Miracle-dz/UniFAR-FTUs huggingface dataset:
What Drives Low-Severity Fire in the Southwestern USA?

Many dry conifer forests in the southwestern USA and elsewhere historically (prior to the late 1800’s) experienced fairly frequent surface fire at intervals ranging from roughly five to 30 years. Due to more than 100 years of successful fire exclusion, however, many of these forests are now denser and more homogenous, and therefore they have a greater probability of experiencing stand-replacing fire compared to prior centuries. Consequently, there is keen interest in restoring such forests to conditions that are conducive to low-severity fire. Yet, there have been no regional assessments in the southwestern USA that have specifically evaluated those factors that promote low-severity fire. Here, we defined low-severity fire using satellite imagery and evaluated the influence of several variables that potentially drive such fire; these variables characterize live fuel, topography, climate (30-year normals), and inter-annual climate variation. We found that live fuel and climate variation (i.e., year-of-fire climate) were the main factors driving low-severity fire; fuel was ~2.4 times more influential than climate variation. Low-severity fire was more likely in settings with lower levels of fuel and in years that were wetter and cooler than average. Surprisingly, the influence of topography and climatic normals was negligible. Our findings elucidate those conditions conducive to low-severity fire and provide valuable information to land managers tasked with restoring forest structures and processes in the southwestern USA and other regions dominated by dry forest types.
Additive response to multiple environmental stressors in the seagrass Zostera marina L.

Ongoing climate changes alter a broad range environmental variables in coastal ecosystems, which may lead to changes in species range distributions or collapse of populations. It is often assumed that changes in environmental parameters affect organisms in a nonadditive way and multifactorial experiments are therefore needed to obtain a better prediction of the effects of climate change. We studied experimentally how combinations of high temperature, low light and high nitrogen (HN) availability affect eelgrass (Zostera marina), which is an important foundation species on the northern hemisphere. Plants were cultured under optimal (15°C) and high (25°C) temperature, limiting and saturating light, and low and high ammonium availability in a 3‐factorial design. We found that individual exposure to heat and shade, respectively, had a negative effect on eelgrass while the effect of exposure to HN‐availability alone was less harmful. Exposure to combinations of two or three stressors simultaneously had a stronger (negative) effect on eelgrass than exposure to each stressor individually, but the combined effects of exposure to multiple stressors were largely similar to the expected additive responses. A synergetic effect was only found in case of mortality when eelgrass plants were exposed to all three stressors simultaneously. The effects of exposure to single or multiple stressors could largely be explained from alterations in the C‐budget of the plants: exposure to one or more stressors lowered the acquisition of C, drained the C‐reserves and sometimes allocated energy to defense or repair processes instead of growth resulting in reduced growth and higher mortality.
Bayesian and likelihood placement of fossils on phylogenies from quantitative morphometries

Jointly developing a comprehensive tree of life from living and fossil taxa has long been a fundamental goal in evolutionary biology. One major challenge has stemmed from difficulties in merging evidence from extant and extinct organisms. While these efforts have resulted in varying stages of synthesis, they have been hindered by their dependence on qualitative descriptions of morphology. Though rarely applied to phylogenetic inference, traditional and geometric morphometric data can improve these issues by generating more rigorous ways to quantify variation in morphological structures. They may also facilitate the rapid and objective aggregation of large morphological datasets. I describe a new Bayesian method that leverages quantitative trait data to reconstruct the positions of fossil taxa on fixed reference trees composed of extant taxa. Unlike most formulations of phylogenetic Brownian motion models, this method expresses branch lengths in units of morphological disparity, suggesting a new framework through which to construct Bayesian node calibration priors for molecular dating and explore comparative patterns in morphological disparity. I am hopeful that the approach described here will help to facilitate a deeper integration of neo- and paleontological data to move morphological phylogenetics further into the genomic era.
Planned missing data design: stronger inferences, increased research efficiency and improved animal welfare in ecology and evolution

Ecological and evolutionary research questions are increasingly requiring the integration of research fields along with larger datasets to address fundamental local and global scale problems. Unfortunately, these agendas are often in conflict with limited funding and a need to balance animal welfare concerns. Planned missing data design (PMDD), where data are randomly and deliberately missed during data collection, is a simple and effective strategy to working under greater research constraints while ensuring experiments have sufficient power to address fundamental research questions. Here, we review how PMDD can be incorporated into existing experimental designs by discussing alternative design approaches and evaluating how data imputation procedures work under PMDD situations. Using realistic examples and simulations of multilevel data we show how a variety of research questions and data types, common in ecology and evolution, can be aided by using a PMDD with data imputation procedures. More specifically, we show how PMDD can improve statistical power in detecting effects of interest even with high levels (50%) of missing data and moderate sample sizes. We also provide examples of how PMDD can facilitate improved animal welfare and potentially alleviate research costs and constraints that would make endeavours for integrative research challenging. Planned missing data designs are still in their infancy and we discuss some of the difficulties in their implementation and provide tentative solutions. Nonetheless, data imputation procedures are becoming more sophisticated and more easily implemented and it is likely that PMDD will be an effective and powerful tool for a wide range of experimental designs, data types and problems in ecology and evolution.
Isolation of phosphate solubilizing Pseudomonas strains from apple rhizosphere in the Trans Himalayan region of Himachal Pradesh, India

Total fifteen phosphate solubilizing bacteria were isolated from rhizosphere soil of apple tree on Kings’ B medium belonging to genus Pseudomonas spp. They were characterized on the basis of morphological and biochemical characteristics. Preliminary selection as phosphate solubilizing bacteria were done on the basis of formation of transparent zone around the colony on Pikovskaya’s agar medium containing 0.5% triclcium phosphate (TCP). Maximum in vitro phosphate solubilization on Pikovskaya’s agar plates after 72h incubation at 28°C was shown by An-15-Mg (46 mm), whereas in case of broth, again this strain showed maximum tricalcium phosphate (TCP) solubilization (76 μg/ml). The pH of each inoculated broth was recorded daily and dropped significantly (pH 7.0-3.99). All the Pseudomonas isolates were further evaluated for overall plant growth promoting traits. Greatest siderophore activity was exhibited by An-14-Mg (71.23 %SU) followed by An-15-Mg (70.12 %SU) which were statiscally at par with each other. Whereas, maximum IAA production was observed again in An-15-Mg (95 μg/ml). This isolate also showed the maximum production of HCN and ammonia. 16S rDNA and phylogenetic analysis showed that strain An-15-Mg exhibits 99% level of similarity with Pseudomonas aeruginosa. Therefore, it was designated as Pseudomonas aeruginosa strain An-15-Mg. HPLC analysis showed that the Pseudomonas aeruginosa strain An-15-Mg produced maximum concentration of succinic acid, malonic, citric and malic acid with small amounts of schimic, quinic, tartaric, fumaric and lactic acids. The strain An-15-Mg possessed phosphate solubilization as major PGP trait along with different PGP traits. The potential phosphate solubilizing strain of Pseudomonas aeruginosa was reported first time as PGPR which lives in close association with apple tree without harming the plant, therefore could be used as a promising phosphate solubilizer and biofertilizer in apple crop grown in high hills of Himachal Pradesh. Authors contribution All authors made significant efforts towards the completion of this research work and preparation of manuscript timely. Author Ranjna Sharma has done collection of soil samples of apple tree from two districts, isolation and characterization of phosphate solubilizing Pseudomonas isolates and their screening for different PGPT’s, phenotypic characteriazation, 16S rRNA analysis and statistical analysis. Author S P Singh has done HPLC analysis at their institute. Author Ankita has done sequence analysis and phylogenetic tree preparation. Author Mohinder Kaur is my mentor and generated idea regarding this work. She guided me in completing this work successfully as well as manuscript writing.
The Role of Fatty Acids on Toll-like Receptor 4 Regulation of Substrate Metabolism with Obesity

Growing evidence suggests that obesity and associated metabolic dysregulation occurs in concert with chronic low-grade inflammation. Toll-like receptors (TLR) are transmembrane receptors that play an important role in innate immunity and the induction of inflammatory responses. Our laboratory has observed that TLR4 expression is elevated in the skeletal muscle of obese humans and is associated with reduced fatty acid (FA) oxidation and increased lipid synthesis. Additionally, activation of this pathway by lipopolysaccharide (LPS), ex vivo, results in a shift in substrate metabolism favoring glucose as an energy substrate and preferential storage of FA in intracellular lipid depots. The purpose of this study was to examine the effects of saturated vs. monounsaturated FA on TLR4 transcription and signaling using ex vivo and in vivo models. C2C12 myotubes were incubated in FA-enriched growth medium with varying ratios of palmitate and oleate for 12 hours. Following FA treatment, cells were either collected for measures of mRNA and protein levels of TLR4 or challenged with LPS (500 ng/mL) for 2 hours to assess TLR4 mediated changes in interleukin-6 (IL6) and glucose and fatty acid metabolism. TLR4 mRNA and protein content were increased in stepwise fashion with higher palmitate concentration (p<0.05). This was associated with an exacerbated LPS effect on IL-6 mRNA and protein levels, and glucose and fatty acid metabolism. To determine if these effects are translated to an invivo model, C57BL/6 mice were fed high saturated fat (HSF), high monounsaturated fat (HMF), and control diets for 10 weeks. Following the dietary intervention, animals were challenged with I.P. injections of either saline or LPS (~25μg/mouse), sacrificed 4 hours post-injection, and red and white gastrocnemius muscle were harvested for measures of expression and protein levels of TLR4 and IL-6, and glucose and fatty acid metabolism. TLR4 mRNA and protein levels were not altered with either the HSF or HMF diets.
Ricinus communis extract inhibits the adipocyte differentiation through activating the Wnt/β-catenin signaling pathway

Ricinus communis, belongs to the family Euphorbiaceae, has been known as medicinal plants for treatment of inflammation, tumors, antidiabetic, hepatoprotective and laxative. Compared to many pharmacological studies, the effect of R. communis extract on regulating adipogenesis as therapeutic drug for treating obesity has not been reported. R. communis extract (RCE) was investigated to determine its effects on the adipogenesis by monitoring the status of Wnt/β-catenin signaling and factors involving the differentiation of adipocytes. The differentiation of 3T3-L1 cells monitored by Oil Red O staining was inhibited in concentration dependent manner by RCE. The luciferase activity of HEK 293-TOP cells containing pTOPFlash with Tcf4 response element-luciferase gene was increased approximately 2-folds by the treatment of RCE at concentrations of 100 μg/mL compared to the control. Activation of the Wnt/β-catenin pathway by RCE was further confirmed by immunocytochemical analysis which shows an increment of nuclear localization of β-catenin. In addition, safety of RCE was verified through performing neural stem cell morphology assay. Among the identified flavonoids in RCE, isoquercitrin was the most abundant. Therefore, these results indicate that the adipocyte differentiation was significantly reduced by isoquercitrin in R. communis. In this study, RCE suppresses the adipogenesis of 3T3-L1 cells via the activation of Wnt/β-catenin signaling.
Precision Agriculture-Machine Learning Based Approach

In this paper Real-time use of precision agriculture with the help of IoT and Machine learning is demonstrated. The NodeMCU-ESP12E and other sensor networks has been used for monitoring and controlling smart irrigation system, which is simple in design and also cost-effective. It is advantageous for farmers to irrigate their land by the application of smart irrigation system. This smart irrigation system has Capacitive Soil moisture Sensor-v2.0, Temperature and Humidity sensor-DHT22, Rain drop Sensor. solenoid valves are used to control the water flow. Data from the farm-field is sent to cloud by NodeMCU-ESP12E transmitter wirelessly. At the receiver side, based on the sensor data NodeMCU-ESP12E drives the 3-Phase motor starter. This enables the remote-control mechanism through an application. Users can control motor, sprinklers and solenoid valves through the application.This paper also focuses on fertilizer recommendation system based on machine learning, the ML model takes the inputs such as soil moisture, temperature, humidity, soil type, crop type and N-P-K values to predict the suitable fertilizer which can be used for the respective farm-field. so that farm-field nutrition will be improved.
DNA fingerprinting in African marigold (Tagetes erecta L.) genotypes using ISSR and URP markers

Genetic diversity of 22 marigold (Tagetes erecta L.) genotypes was evaluated with Inter Simple Sequence Repeats (ISSR) and Universal Rice Primers (URP) markers. A total of 31 molecular markers comprising of 19ISSR and 12 URP markers were utilized for the study. A total of 184 amplicons were amplified using 19 ISSR primers, out of which 171 (92.73%) were polymorphic. The polymorphic information content (PIC) ranged from 0.23 to 0.47 with an average of 0.34. The resolving power (RP) ranged from 7.00 to 16.00 with average of 11.20. The marker index (MI) ranged from 0.77 to 4.83 with an average of 2.93. In case of URP markers, a total of 131amplicons were amplified of which 122 (93.08%) were polymorphic with 12 URP primers. The polymorphic information content (PIC) ranged from 0.17 to 0.39 with an average of 0.32. The resolving power (RP) rangedfrom 8.82 to 22.45 with average of 13.75. The marker index (MI) ranged from 0.55 to 5.87 with an average of 3.17. The Jaccard's similarity coefficient ranged from 0.33 to 0.81 in ISSR markers and 0.33 to 0.86 for URP markers which suggests a wide range of genetic divergence for marigold genotypes. UPGMA method was used for cluster analysis which categorised 22 genotypes in two main clusters at 0.44 similarity coefficient in both ISSR and URP markers. The two male sterile lines formed a distinct group as confirmed through both the marker systems.
Self-Balancing System and Control Design for Two-Wheeled Single-Track Vehicles

This study presents a novel approach to achieve self-balance by employing a proportional integral derivative (PID) control system. Simply put, the innovative design consists of two electric ducted fans (EDF) that propel air against the direction of fall and thereby maintain balance. If these motors are allowed to move in two degrees of freedom, the EDF motors will propel and reduce weight of the two-wheeler while maintaining stability. To the best of our knowledge, no study has proposed a system that simultaneously provides propulsion and weight reduction along with achieving self-balance. The working mechanism of the utilized PID arducopter controller is elucidated which utilizes an IMU sensor and employs a nonlinear complementary filter on the special orthogonal group to determine the lean angles at any instant of time and a feedback loop to maintain the system’s position at the desired upright zero degrees lean angle. Next, the proposed PID controller is first tested on a small-scale model to validate the developed concept to achieve self-balance by employing EDF motors. After achieving successful results on the small-scale model and thereby attaining the step of validation, the proposed concept is tested against a full-scale model (motorbike) by designing the mechanical and electrical parts. The methodology is divided into three major steps – mechanical parts design and manufacture, electrical components design and control system design. Furthermore, three mechanisms are designed to control steering, braking and throttle via a remote transmitter receiver control and autonomous control.
RocS drives chromosome segregation and nucleoid occlusion in Streptococcus pneumoniae

Segregation of replicated chromosomes in bacteria is poorly understood outside some prominent model strains and even less is known about how it is coordinated with other cellular processes. Here we report that RocS is crucial for chromosome segregation in the opportunistic human pathogen Streptococcus pneumoniae. RocS is membrane-bound and interacts both with DNA and the chromosome partitioning protein ParB to properly segregate the origin of replication region to new daughter cells. In addition, we show that RocS interacts with the tyrosine-autokinase CpsD required for polysaccharide capsule biogenesis, which is crucial for S. pneumoniae’s ability to prevent host immune detection. Altering the RocS-CpsD interaction drastically hinders chromosome partitioning and cell division. Altogether, this work reveals that RocS is the cornerstone of an atypical nucleoid occlusion system ensuring proper cell division in coordination with the biogenesis of a protective capsular layer.
Modulation of input sensitivity and output gain by retinal amacrine cells

The prevailing hierarchical view of the visual system consists of parallel circuits that begin in the retina, which then sum effects across sequential levels, increasing in complexity. Yet a separate type of interaction, whereby one visual pattern changes the influence of another, known as modulation, has received much less attention in terms of its circuit mechanisms. Retinal amacrine cells are a diverse class of inhibitory interneurons that are thought to have modulatory effects, but we lack a general understanding of their functional types. Using dynamic causal experiments in the salamander retina perturbing amacrine cells along with an unsupervised computational framework, we find that amacrine cell modulatory effects cluster into two distinct types. One type controls ganglion cell sensitivity to individual visual features, and a second type controls the ganglion cell’s output gain, acting to gate all features. These results establish three separate general roles of amacrine cells – to generate primary visual features, to use context to select specific visual features and to gate retinal output.
Dam removal and fish passage improvement influence fish assemblages in the Penobscot River, Maine.

Dams and their impoundments disrupt river habitat connectivity to the detriment of migratory fishes. Removal of dams improves riverine connectivity and lotic habitat, which benefits not only these fishes but also resident fluvial specialist species. Restoration efforts on the Penobscot River, Maine, are among the largest recently completed in the United States and include the removal of the two lowermost dams and improvements to fish passage at several remaining barriers. We assessed fish assemblages in the main-stem river and several major tributaries before (2010–2012) and after (2014–2016) dam removal using boat electrofishing surveys and a stratified random sampling design. In total, we sampled 303 km of shoreline and captured 107,335 individual fish representing 39 species. Similarity indices and rarefaction curves indicated that significant changes in fish assemblage composition occurred in reaches that underwent both habitat and connectivity changes (i.e., directly above removed dams). The newly connected reaches became more similar in fish assemblage composition, as demonstrated by an average increase of 31% in similarity scores. The changes in similarity score in these reaches were driven by increasing access for anadromous fishes and decreasing abundances of slow-water specialist species. For example, we observed a marked reduction in lacustrine species in former impoundments. These assemblage shifts were further illustrated by nonmetric multidimensional scaling in which sites directly above former dams exhibited the largest ordinal shifts immediately following dam removal. We also found all anadromous species in greatest abundance below the lowermost dam during each respective sampling period, though we did find some anadromous species above the lowermost dam during postremoval sampling. Our results demonstrate the potential for large dam removal projects to restore both fluvial and anadromous fish assemblages. Dams fundamentally alter the flow, temperature, sediment dynamics, and connectivity of rivers, which results in changes to aquatic and riparian biota (Petts 1980; Poff et al. 1997). Such biotic changes include reduced biodiversity in impoundment habitat (Santucci et al. 2005; Guenther and Spacie 2006; Slawski et al. 2008), reduction in *Corresponding author: jonathan.watson@maine.edu Received June 24, 2017; accepted February 16, 2018 Transactions of the American Fisheries Society 147:525–540, 2018 © 2018 American Fisheries Society ISSN: 0002-8487 print / 1548-8659 online DOI: 10.1002/tafs.10053
Effect of Fermentation and Variety on Quality Attributes of Okra Seed (Abelmoschus esculentus (L) Moench) Flour

Effect of Fermentation and Variety on Quality Attributes of Okra Seed (Abelmoschus esculentus (L) Moench) Flour Oluyemisi Elizabeth Adelakun*, Bosede Folake Olanipekun, Oluyemisi Akingbaso and Bhaskar Mani Adhikar Department of Biological Sciences, Covenant University, Ota, Ogun State, Nigeria. Department of Food Science and Engineering, Ladoke Akintola University of Technology, PMB 4000, Ogbomoso, Oyo State, Nigeria. Department of Food Technology, National College of Food Science and Technology, Kathmandu, Nepal