Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro Antibiotic Susceptibility, Virulence Genes Distribution and Biofilm Production of Staphylococcus aureus Isolates from Bovine Mastitis in the Liaoning Province of China

Purpose The aim of this study was to identify the subtype, characterize the antimicrobial resistance, determine the virulence gene distribution, and analyze the biofilm production of Staphylococcus aureus isolates from bovine mastitis milk samples in the Liaoning Province of China. Materials and Methods In ﻿total, 56 Staph. aureus isolates were collected and identified in this study; the isolates were divided into different spa types based on the sequence of the polymorphic X region of the spa gene. Additionally, antimicrobial susceptibility was investigated using the broth microdilution method, and 18 virulence genes were detected using PCR. Biofilm formation was measured by spectrophotometry with crystal violet staining and observed using confocal laser scanning microscopy. Results There were 12.12% (56/462) milk samples that were positive for Staph. aureus. These isolates were nonsusceptible to sulfamethoxazole (100%), penicillin (76.9%), daptomycin (76.79%), clindamycin (69.64%), and oxacillin (60.71%); however, the majority of the isolates (80.4%) were susceptible to amoxicillin/clavulanate. The predominant virulence genes encoded the cytotoxins, hla (94.64%) and hlb (89.29%), and the adhesion factors clfA (89.29%), clfB (89.29%), and fnbB (80.36%). Comparatively, virulence genes related to other adhesion factors such as cna (8.93%) and enterotoxins, such as seg (26.79%), sea (16.07%), seb (7.14%), and sec (7.14%) were detected at relatively lower rates. The following eight spa types were identified: t267 (35.84%), t730 (22.64%), t518 (15.09%), t1190 (11.32%), t1456 (9.43%), t224 (1.88%), t9129 (1.88%), and t177 (1.88%). The highest biofilm production was observed for t267. Staph. aureus exhibited various patterns of biofilm formation, with the biofilm often being associated with a tower-shaped structure or a thicker biofilm. Conclusion Our results indicated that Staph. aureus isolates from dairy cows with mastitis in the Liaoning Province of China were non-susceptible to sulfamethoxazole, penicillin, daptomycin, oxacillin, and clindamycin. Additionally, the most prevalent subtype was t267, which displayed resistance to multiple antimicrobial agents and harbored several virulence genes, including clfA, clfB, fnbB, hla, and hlb.
Oncology during the COVID-19 pandemic: challenges, dilemmas and the psychosocial impact on cancer patients

COVID-19 has caused unprecedented societal turmoil, triggering a rapid, still ongoing, transformation of healthcare provision on a global level. In this new landscape, it is highly important to acknowledge the challenges this pandemic poses on the care of the particularly vulnerable cancer patients and the subsequent psychosocial impact on them. We have outlined our clinical experience in managing patients with gastrointestinal, hematological, gynaecological, dermatological, neurological, thyroid, lung and paediatric cancers in the COVID-19 era and have reviewed the emerging literature around barriers to care of oncology patients and how this crisis affects them. Moreover, evolving treatment strategies and novel ways of addressing the needs of oncology patients in the new context of the pandemic are discussed.
Non-destructive DNA extraction for small pelagic copepods to perform integrative taxonomy

Molecular analyses of small-sized copepods (≤1 mm) generally involve the complete destruction of the specimens. Consequently, incongruences between the molecular and morphological results cannot be investigated since no specimen vouchers remain. The present study provides a modified column-based DNA extraction method to retain the exoskeleton of the specimen and thus, to enable molecular and morphological analysis of the same specimens. The method has been tested on ethanol preserved specimens of nine pelagic copepod genera.
Biochemical responses associated with bacterial blight of rice (Oryza sativa)

Biochemical response of susceptible cultivar TN 1 and resistant near isogenic lines IRBB 13 and IRBB 21 of rice to Xanthomonas oryzae pv. oryzae (Xoo) was studied at different stages of infection. The activities of the defence related enzymes peroxidase (PO), phenylalanine ammonia lyase (PAL) and tyrosine ammonia lyase (TAL) were found to be significantly higher in the resistant isogenic lines, IRBB 13 and IRBB 21 than in the susceptible cultivar TN 1. Total phenols, ortho-dihydroxyphenols and flavonols content also exhibited a similar trend as that of the enzymes. After bacterial infiltration a significant increase in the levels of total phenols, o-dihydroxyphenols, flavonols, PO, PAL and TAL was observed. However, this increase was comparatively rapid and higher in resistant near isogenic lines when compared with the susceptible line. Total sugars, reducing sugars and starch content were significantly higher in the leaves of the susceptible variety TN 1 than in the resistant near isogenic lines IRBB 13 and IRBB 21.
Evaluation of greenhouse gas emissions from HOG manure application in a Canadian cow-calf production system using whole-farm models

The development of beneficial management practices is a key strategy to reduce greenhouse gas (GHG) emissions from animal agriculture. The objective of the present study was to evaluate the impact of time and amount of hog manure application on farm productivity and GHG emissions from a cow–calf production system using two whole-farm models. Detailed model inputs (climate, soil and manure properties, farm operation data) were collected from a 3-year field study that evaluated the following three treatments: no application of hog manure on grassland (baseline); a single application of hog manure on grassland in spring (single); and two applications of hog manure as fall and spring (split). All three treatments were simulated in a representative cow–calf production system at the farm-gate using the following whole-farm models: a Coupled Components Model (CCM) that used existing farm component models and the Integrated Farm System Model (IFSM). Annual GHG intensities for the baseline scenario were 17.7 kg CO2-eq/kg liveweight for CCM and 18.1 kg CO2-eq/kg liveweight for IFSM. Of the total farm GHG emissions, 73–77% were from enteric methane production. The application of hog manure on grassland showed a mean emission increase of 7.8 and 8.4 kg CO2-eq/kg liveweight above the baseline for the single and split scenarios, respectively. For the manured scenarios, farm GHG emissions were mainly from enteric methane (47–54%) and soil nitrous oxide (33–41%). Emission estimates from the different GHG sources in the farm varied between models for the single and split application scenarios. Although farm productivity was 3–4% higher in the split than in single application (0.14 t liveweight/ha), the environmental advantage of applying manure in a single or split application was not consistent between models for farm emission intensity. Further component and whole-farm assessments are required to fully understand the impact of timing and the amount of livestock manure application on GHG emissions from beef production systems.
Prevalence of Current Smoking and Association with Adverse Outcome in Hospitalized COVID-19 Patients: A Systematic Review and Meta-Analysis

Background: The purpose of this study was to examine the prevalence and effects of current smoking on adverse outcomes among hospitalized COVID-19 patients. Methods: We performed a systematic review of the literature (PubMed) for studies published until April 25. Studies were included into the analysis if they satisfied all of the following criteria: 1. To present hospitalized patients with COVID-19. 2. To classify patients into less and more severe disease, irrespective of the severity definition (defined as “adverse ourtcome”). 3. To present data on the smoking status, separately for each severity classification. We identified 18 (from a total of 1398) relevant studies. Pooled current smoking prevalence was compared with the gender-adjusted, population-based expected prevalence by calculating Prevalence Odds Ratio (POR). The association between current, compared to non-current and former, smoking and adverse outcome was examined by calculating Odds Ratio (OR). All analyses were performed using random-effects meta-analysis. Results: Among 6515 patients, 440 of whom were current smokers, the pooled prevalence of current smoking was 6.8% (95%CI: 4.8-9.1%) and the POR was 0.21 (95%CI: 0.16-0.26, P < 0.001). In Chinese studies only, the POR was 0.22 (95%CI: 0.17-0.27, P < 0.001). Current smokers were more likely to have an adverse outcome compared to non-current smokers (OR: 1.53, 95%CI: 1.06-2.20, P = 0.022). However, they were less likely to have an adverse outcome compared to former smokers (OR: 0.42, 95%CI: 0.27-0.74, P = 0.003). Conclusion: An unexpectedly low prevalence of current smoking was observed among hospitalized patients with COVID-19. Hospitalized current smokers had higher odds compared to non-current smokers but lower odds compared to former smokers for an adverse outcome. The possibility that nicotine may have a protective effect in COVID-19 which may be masked by smoking-related toxicity and by the abrupt cessation of nicotine intake when smokers are hospitalized should be explored.
Traffic Offloading for Content Distribution Assisted With Device-to-Device Communications

While mobile networks are evolving rapidly, the battle between ever-growing traffic demands and out-paced network capacities will continue and require more efficient solutions. Emerging techniques such as mobile edge computing and device-to-device (D2D) communications can help relieve traffic at the mobile edge and accommodate surging traffic demands from various content-centric services. In this work, we focus on exploiting device caching and user collaboration to offload content distribution traffic. Specifically, we investigate the request offloading problem, which aims to appropriately select caching devices and maximize the content requests that can be fulfilled through D2D communications. Given the constraints of individual transmission and caching capacities, the number of available D2D channels, and information privacy with social-awareness, we can decouple the request offloading problem into two subproblems, i.e., the device caching and matching problem, and the D2D channel allocation problem. As we prove that both problems are NP-hard, we propose efficient algorithms that iteratively make a best local decision in each step. Simulation results show that the proposed algorithms perform fairly closely to optimal solutions in small-scale instances and outperform the reference schemes under various situations.
Alien and native plant species play different roles in plant community structure

Although impacts of alien plants on species richness are widely reported, it remains unclear how common such effects might be and whether they differ from those due to native species. To date, too few studies have examined the impacts of a wide enough spectrum of native and alien species to address the importance of geographic origin on the richness of plant communities. We investigated how total plant species richness, as well as its separate alien and native components, varied with the abundance of 115 alien and 146 native plant species across Banks Peninsula in New Zealand. Using null models, we tested whether significant correlations between the abundance of each focal species and species richness were more frequent than expected by chance. Examination of the differences in the relationships with species abundance found for native and alien richness can shed light as to whether alien species might be acting as drivers of biodiversity change or passengers responding to external environmental factors. Significant relationships were rarely found for total richness due to contrasting trends of native and alien richness with species abundance. In contrast to natives, an increase in the abundance of an alien species revealed more frequent negative relationships with native richness and positive correlations with alien richness. The relationship with species abundance found for native and alien components of richness differed between grasslands and woodlands. While we found putative support for negative impacts on native richness for several alien species in grasslands, the similar negative correlations in woodlands were more likely to reflect the shade intolerance of alien grasses where native species richness was high. Synthesis. Our analyses reveal that widespread alien and native species play different roles in the plant communities in which they co‐occur. Separately analysing the relationship with species abundance for alien and native components of richness can help distinguish between situations where aliens may be acting as the primary drivers in plant community changes or simply passengers. This is an essential first step in designing further experimental studies to determine the underlying ecological processes and potential ecosystem impacts of alien species.
Characterization of brown planthopper strains based on their differential responses to introgressed resistance genes and on mitochondrial DNA polymorphism

Biotypes cause a serious problem in controlling brown planthopper (BPH), Nilaparvata lugens Stal (Homoptera: Delphacidae). We characterized four BPH strains, which were collected in different localities in Japan and maintained by random mating within each strain for different periods. The virulence of the BPH strains was evaluated based on their postembryonic development on susceptible and resistant rice lines and inhibition of rice seedling growth. Two single resistance gene introgression lines, “Norin-PL3 (Bph1 carrier)” and “Norin-PL4” (bph2 carrier), and a pyramided line in which both genes were combined were used with a susceptible japonica recurrent parent “Tsukushibare” as a control. Sequence comparison of the mitochondrial cytochrome oxidase-I (COXI) gene was also performed in the characterization. The four BPH strains were classified into two or three groups with unique virulence spectra. The oldest strain showed avirulence against both introgressed resistance genes, while the three younger strains showed strong virulence against one or both genes. The different virulence spectra suggested the sequential adaptation of these BPH strains to the two resistance genes. Pyramiding of the resistance genes had no additive effect on rice seedlings carrying them even against avirulent and less-virulent BPH strains.
THE NUTRIENT CONTENT IN SUBSTRATES AND LEAVES OF GREENHOUSE TOMATO

Organic substrata applied in greenhouse cultivations are biodegradable. De- composition occurs during vegetation and as a waste during composting or ploughed in the field. The aim of the presented studies, conducted in the years 2008 and 2009 was to demonstrate the contents of macrocomponents in the solution from root environment of substrata and in tomato leaves. The tomato of Admiro F1 cultivar was grown in the fol- lowing substrata: 1) triticale straw, 2) triticale straw + high peat (3:1 v/v), 3) triticale straw + pine bark (3:1 v/v), 4) rockwool. Straw, cut into 2-3 cm pieces, straw with peat and bark were placed in plastic boxes (height twice as large as width). There was 15 dm 3 of organic substrata and rockwool. During tomato vegetation in organic substrata there was the least of N-NO3 at the beginning of growing (March), which could be related to biological sorption of nitrogen. In the subsequent months of cultivation the content of this nutrient was normal, according to the leaves recommended for tomato. Mean content of N-NH4, N-NO3, K, Ca, Mg in organic substrata did not significantly differ compared to rockwool. The EC value in organic and rockwool substrata was optimal during the whole vegetation period. The correct growth and high yield of tomato grown in organic substrata was obtained at the following mean contents in solution from root environment (mg dm -3 ): N-NH4 - 26.8, N-NO3 - 242.8, P -78.1, K - 295.6, Ca - 315.3, Mg - 107.5.
Grammatical conformity in question-answer sequences: The case of meiyou in Mandarin conversation

This article probes into grammatical conformity in Mandarin by examining meiyou, a multifunctional negative form, in question-answer sequences. Using a conversation analysis approach, it discovers that, as a conforming answer to polar questions, meiyou acquiesces to all the terms and constraints of the question and maximizes the progressivity of the sequence. As a non-conforming response to polar questions, it mitigates the disagreement by avoiding a pointed syntactic negation. Meiyou can also respond to Q-word questions, problematizing the inference incorporated in the question. This study not only contributes to the cross-linguistic research on negative particles in talk-in-interaction but also reveals that grammatical conformity is a crucial dimension in Mandarin response design, providing further confirmation of the link between grammar, action, and sequence organization.
Modeling Soil Water–Heat Dynamic Changes in Seed-Maize Fields under Film Mulching and Deficit Irrigation Conditions

The Soil–Water–Atmosphere–Plant (SWAP) model does not have a mulching module to simulate the effect of film mulching on soil water, heat dynamics and crop growth. In this study, SWAP model parameters were selected to simulate the soil water–heat process and crop growth, taking into account the effect of film mulching on soil evaporation, temperature, and crop growth, in order to predict the influence of future climate change on crop growth and evapotranspiration (ET). A most suitable scheme for high yield and water use efficiency (WUE) was studied by an experiment conducted in the Shiyang River Basin of Northwest China during 2017 and 2018. The experiment included mulching (M1) and non-mulching (M0) under three drip irrigation treatments, including full (WF), medium (WM), low (WL) water irrigation. Results demonstrated that SWAP simulated soil water storage (SWS) well, soil temperature at various depths, leaf area index (LAI) and aboveground dry biomass (ADB) with the normalized root mean square error (NRMSE) of 16.2%, 7.5%, 16.1% and 16.4%, respectively; and yield, ET, and WUE with the mean relative error (MRE) of 10.5%, 12.4% and 14.8%, respectively, under different treatments on average. The measured and simulated results showed film mulching could increase soil temperature, promote LAI during the early growth period, and ultimately improve ADB, yield and WUE. Among the treatments, M1WM treatment with moderate water deficit and film mulching could achieve the target of more WUE, higher yield, less irrigation water. Changes in atmospheric temperature, precipitation, and CO2 concentration are of worldwide concern. Three Representative Concentration Pathway (RCP) scenarios (RCP2.6, RCP4.5, RCP8.5) showed a negative effect on LAI, ADB and yield of seed-maize. The yield of seed-maize on an average decreased by 33.2%, 13.9% under the three RCPs scenarios for film mulching and non-mulching, respectively. Predicted yields under film mulching were lower than that under non-mulching for the next 30 years demonstrating that current film mulching management might not be suitable for this area to improve crop production under the future climate scenarios.
Phylogenetic relationships of Microdontinae (Diptera: Syrphidae) based on molecular and morphological characters

The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister‐group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k‐values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.
Complex Behaviors of Epidemic Model with Nonlinear Rewiring Rate

An SIS propagation model with the nonlinear rewiring rate on an adaptive network is considered. It is found by bifurcation analysis that the model has the complex behaviors which include the transcritical bifurcation, saddle-node bifurcation, Hopf bifurcation, and Bogdanov–Takens bifurcation. Especially, a bifurcation curve with “S” shape emerges due to the nonlinear rewiring rate, which leads to multiple equilibria and twice saddle-node bifurcations. Numerical simulations show that the model admits a homoclinic bifurcation and a saddle-node bifurcation of the limit cycle.
Standardized approaches in effectiveness monitoring programs and regional relevance: lessons from the Bowron River Watershed Riparian Evaluation Project

Streams and riparian areas in the Bowron River watershed were assessed using the riparian management routine effectiveness evaluation, a protocol developed for postharvest operational monitoring in British Columbia. Located in the British Columbia interior, the study watershed has had several decades to recover since a period of intensive salvage log- ging from 1977 to 1987 in response to a spruce beetle (Dendroctonus rufipennis) outbreak. Correlations were found with site-specific watershed characteristics and attributes that are used to answer the protocol indicator questions. Channel width was the strongest covariate, exhibiting the most significant relationships with the stream and riparian attributes. Sugges- tions on how to adjust standard protocols for stream size and landscape heterogeneity are discussed and include the use of appropriate reference sites for baseline data. We used correlations with watershed characteristics and multiple regressions based on regional reference sites to predict upper and lower threshold values by which attribute measurements could be compared. Sites that were assessed above or below threshold values for an attribute were considered to be outside the range of natural variation and were given a failing score. Attributes with the most failures 20-30 years postharvest were disturbed ground, bare soil, undercut banks, and shade.