mo, SD 4y 2mo). All had moderate to severe spastic or mixed spastic CP at Gross Motor Function Classification System level III (n=8, 10%); level IV (n=21, 26%); or level V (n=51, 64%). Skeletal maturation was assessed by the detailed Fels method of scoring hand‐wrist radiographs. Each evaluation included clinical and anthropometric assessments, Tanner staging, bone density measurements, and the Children's Health Status Questionnaire. Follow‐up evaluations were obtained for 41 participants, providing a total of 143 evaluations. Median interval between first and last evaluations was 24.7 months (range 11.9 to 45mo). For the study group as a whole there was no significant difference between a child's skeletal age and chronological age. However, there was a high prevalence of individual participants in whom skeletal age was advanced (7%) or delayed (10%), relative to chronological age, by more than 2 years. In multivariant analyses it was found that diminished linear growth (height), low lumbar‐spine bone density, and low body fat as measured by triceps skinfolds were all independently associated with delays in skeletal maturation. Multiple aspects of skeletal growth and development, including skeletal maturation, are frequently altered in children with moderate to severe CP.
A SECURE DATA SHARING AND REVOCATION IN CLOUD USING IDE

—In this paper, we presented a secure data sharing and revocation using Identity Based Encryption (IBE) In cloud . Cloud storage means “the storage of data online in the cloud”, however, the cloud storage is not completely trusted. To tackle this issue outsourcing Revocable IBE scheme for efficient key generation and key updating process is introduce. Also to improve the efficiency of cloud server in terms of storage new secure data self-destructing system in cloud computing is used. In this system, each cipher text (encrypted file) is labeled with a time interval. If the attributes associated with the cipher text satisfy the keys access structure and both the time instant is in the allowed time interval then the cipher text is decrypted. After a user -specified end time the data at cloud server will be securely self-destructed.
Nutrient regeneration from feces and pseudofeces of mussel Mytilus edulis spat

Suspension-feeding mussels exert top-down grazing control on primary producers, and provide bottom-up feedback of regenerated nutrients. Besides direct excretion, an important pathway of nutrient regeneration is through the decomposition of feces and pseudofeces, of which mussels can produce large quantities. Information on mussel feces and pseudofeces quality and nutrient regeneration rates is scarce. Feces and pseudofeces, produced in varying proportions, are commonly treated as one pool. We determined nutrient regeneration rates of feces and pseudofeces decomposition in incubations using natural seawater and juvenile Mytilus edulis from spat collectors. Apart from one 1993 trial, our results are the first to present nutrient regeneration dynamics of feces and pseudofeces separately. Dissolved inorganic nitrogen (DIN) and phosphate regeneration continued at stable rates for approximately 3 wk, after which 13.1 and 12.4% of the available N and 8.7 and 7.9% of the available P was regenerated from feces and pseudofeces, respectively. Rates of silicate regeneration declined continuously, which we attribute to its accumulation in the experimental setup. Coinciding environmental levels of DIN and silicate at growth-limiting levels indicate the potential ecological relevance of biodeposit decomposition. Overall DIN regeneration rates were similar between feces and pseudofeces, but depletion of ammonia was initially more rapid for pseudofeces due to stronger nitrification. Phosphate and silicate regeneration rates were 1.1 and 1.4 times greater from feces than pseudofeces, respectively. Future research should clarify the role of bivalve suspension feeders in controlling Si and P availability in coastal ecosystems in relationship to the proportion of pseudofeces generated, which depends on food concentration.
Biogeochemistry and Nutrient Limitation of Microbial Biofilms in Devils Hole, Nevada

Abstract Little is known about the role of microbial biofilms in nutrient cycling and ecosystem processes within desert springs. However, biofilms produce microscale physicochemical variation important to ecosystem function. We used microelectrodes to measure microscale physicochemical (temperature, pH, O2, and H2S) heterogeneity in biofilms at Devils Hole, Nevada. Additionally, we measured water column and pore water nutrient concentrations in 2 autotrophic (Spirogyra, cyanobacteria) and 1 heterotrophic (Beggiatoa) biofilm types. Spirogyra and cyanobacteria followed similar physicochemical trends; however, Spirogyra had more pronounced diurnal and seasonal variation. Oxygen concentrations within the biofilms varied with sample month, light availability, and biofilm type. We also assessed the nutrient limitation of desert spring microbial biofilms using a nutrient-diffusing substrata experiment. Autotrophic and heterotrophic biofilms responded differently to nutrient treatments. The differences between cyanobacteria and Spirogyra have implications on the ecosystem function of desert springs, as well as other ecosystems with diverse biofilm communities, and suggest that a change in microbial biofilms could alter ecosystem biogeochemical dynamics.
Grafting tomato onto tobacco rootstocks is a practical and feasible application for higher growth and leafing in different tobacco–tomato unions

Abstract A previously developed grafting strategy was applied to graft a commercial cultivated variety of tomato (Solanum lycopersicum L. H-2274) onto Nicotiana rustica L. (cv. Hasankeyf) and Nicotiana tabacum L. (cv. Samsun) rootstocks. Higher growth and leafing, and earlier flower onset were found in grafted than in non-grafted and self-grafted plants. Significant 22.7 and 34.3% increases in fruit yield were obtained with Samsun and Hasankeyf rootstocks, respectively. Leaves of tobacco-grafted plants had significantly elevated levels of nicotine, and highest leaf nicotine levels were measured at 90 days after transplantation (DAT). Leaves from upper sampling levels of plants had significantly less nicotine independent of the sampling DAT. Fruits of all tobacco-grafted plants had significantly higher amounts of nicotine than non-grafted scions. Nicotine levels were higher in fruits sampled from lower parts of the plants for different harvest DAT and rootstocks. Increases in leaf nicotine concentration of tobacco-grafted plants were higher when compared with that of fruit. Grafting tomato onto tobacco rootstocks is a practical and feasible application for different tobacco–tomato unions.
Language Edit Distance Approximation via Amnesic Dynamic Programming

In 1975, a breakthrough result of L. Valiant showed that parsing context free grammars can be reduced to Boolean matrix multiplication, resulting in a running time of O ( n ω ) for parsing where ω ≤ 2 . 373 is the exponent of fast matrix multiplication, and n is the string length. Recently, a remarkable result of Abboud, Backers and V. Williams (FOCS 2015) showed that this is essentially optimal; moreover, a combinatorial o ( n 3 ) algorithm is unlikely to exist for the general parsing problem. Language edit distance is a signiﬁcant generalization of the parsing problem, which computes the minimum edit distance of a given string (insertion, deletion and substitution) to any valid string in the language. Clearly, the lower bound for parsing rules out any algorithm running in o ( n ω ) time that can return a nontrivial multiplicative approximation of the language edit distance problem. However, combinatorial algorithms with cubic running time, or algorithms that use fast matrix multiplication, are often not desirable in practice. To break this n ω hardness barrier, in this paper we study additive approximation algorithms for language edit distance. We propose a generic technique of amnesic dynamic programming which, given any high-dimensional dynamic programming problem, selectively forgets some of the intermediate states. By performing fewer look-ups, this speeds up the running time at the cost of returning an approximate answer. We believe that this technique will ﬁnd widespread applications. Our