Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycoavidus sp. Strain B2-EB: Comparative Genomics Reveals Minimal Genomic Features Required by a Cultivable Burkholderiaceae-Related Endofungal Bacterium

This study attempted the isolation of a novel endobacterium, Mycoavidus sp. B2-EB (JCM 33615), harbored in the fungal host Mortierella parvispora E1425 (JCM 39028). We report the complete genome sequence of this strain, which possesses a reduced genome size with relatively high genome completeness and a streamlined genome structure. The information indicates the minimal genomic features required by both the endofungal lifestyle and artificial cultivation, which furthers our understanding of genome reduction in fungal endosymbionts and extends the culture resources for biotechnological development on engineering synthetic microbiomes. ABSTRACT Obligate bacterial endosymbionts are critical to the existence of many eukaryotes. Such endobacteria are usually characterized by reduced genomes and metabolic dependence on the host, which may cause difficulty in isolating them in pure cultures. Family Burkholderiaceae-related endofungal bacteria affiliated with the Mycoavidus-Glomeribacter clade can be associated with the fungal subphyla Mortierellomycotina and Glomeromycotina. In this study, a cultivable endosymbiotic bacterium, Mycoavidus sp. strain B2-EB, present in the fungal host Mortierella parvispora was obtained successfully. The B2-EB genome (1.88 Mb) represents the smallest genome among the endofungal bacterium Mycoavidus cysteinexigens (2.64–2.80 Mb) of Mortierella elongata and the uncultured endosymbiont “Candidatus Glomeribacter gigasporarum” (1.37 to 2.36 Mb) of arbuscular mycorrhizal fungi. Despite a reduction in genome size, strain B2-EB displays a high genome completeness, suggesting a nondegenerative reduction in the B2-EB genome. Compared with a large proportion of transposable elements (TEs) in other known Mycoavidus genomes (7.2 to 11.5% of the total genome length), TEs accounted for only 2.4% of the B2-EB genome. This pattern, together with a high proportion of single-copy genes in the B2-EB genome, suggests that the B2-EB genome reached a state of relative evolutionary stability. These results represent the most streamlined structure among the cultivable endofungal bacteria and suggest the minimal genome features required by both an endofungal lifestyle and artificial culture. This study allows us to understand the genome evolution of Burkholderiaceae-related endosymbionts and to elucidate microbiological interactions. IMPORTANCE This study attempted the isolation of a novel endobacterium, Mycoavidus sp. B2-EB (JCM 33615), harbored in the fungal host Mortierella parvispora E1425 (JCM 39028). We report the complete genome sequence of this strain, which possesses a reduced genome size with relatively high genome completeness and a streamlined genome structure. The information indicates the minimal genomic features required by both the endofungal lifestyle and artificial cultivation, which furthers our understanding of genome reduction in fungal endosymbionts and extends the culture resources for biotechnological development on engineering synthetic microbiomes.
Windrow Burning Eliminates Italian Ryegrass (Lolium perenne ssp. multiflorum) Seed Viability

Windrow burning is one of several harvest weed seed control strategies that have been developed and evaluated in Australia to address the widespread evolution of multiple herbicide resistance in annual weeds. Herbicide-resistant Italian ryegrass populations are common in the Palouse region of eastern Washington and northern Idaho. Field and greenhouse studies were conducted to evaluate the effects of burning standing stubble and narrow windrows on the survival of Italian ryegrass seed on the soil surface and to determine the amount of crop residue remaining after both practices. Italian ryegrass emergence was 63, 48, and 1% for the nonburned check, burned standing stubble, and burned windrow treatments, respectively. Crop-residue dry weights were 9.94, 5.69, and 5.79 Mg ha−1 for these same treatments. Windrow burning can be an effective tactic in an integrated weed management strategy for Italian ryegrass control in the Palouse region of eastern Washington and northern Idaho. Nomenclature: Italian ryegrass, Lolium perenne L. ssp. multiflorum (Lam.) Husnot; wheat, Triticum aestivum L. La quema de residuos de cultivo apilados en bandas es una de las estrategias de control de semillas de malezas durante la cosecha que han sido desarrolladas y evaluadas en Australia para enfrentar la ampliamente distribuida evolución de resistencia múltiple a herbicidas en malezas anuales. Poblaciones de Lolium perenne ssp. multiflorum resistentes a herbicidas son comunes en la región Palouse en el este de Washington y en el norte de Idaho. Se realizaron estudios de campo y de invernadero para evaluar los efectos de la quema de los residuos en pie del cultivo después de la cosecha y de la quema de los residuos de cultivos apilados en bandas, sobre la sobrevivencia de la semilla de L. perenne en la superficie del suelo, y para determinar la cantidad de residuo de cultivo que queda después de ambas prácticas. La emergencia de L. perenne fue 63, 48, y 1% para el testigo sin quema, la quema de los residuos en pie del cultivo, y la quema de los residuos en bandas, respectivamente. La quema de residuos de cultivos apilados en bandas puede ser una táctica efectiva dentro de una estrategia de manejo integrado de malezas para el control de L. perenne en la región Palouse en el este de Washington y en el norte de Idaho.
Peer-Prediction in the Presence of Outcome Dependent Lying Incentives

We derive conditions under which a peer-consistency mechanism can be used to elicit truthful data from non-trusted rational agents when an aggregate statistic of the collected data affects the amount of their incentives to lie. Furthermore, we discuss the relative saving that can be achieved by the mechanism, compared to the rational outcome, if no such mechanism was implemented. Our work is motivated by distributed platforms, where decentralized data oracles collect information about real-world events, based on the aggregate information provided by often self-interested participants. We compare our theoretical observations with numerical simulations on two public real datasets.
BlueMemo: Depression Analysis through Twitter Posts

The use of social media runs through our lives, and users' emotions are also affected by it. Previous studies have reported social organizations and psychologists using social media to find depressed patients. However, due to the variety of content published by users, it isn't effortless for the system to consider the text, image, and even the hidden information behind the image. To address this problem, we proposed a new system for social media screening of depressed patients named BlueMemo. We collected real-time posts from Twitter. Based on the posts, learned text features, image features, and visual attributes were extracted as three modalities and were fed into a multi-modal fusion and classification model to implement our system. The proposed BlueMemo has the power to help physicians and clinicians quickly and accurately identify users at potential risk for depression.
Ex situ plant conservation initiative in developing country: Nepal as a case study

With the increased loss of plant biodiversity, the ex situ seed conservation has become of strategic importance. International treaties and conventions encourage more developed countries to cooperate in providing financial and other supports for the establishment and maintenance of ex situ conservation facilities in developing countries. In this regard, the Nepal Academy of Science and Technology (Nepal) and the Ev-K2-CNR (Italy) set up the Himalayan Seed Bank, with the goal of establishing ex situ seed conservation facility of rare, endemic and endangered plants in Nepal. Here, we discuss the importance of training on seed curation, management and research for the seed bank operators in developing countries. Particular attention is given to the procedures for providing power supply and for optimizing seed longevity in dry storage. Finally, the importance of duplicates in high-standard international seed banks is also discussed.
In Vitro Antimycobacterial Activity and Physicochemical Characterization of Diaryl Ether Triclosan Analogues as Potential InhA Reductase Inhibitors

Two sets of diphenyl ether derivatives incorporating five-membered 1,3,4-oxadiazoles, and their open-chain aryl hydrazone analogs were synthesized in good yields. Most of the synthesized compounds showed promising in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv. Three diphenyl ether derivatives, namely hydrazide 3, oxadiazole 4 and naphthylarylidene 8g exhibited pronounced activity with minimum inhibitory concentrations (MICs) of 0.61, 0.86 and 0.99 μg/mL, respectively compared to triclosan (10 μg/mL) and isoniazid (INH) (0.2 μg/mL). Compounds 3, 4, and 8g showed the InhA reductase enzyme inhibition with higher IC50 values (3.28–4.23 µM) in comparison to triclosan (1.10 µM). Correlation between calculated physicochemical parameters and biological activity has been discussed which justifies a strong correlation with respect to the inhibition of InhA reductase enzyme. Molecular modeling and drug-likeness studies showed good agreement with the obtained biological evaluation. The structural and experimental information concerning these three InhA inhibitors will likely contribute to the lead optimization of new antibiotics for M. tuberculosis.
A Dietary Sugarcane-Derived Polyphenol Mix Reduces the Negative Effects of Cyclic Heat Exposure on Growth Performance, Blood Gas Status, and Meat Quality in Broiler Chickens

Simple Summary Heat stress is a main reason of systemic oxidative stress, which compromises broiler meat production and quality. To improve the productivity of poultry meat production, studies have investigated different heat stress amelioration strategies. Among these strategies, low-cost feed supplementations are introduced to potentially reduce the negative effects of heat stress. Previous studies have also investigated the effects of different antioxidants on growth performance and meat quality, while a limited number of studies have been made regarding the impacts of the polyphenols at different doses. Polyphenols with antioxidant properties have positive effects against oxidative stress, and are naturally available in high amounts in plants, which makes them a novel feed supplementation for improving meat production as well as meat quality in heat-stressed broiler chickens. Therefore, this study attempted to investigate the effects of different doses of polyphenols supplementation on growth performance, physiological responses, and meat quality in broiler chickens exposed to cyclic heat stress. Abstract Heat stress (HS) compromises growth performance and meat quality of broiler chickens by interrupting lipid and protein metabolism, resulting in increased oxidative damages. The experiment attempted to investigate whether dietary polyphenols (Polygain (POL)) could ameliorate the aforementioned adverse effects of HS on performance and meat quality. One hundred and twenty one day-old-male chicks were allocated to two temperature conditions, thermoneutral (TN) or HS, and fed with either a control diet (CON) or the CON plus four different doses of POL (2, 4, 6 and 10 g/kg). Heat stress caused respiratory alkalosis as evidenced by increased rectal temperature (p < 0.001) and respiration rate (p < 0.001) due to increased blood pH (p < 0.001). Heat stress decreased final body weight (p = 0.061) and breast muscle water content (p = 0.013) while POL improved both (p = 0.002 and p = 0.003, respectively). Heat stress amplified muscle damages, indicated by increased thiobarbituric acid reactive substances (p < 0.001) and reduced myofibril fragmentation index (p = 0.006) whereas POL improved both (p = 0.037 and p = 0.092, respectively). Heat stress impaired meat tenderness (p < 0.001) while POL improved it (p = 0.003). In conclusion, HS impaired growth performance and meat quality whereas POL ameliorated these responses in a dose-dependent manner, and effects of POL were evident under both temperature conditions.
What Can Social Media Tell Us About Patient Symptoms

Background Ovarian cancer (OvCa) patients suffer from symptoms that severely affect quality of life. To optimally manage these symptoms, their symptom experiences must be better understood. Social media have emerged as a data source to understand these experiences. Objective The objective of this study was to use topic modeling (ie, latent Dirichlet allocation [LDA]) to understand the symptom experience of OvCa patients through analysis of online forum posts from OvCa patients and their caregivers. Interventions/Methods Ovarian cancer patient/caregiver posts (n = 50 626) were collected from an online OvCa forum. We developed a symptom dictionary to identify symptoms described therein, selected the top 5 most frequently discussed symptoms, extracted posts that mentioned at least one of those symptoms, and conducted LDA on those extracted posts. Results Pain, nausea, anxiety, fatigue, and skin rash were the top 5 most frequently discussed symptoms (n = 4536, 1296, 967, 878, and 657, respectively). Using LDA, we identified 11 topic categories, which differed across symptoms. For example, chemotherapy-related adverse effects likely reflected fatigue, nausea, and rash; social and spiritual support likely reflected anxiety; and diagnosis and treatment often reflected pain. Conclusion The frequency of a symptom discussed on a social media platform may not include all symptom experience and their severity. Indeed, users, who are experiencing different symptoms, mentioned different topics on the forum. Subsequent studies should consider the influence of additional factors (eg, cancer stage) from discussions. Implications for Practice Social media have the potential to prioritize and answer the questions about clinical care that are frequently asked by cancer patients and their caregivers.
SECURITY BASED VOLT/VAR CONTROL IN DISTRIBUTION SYSTEM IN THE PRESENCE OF DISTRIBUTED GENERATORS USING TEACHING-LEARNING-BASED OPTIMIZATION ALGORITHM

Different operation conditions along with the existence of distributed generations (DG) are of the most important characteristics of modern distribution networks. Considering this fact, it is essential to add voltage security term to the objective function of voltage and reactive power control. This paper proposed security based voltage and reactive power control in the presence of DG in the distribution network. In the formulation of the objective function of this problem three functions are provided including; minimization of total electrical energy losses, minimization of voltage deviations and maximization of voltage stability. To satisfy these conditions, optimum dispatch schedules for the onload tap changer (OLTC) settings and all shunt capacitors switching on the network should be taken into account. In order to reduce the volume of calculations and the number of switching’s, optimization algorithms are used to classify daily load curves. Furthermore, the teaching-learning-based optimization (TLBO) which is a kind of evolutionary algorithms is proposed to solve the security based volt/var control in the distribution system in the presence of distributed generators. In addition, performance of TLBO algorithm and genetic algorithm for solving this problem are compared. Finally, IEEE 33-bus test system and real-life 77-bus distribution network are considered as the case studies to demonstrate the effectiveness of the proposed method. The results of simulation have shown us: improving voltage stability, decreasing total electrical energy losses and reducing voltage deviations. In addition, the simulation results verify that the TLBO algorithm has better performances in comparison with genetic algorithm.
A rapidly evolved shift in life history timing during ecological speciation is driven by the transition between developmental phases

For insect species in temperate environments, seasonal timing is often governed by the regulation of diapause, a complex developmental program that allows insects to weather unfavorable conditions and synchronize their lifecycles with available resources. Diapause consists of a series of phases that govern initiation, maintenance, and termination of this developmental pathway. The evolution of insect seasonal timing depends in part on how these phases of diapause development and post-diapause development interact to affect variation in phenology. Here, we dissect the physiological basis of a recently evolved phenological shift in Rhagoletis pomonella (Diptera: Tephritidae), a model system for ecological divergence. A recently derived population of R. pomonella shifted from specializing on native hawthorn fruit to earlier fruiting introduced apples, resulting in a 3-4 week shift in adult emergence timing. We tracked metabolic rates of individual flies across post-winter development to test which phases of development may act either independently or in combination to contribute to this recently evolved divergence in timing. Apple and hawthorn flies differed in a number of facets of their post-winter developmental trajectories. However, divergent adaptation in adult emergence phenology in these flies was due almost entirely to the end of the pupal diapause maintenance phase, with post-diapause development having a very small effect. The relatively simple underpinnings of variation in adult emergence phenology suggest that further adaptation to seasonal change in these flies for this trait might be largely due to the timing of diapause termination unhindered by strong covariance among different components of post-diapause development. Data accessibility All data (in the form of tables of all metabolic rate measurements for all individual flies in the study) will be available on DRYAD when the manuscript is published.
Development of a Peroral, Droplet-Dose Bioassay Laboratory Technique and Its Application on a Granulovirus for Thaumatotibia leucotreta (Lepidoptera: Tortricidae)

The false codling moth, Thaumatotibia (= Cryptophlebia)leucotreta Meyrick (1912) (Lepidoptera: Tortricidae) is regarded as a serious pest on citrus and other crops in Africa south of the Sahara (Newton 1998). Biological pesticides have been formulated using entomopathogenic viruses such as granuloviruses (Baculoviridae) (Hunter-Fujita et al. 1998). The efficacy of registered biological control formulations using naturally-occurring South African Cryptophlebia leucotreta granulovirus (CrleGV-SA) needs to be determined as close to field conditions as possible.
Altered complexity of resting-state BOLD activity in Alzheimer’s disease-related neurodegeneration: a multiscale entropy analysis

Brain complexity, which reflects the ability of the brain to adapt to a changing environment, has been found to be significantly changed with age. However, there is less evidence on the alterations of brain complexity in neurodegenerative disorders such as Alzheimer’s disease (AD). Here we investigated the altered complexity of resting-state blood oxygen level-dependent signals in AD-related neurodegeneration using multiscale entropy (MSE) analysis. All participants were recruited from the Alzheimer’s Disease Neuroimaging Initiative, including healthy controls (HC, n=62), amnestic mild cognitive impairment (aMCI, n =81) patients, and Alzheimer’s disease (AD, n=25) patients. Our results showed time scale-dependent MSE differences across the three groups. In scale=1, significantly changed MSE patterns (HC>aMCI>AD) were found in four brain regions, including the hippocampus, middle frontal gyrus, intraparietal lobe, and superior frontal gyrus. In scale=4, reversed MSE patterns (HC<aMCI<AD) were found in the middle frontal gyrus and middle occipital gyrus. Furthermore, the values of regional entropy were significantly associated with cognitive functions positively on the short time scale, while negatively on the longer time scale. Our findings suggest that MSE could be a reliable measure for characterizing brain deterioration in AD, and may provide insights into the neural mechanism of AD-related neurodegeneration.
Characterizing the impact of an exotic soybean line on elite cultivar development

The genetic diversity of North American soybean cultivars has been largely influenced by a small number of ancestors. High yielding breeding lines that possess exotic pedigrees have been developed, but identifying beneficial exotic alleles has been difficult as a result of complex interactions of yield alleles with genetic backgrounds and environments as well as the highly quantitative nature of yield. PI 416937 has been utilized in the development of many high yielding lines that have been entered into the USDA Southern States Uniform Tests over the past ~20 years. The primary goal of this research was to identify genomic regions under breeding selection from PI 416937 and introduce a methodology for identifying and potentially utilizing beneficial diversity from lines prevalent in the ancestry of elite cultivars. Utilizing SoySNP50K Infinium BeadChips, 52 high yielding PI 416937-derived lines as well as their parents were genotyped to identify PI 416937 alleles under breeding selection. Nine genomic regions across three chromosomes and 17 genomic regions across seven chromosomes were identified where PI 416937 alleles were under positive or negative selection. Minimal significant associations between PI 416937 alleles and yield were observed in replicated yield trials of five RIL populations, highlighting the difficulty of consistently detecting yield associations.
Hierarchical Instance Feature Alignment for 2D Image-Based 3D Shape Retrieval

2D image-based 3D shape retrieval has become a hot research topic since its wide industrial applications and academic significance. However, existing view-based 3D shape retrieval methods are restricted by two settings, 1) learn the common-class features while neglecting the instance visual characteristics, 2) narrow the global domain variations while ignoring the local semantic variations in each category. To overcome these problems, we propose a novel hierarchical instance feature alignment (HIFA) method for this task. HIFA consists of two modules, cross-modal instance feature learning and hierarchical instance feature alignment. Specifically, we first use CNN to extract both 2D image and multi-view features. Then, we maximize the mutual information between the input data and the high-level feature to preserve as much as visual characteristics of an individual instance. To mix up the features in two domains, we enforce feature alignment considering both global domain and local semantic levels. By narrowing the global domain variations we impose the identical large norm restriction on both 2D and 3D feature-norm expectations to facilitate more transferable possibility. By narrowing the local variations we propose to minimize the distance between two centroids of the same class from different domains to obtain semantic consistency. Extensive experiments on two popular and novel datasets, MI3DOR and MI3DOR-2, validate the superiority of HIFA for 2D image-based 3D shape retrieval task.
Mutation Research/Reviews in Mutation Research

Night is no longer dark in the modern world, and the Milky Way has disappeared. Electric light has benefits but there are also a few detriments. These are (1) loss of the night sky, (2) wasted energy, (3) harm to animal and plant life, (4) and perhaps increases in some severe human maladies such as cancers of breast and prostate. The science on phototransduction for the circadian system and on clock gene function is evolving rapidly, and it provides a rationale for the idea that circadian disruption from light at night could cause disease. Direct evidence from humans and rodent models has also accumulated to the point where the idea is no longer fanciful. Although it may seem logical now, the journey on the path