Miracle-dz/UniFAR-FTUs huggingface dataset:
Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus

The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1173 genes, with the accessory genome containing 4941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.
Voluntary or Forced: Different Effects of Personal and Social Norms on Urban Residents’ Environmental Protection Behavior

It is well known that environmental protection behaviors are influenced by both individual internal motivation and external environmental pressure, but few studies have looked at the two kinds of factors together. In order to study the influence mechanism of these two kinds of factors on the environmental protection behavior of urban residents, especially the difference between these two kinds of factors, we take personal norms and social norms as independent variables into the theoretical model. Results based on survey data of 731 urban residents revealed that personal norms and social norms both are positively associated with environmental protection behavior. Moreover, environmental protection willingness was found to mediate the relationship of personal and social norms with environmental protection behavior. We also found that the direct and indirect influences of personal norms on environmental protection behavior are greater than that of social norms. Further, the study revealed that cost consciousness moderates the relationship between personal norms, environmental protection willingness, and environmental protection behavior. Our results suggest that personal norms have a greater impact on environmental protection behavior than social norms. Therefore, we need to make greater efforts to promote environmental education and cultivate young people’s sense of environmental responsibility from an early age. At the same time, it is necessary to maintain appropriate environmental pressure and reduce the environmental cost in the daily life of residents.
Chagas Disease: Detection of Trypanosoma cruzi by a New, High-Specific Real Time PCR

Background: Chagas disease (CD) is a major burden in Latin America, expanding also to non-endemic countries. A gold standard to detect the CD causing pathogen Trypanosoma cruzi is currently not available. Existing real time polymerase chain reactions (RT-PCRs) lack sensitivity and/or specificity. We present a new, highly specific RT-PCR for the diagnosis and monitoring of CD. Material and Methods: We analyzed 352 serum samples from Indigenous people living in high endemic CD areas of Colombia using three leading RT-PCRs (k-DNA-, TCZ-, 18S rRNA-PCR), the newly developed one (NDO-PCR), a Rapid Test/enzyme-linked immuno sorbent assay (ELISA), and immunofluorescence. Eighty-seven PCR-products were verified by sequence analysis after plasmid vector preparation. Results: The NDO-PCR showed the highest sensitivity (92.3%), specificity (100%), and accuracy (94.3%) for T. cruzi detection in the 87 sequenced samples. Sensitivities and specificities of the kDNA-PCR were 89.2%/22.7%, 20.5%/100% for TCZ-PCR, and 1.5%/100% for the 18S rRNA-PCR. The kDNA-PCR revealed a 77.3% false positive rate, mostly due to cross-reactions with T. rangeli (NDO-PCR 0%). TCZ- and 18S rRNA-PCR showed a false negative rate of 79.5% and 98.5% (NDO-PCR 7.7%), respectively. Conclusions: The NDO-PCR demonstrated the highest specificity, sensitivity, and accuracy compared to leading PCRs. Together with serologic tests, it can be considered as a reliable tool for CD detection and can improve CD management significantly.
Microwave Irradiation Synthesis and Characterization of Reduced-(Graphene Oxide-(Polystyrene-Polymethyl Methacrylate))/Silver Nanoparticle Nanocomposites and Their Anti-Microbial Activity

Herein, we report a facile process for the preparation of styrene and methyl-methacrylate copolymer nanocomposites containing reduced graphene oxide and silver nanoparticles ((R-(GO-(PS-PMMA))/AgNPs)) by using (i) microwave irradiation (MWI) to obtain R-(GO-(PS-PMMA))/AgNPs and (ii) the in situ bulk polymerization technique to produce RGO/AgNPs-(PS-PMMA). Various characterization techniques, including FT-IR, XPS, Raman spectroscopy, XRD, SEM, HR-TEM, DSC, and TGA analysis, were used to characterize the prepared nanocomposites. The Berkovich nanoindentation method was employed to determine the hardness and elastic modulus of the nanocomposites. The results showed that the MWI-produced nanocomposites were found to have enhanced morphological, structural, and thermal properties compared with those of the nanocomposites prepared by the in situ method. In addition, the antibacterial activity of the prepared nanocomposites against the E. coli HB 101 K-12 was investigated, whereby an inhibition zone of 3 mm (RGO/AgNPs-(PS-PMMA) and 27 mm (R-(GO-(PS-PMMA))/AgNPs) was achieved. This indicates that the MWI-prepared nanocomposite has stronger antibacterial activity than the in situ-prepared nanocomposite.
Sand Prairie Communities of Matanzas Nature Preserve, Mason County, Illinois

ABSTRACT The Matanzas Prairie Nature Preserve is located near Bath, Mason County, Illinois, in the extensive glacial sand deposits associated with the Illinois River. This Preserve contains the only remaining high quality wet-mesic sand prairie, shrub prairie, and sedge meadow associated with the Illinois River sand deposits. The sedge meadow, about 5 ha in size, was dominated by Carex stricta (Importance Value or IV of 66.6 out of 200), Calamagrostis canadensis, and Rosa palustris (both with IV's of 28.3). The wet-mesic sand prairie occurred on slightly higher ground and was dominated by Solidago canadensis (IV of 34.2), Andropogon gerardii (IV of 25.9), Carex stricta (IV of 21.9), Poa pratensis (IV of 18.0), and Euthamia graminifolia (IV of 17.7). Parts of the Preserve were shrub prairie with a ground layer similar to the wet-mesic sand prairie community. A total of 340 species of vascular plants were encountered on the Preserve: 5 fern and fern-allies; 100 monocots; and, 235 dicots. Except for Poa pratensis, which was among the dominant species in the wet-mesic sand prairie and shrub prairie, the 38 exotic species were rarely encountered (11% of the flora). The Floristic Quality Index (including exotic species) for the sedge meadow was 38.80, the wet-mesic sand prairie 43.65, and the shrub prairie 31.76.
Influence of MgO-Lignin Dual Component Additives on Selected Properties of Low Density Polyethylene

The presented study describes the application of lignin-based dual component fillers into low-density polyethylene (LDPE) and an examination of their selected properties. The main experimental procedure was focused on the preparation of thin sheet films using polyethylene and its composites with 5% by wt. of fillers: MgO, MgO-lignin dual phase systems with varying amounts of lignin and pristine lignin. Analysis of morphology revealed that elongated voids appeared in the structure for hybrid filler with a higher content of lignin (min. 50% by wt. of lignin versus MgO) and also for pristine lignin. Moreover, the prepared sheets were subjected to the thermoforming process by using the positive forming method (male mold). The thermoforming ability of all composites was evaluated by means of a comparison of wall thickness distribution on thermoformed shapes. The most noticeable percentage of wall thinning occurred for films which consisted of LDPE/MgO-lignin (5:1 wt./wt.) composite. In contrast, the best material arrangement and the highest mean percentage wall thickness were observed in the case of the shape formed with LDPE/MgO-lignin (1:5 wt./wt.). In addition, as part of research studies, the measurements of the contact angle have been conducted. The analysed LDPE films, in particular LDPE/MgO-L, have been recognized as materials with high wettability.
A rapid determination of the total sugar content and the average inulin chain length in roots of chicory (Cichorium intybusL)

A method is proposed to the chicory breeder for the fast screening of total sugar content and average inulin chain length of lots of chicory roots. The determination of the refractive index of the chicory root juice by refractometer is the first step. This rapid analysis gives a good estimation of the total sugar content (r=0·85; RSD=3·8%). In the next step extracts of chicory roots with a high total sugar content are hydrolysed and analysed by chromatography. The calculated fructose/glucose ratio predicts the average inulin chain length well (r=0·91; RSD=5·3%). The molecular weight distribution of the inulin was analysed by anion exchange HPLC with pulsed amperometric detection. © 1998 SCI
Effects of changing cow production and fitness traits on profit and greenhouse gas emissions of UK dairy systems

SUMMARY The aim of the present study was to compare the effect of changing a range of biological traits on farm profit and greenhouse gas (GHG) emissions (expressed as carbon dioxide equivalent, CO2-eq.) in the UK dairy cow population. A Markov chain approach was used to describe the steady-state herd structure of the average milk-recorded UK dairy herd, as well as to estimate the CO2-eq. emissions per cow, and per kilogram of milk solids (MS). Effects of changing each herd production and fitness trait by one unit (e.g. 1 kg milk; 1% mastitis incidence) were assessed, with derived values for change in profit (economic values) being used in a multi-trait selection index. Of the traits studied, an increase in survival and reductions in milk volume, live weight, residual feed intake, somatic cell count, mastitis incidence, lameness incidence and calving interval were traits that would be both profitable and reduce CO2-eq. emissions per cow and per kg MS of a dairy herd. A multi-trait selection index was used to estimate the annual response in production and fitness traits and the economic response, with an estimate of annual profit per cow from selection on multiple traits. Milk volume, milk fat and protein yield, live weight, survival and dry matter intake were estimated to increase each year and body condition score, residual feed intake, somatic cell count, mastitis incidence, lameness incidence and calving interval were estimated to decrease, with selection on these traits estimated to result in an annual increase of 1% per year in GHG emissions per cow, but a reduction of 0·9% per unit product. Improved efficiencies of production associated with a reduction in milk volume (and increasing fat and protein content), live weight and feed intake (gross and metabolic efficiency, respectively), and increase in health, fertility and overall survival will increase farm annual profit of UK dairy systems and reduce their environmental impact.
INDICES OF GENETIC IDENTITY AND DISTANCE IN THREE TAXA WITHIN THE BALANUS AMPHITRITE DARWIN COMPLEX (CIRRIPEDIA, THORACICA)

[Balanus amphitrite ist eine auserordentlich variable Art innerhalb der balanomorphen Cirripedier. Aufgrund unvollstandiger Diagnosen der fruher beschriebenen Erscheinungsformen ergab sich eine betrachtliche Verwirrung in der Taxonomie der B. amphitrite-Gruppe. Durch elektrophoretische Analysen die bis zu 18 Enzymloci fasten, wurden die Indices der genetischen Identitat bzw. Divergenz fur drei Taxa innerhalb der B. amphitrite-Gruppe ermittelt. Die Ergebnisse fuhren zu dem Schlus, das Balanus amphitrite saltonensis neu klassifiziert werden sollte als Balanus amphitrite amphitrite, Balanus variegatus konnte in seiner taxonomischen Stellung als Art bestatigt werden. , Balanus amphitrite ist eine auserordentlich variable Art innerhalb der balanomorphen Cirripedier. Aufgrund unvollstandiger Diagnosen der fruher beschriebenen Erscheinungsformen ergab sich eine betrachtliche Verwirrung in der Taxonomie der B. amphitrite-Gruppe. Durch elektrophoretische Analysen die bis zu 18 Enzymloci fasten, wurden die Indices der genetischen Identitat bzw. Divergenz fur drei Taxa innerhalb der B. amphitrite-Gruppe ermittelt. Die Ergebnisse fuhren zu dem Schlus, das Balanus amphitrite saltonensis neu klassifiziert werden sollte als Balanus amphitrite amphitrite, Balanus variegatus konnte in seiner taxonomischen Stellung als Art bestatigt werden. ]
Quality of the reef fish Upeneus tragula (Mullidae) at settlement: is size a good indicator of condition?

The quality at settlement of the goatfish Upeneus tragula (family Mullidae) was examined from 10 samples collected over 2 summers (1990/1991, 1991/1992), at 1 location near Lizard Island on the northern Great Barrier Reef. Australia. Nine commonly used measures of fish condition were employed: standard length (SL), body depth at the pectoral fin, total lipid content, carbohydrate content, protein content, water content, growth rate, burst swimming speed and Fulton's condition factor (K = weight / S L ~ ) . High and significant levels of variability were found in all measures of condition over the 10 san~ples. There was no relationship between the age of the fish at settlement and total carbohydrate and lipid content or burst speed of fish. Correlations of measures of condition with fish length were very poor. Specifically, burst speed and stored energy levels (lipids, carbohydrates) had particularly low correlations with fish length ( r < 0.2). An experiment determined that burst speed of a fish at settlement was not related to its feeding history within the larval stage. Feeding history only accounted for 6% of the total variation in burst speeds. Most of the var~abil~ty In measures of condition were due to differences among individuals. The poor correlations between all measures of fish quallty (with exception of morphological measures) suggest no single measure gives an adequate description of a fish's survival potential. Furthermore, this study cautions against the direct transfer of size-based theories of success (i.e. 'bigger is better') to the variability within a specific developmental stage.
Melioidosis in a Resident of Texas with No Recent Travel History, United States

To our knowledge, environmental isolation of Burkholderia pseudomallei, the causative agent of melioidosis, from the continental United States has not been reported. We report a case of melioidosis in a Texas resident. Genomic analysis indicated that the isolate groups with B. pseudomallei isolates from patients in the same region, suggesting possible endemicity to this region.
Research on the Stationarity of Hexapod Robot Posture Adjustment

This paper proposes a smooth adjustment method for the instability problem that occurs during the start and stop of a multi-footed robot during attitude change. First, kinematics analysis is used to establish the mapping relationship between the joint angles of the robot support legs and the body posture. The leg joint angle is a known quantity that can be measured accurately and in real time. Therefore, when the position of the foot end of the support leg is unchanged, a unique set of joint angles can be obtained with the change of body posture at a certain moment. Based on the designed mapping model, the smooth adjustment of the posture can be achieved by the smooth adjustment of the support legs. Second, a constraint index that satisfies the requirements of the robot’s steady adjustment of the robot is given. The S-curve acceleration/deceleration method is used to plan the body’s attitude angle transformation curve, and then the mapping control relationship is used to obtain the control trajectory requirements of the joint to achieve smooth adjustment. In addition, this paper also gives a simple choice and motion control method for the redundancy problem caused by the number of support legs of a multi-footed robot when the attitude is changed. The simulation and prototype experiments verify and analyze the proposed method. The results of comparative experiments show that the posture adjustment method proposed in this paper has continuous acceleration without breakpoints, the speed changes gently during the start and stop phases of the attitude transformation, and there is no sudden change in the entire process, which improves the consistency of the actual values of the attitude planning curve with the target values. The physical prototype experiment shows that the maximum deviation between the actual value of the attitude angular velocity and the target value changes from 62.5% to 5.5%, and the degree of fit increases by 57.0%. Therefore, this study solves the problem of the instability of the fuselage when the robot changes its attitude, and it provides an important reference for the multi-footed robot to improve the terrain adaptability.
Influenza A virus utilizes noncanonical cap-snatching to diversify its mRNA/ncRNA

Influenza A virus (IAV) utilizes cap-snatching to obtain host capped small RNAs for priming viral mRNA synthesis, generating capped hybrid mRNAs for translation. Previous studies have been focusing on canonical cap-snatching, which occurs at the very 5′ end of viral mRNAs. Here we discovered noncanonical cap-snatching, which generates capped hybrid mRNAs/noncoding RNAs mapped to the region ∼300 nucleotides (nt) upstream of each mRNA 3′ end, and to the 5′ region, primarily starting at the second nt, of each virion RNAs (vRNA). Like canonical cap-snatching, noncanonical cap-snatching utilizes a base-pairing between the last nt G of host capped RNAs and a nt C of template RNAs to prime RNA synthesis. However, the nt upstream of this template C is usually A/U rather than just U; prime-realignment occurs less frequently. We also demonstrate that IAV can snatch capped IAV RNAs in addition to host RNAs. Noncanonical cap-snatching likely generates novel mRNAs with start AUG encoded in viral or host RNAs. These findings expand our understanding of cap-snatching mechanisms and suggest that IAV may utilize noncanonical cap-snatching to diversify its mRNAs/ncRNAs.
Underreporting of Death by COVID-19 in Brazil's Second Most Populous State

The COVID-19 pandemic brings to light the reality of the Brazilian health system. The underreporting of COVID-19 deaths in the state of Minas Gerais (MG), where the second largest population of the country is concentrated, reveals government unpreparedness, as there is a low capacity of testing in the population, which prevents the real understanding of the general panorama of SARS-CoV-2 dissemination. The goals of this research are to analyze the causes of deaths in different Brazilian government databases (Civil Registry Transparency Portal and InfoGripe) and to assess whether there are sub-records showing an unexpected increase in the frequency of deaths from causes clinically similar to COVID-19. A descriptive and quantitative analysis of the number of deaths by COVID-19 and similar causes was performed in different databases. Our results demonstrate that different official sources had a discrepancy of 109.45% between these data referring to the same period. There was also a 758.57% increase in SARI deaths in 2020, when compared to the average of previous years. Finally, it was shown that there was an increase in the rate of pneumonia and respiratory insufficiency (RI) by 6.34 and 6.25%, respectively. In conclusion, there is an underreporting of COVID-19 deaths in MG due to the unexplained excess of deaths caused by SARI, respiratory insufficiency, and pneumonia compared to previous years.
Patatin-Related Phospholipase pPLAIIIγ Involved in Osmotic and Salt Tolerance in Arabidopsis

Patatin-related phospholipases (pPLAs) are acyl-hydrolyzing enzymes implicated in various processes, including lipid metabolism, signal transduction, plant growth and stress responses, but the function for many specific pPLAs in plants remains unknown. Here we determine the effect of patatin-related phospholipase A pPLAIIIγ on Arabidopsis response to abiotic stress. Knockout of pPLAIIIγ rendered plants more sensitive whereas overexpression of pPLAIIIγ enhanced plant tolerance to NaCl and drought in seed germination and seedling growth. The pPLAIIIγ-knockout and overexpressing seedlings displayed a lower and higher level of lysolipids and free fatty acids than that of wild-type plants in response to NaCl stress, respectively. These results indicate that pPLAIIIγ acts a positive regulator of salt and osmatic stress tolerance in Arabidopsis.
Extremely Low Forces Induce Extreme Axon Growth

Stretch-growth has been defined as a process that extends axons via the application of mechanical forces. In the present article, we used a protocol based on magnetic nanoparticles (NPs) for labeling the entire axon tract of hippocampal neurons, and an external magnetic field gradient to generate a dragging force. We found that the application of forces below 10 pN induces growth at a rate of 0.66 ± 0.02 µm h−1 pN−1. Calcium imaging confirmed the strong increase in elongation rate, in comparison with the condition of tip-growth. Enhanced growth in stretched axons was also accompanied by endoplasmic reticulum (ER) accumulation and, accordingly, it was blocked by an inhibition of translation. Stretch-growth was also found to stimulate axonal branching, glutamatergic synaptic transmission, and neuronal excitability. Moreover, stretched axons showed increased microtubule (MT) density and MT assembly was key to sustaining stretch-growth, suggesting a possible role of tensile forces in MT translocation/assembly. Additionally, our data showed that stretched axons do not respond to BDNF signaling, suggesting interference between the two pathways. As these extremely low mechanical forces are physiologically relevant, stretch-growth could be an important endogenous mechanism of axon growth, with a potential for designing novel strategies for axonal regrowth. SIGNIFICANCE STATEMENT Axon growth involves motion, and motion is driven by forces. The growth cone (GC) itself can generate very low intracellular forces by inducing a drastic cytoskeleton remodeling, in response to signaling molecules. Here, we investigated the key role of intracellular force as an endogenous regulator of axon outgrowth, which it has been neglected for decades because of the lack of methodologies to investigate the topic. Our results indicate a critical role of force in promoting axon growth by facilitating microtubule (MT) polymerization.