Miracle-dz/UniFAR-FTUs huggingface dataset:
Disparate evolution of virus populations in upper and lower airways of mechanically ventilated patients

In routine surveillance and diagnostic testing, influenza virus samples are typically collected only from the upper respiratory tract (URT) due to the invasiveness of sample collection from the lower airways. Very little is known about virus variation in the lower respiratory tract (LRT) and it remains unclear if the virus populations at different sites of the human airways may develop to have divergent genetic signatures. We used deep sequencing of serially obtained matched nasopharyngeal swabs and endotracheal aspirates from four mechanically ventilated patients with influenza A/H3N2 infections. A physical barrier separating both compartments of the respiratory tract introduced as part of the medical procedures enabled us to track and compare the genetic composition of the virus populations during isolated evolution in the same host. Amino acid variants reaching majority proportions emerged during the course of infection in both nasopharyngeal swabs and endotracheal aspirates, and amino acid variation was observed in all influenza virus proteins. Genetic variation of the virus populations differed between the URT and LRT and variants were frequently uniquely present in either URT or LRT virus populations of a patient. These observations indicate that virus populations in spatially distinct parts of the human airways may follow different evolutionary trajectories. Selectively sampling from the URT may therefore fail to detect potentially important emerging variants. Importance Influenza viruses are rapidly mutating pathogens that easily adapt to changing environments. Although advances in sequencing technology make it possible to identify virus variants at very low proportions of the within-host virus population, several aspects of intrahost viral evolution have not been studied because sequentially collected samples and samples from the lower respiratory tract are not routinely obtained for influenza surveillance or clinical diagnostic purposes. Importantly, how virus populations evolve in different parts of the human respiratory tract remains unknown. Here we used serial clinical specimens collected from mechanically ventilated influenza patients to compare how virus populations develop in the upper and lower respiratory tract. We show that virus populations in the upper and lower respiratory tract may evolve along distinct evolutionary pathways, and that current sampling and surveillance regimens likely capture only part of the complete intrahost virus variation.
Analysis of Single Nucleotide Variants in CRISPR-Cas9 Edited Zebrafish Exomes Shows No Evidence of Off-Target Inflation

Therapeutic applications of CRISPR-Cas9 gene editing have spurred innovation in Cas9 enzyme engineering and single guide RNA (sgRNA) design algorithms to minimize potential off-target events. While recent work in rodents outlines favorable conditions for specific editing and uses a trio design to control for the contribution of natural genome variation, the potential for CRISPR-Cas9 to induce de novo mutations in vivo remains a topic of interest. In zebrafish, we performed whole exome sequencing (WES) on two generations of offspring derived from the same founding pair: 54 exomes from control and CRISPR-Cas9 edited embryos in the first generation (F0), and 16 exomes from the progeny of inbred F0 pairs in the second generation (F1). We did not observe an increase in the number of transmissible variants in edited individuals in F1, nor in F0 edited mosaic individuals, arguing that in vivo editing does not precipitate an inflation of deleterious point mutations.
Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning

Microbial communities in nature often feature complex compositional dynamics yet also stable coexistence of diverse species. The mechanistic underpinnings of such dynamic stability remain unclear as system-wide studies have been limited to small engineered communities or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community, realizes stable coexistence through spatio-temporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a dynamic fashion with early members opening metabolic niches for the followers. Through large-scale mapping of metabolic preferences and inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate, the community through metabolic cooperation and uneven partitioning between the grain and the liquid phase. Overall, our findings reveal how spatio-temporal dynamics promote stable coexistence and have implications for deciphering and modulating complex microbial ecosystems.
Cataract and its risk factor among adults residing in South Bihar, India

Background: Cataract is considered as one of the most common causes of visual impairment and the leading cause of blindness in the world. Age related cataract occurs in people above 50 years of age and the its pathogenesis is multifactorial. Therefore, the present study was aimed to assess the prevalence and risk factors for cataract. Methods: Community based cross sectional study was conducted among adults residing at urban areas of South Bihar. The data was collected by interview method, using pre-tested semi-structured questionnaire which contains socio-demographic data, dietary habits, history of diabetes or hypertension, family history of cataract and long-term sun exposure. Results: Among 240 participants, 94 (39.2%) were male and 146 (60.8%) were female. Maximum participants were aged more than 70 years. The prevalence of cataract was 52.1%. Conclusions: The prevalence of cataract was quite high and was significantly associated with age, long term sun exposure and family history of cataract.
Growth and Photosynthetic Response of Capsicum annuum L. in Biochar Amended Soil

The present study investigated the growth of Capsicum annuum L. (pepper) in an outdoor pot experiment. Changes in the plants’ aboveground and root biomass, leaf area, plant height, stem thickness, and yield, as a response to different doses of biochar amendments were observed. During the 12.5-week-long study, four treatments with biochar amounts of 0, 0.5%, 2.5%, and 5.0% (by weight) were added to silt loam soil. Photochemical responses of plants, the plants photochemical reflectance index (PRI) modified by the different doses of biochar were continuously monitored. Plant height and fruit yield were initially the highest for BC5.0; however, by the end of the experiment, both parameters showed higher values for BC2.5, e.g., 15.9 and 9.1% higher plant height and 32.5 and 22.6% higher fruit yield for BC2.5 and BC5.0 compared to control, respectively. By the end of the experiment the BC2.5 treatments had significantly higher stem thickness (p < 0.001) compared to all other amendments. Root dry matter in biochar treatments increased relative to controls with the highest values (54.9% increase) observed in the BC2.5 treatment. Biochar treatment increased leaf area index (LAI) values for the higher doses (1.58, 1.59, 2.03, and 1.89 for C, BC0.5, BC2.5, and BC5.0, respectively). Significant differences between control and biochar amended soils’ PRI measurements were observed (p < 0.001), showing less plant sensitivity to environmental changes when biochar was applied to the soil. While biochar amendment could greatly enhance plant growth and development, there is an optimal amount of biochar after which additional amount might not result in substantial differences, or even can result in lower fruit yield as found in the present study.
Perceived Morbidity Patterns among Workers in the Oil Industry of Nigeria

Background: Globally, the oil industry is replete with several high-risk activities as seen in seismic exploration, construction, drilling, production, and maintenance. Generated hazards could impact exposed workers. Exposure to associated hazards and rigour of activities usually puts workers in oil and gas installations at risk of developing several occupational illnesses. Environmental problems have also been reportedly associated with these activities as well. This study was thus aimed at determining the perceived environmental effects and morbidity patterns among staff of an oil and gas installation in the Niger Delta Region of Nigeria. Methods: A descriptive, cross-sectional study design was used in conducting this study in an onshore oil and gas hub in Nigeria. Study group comprised engineers and technicians of various oil and gas specialties. A random sampling method was used to select 256 personnel from the study population. A self-administered questionnaire was administered to the personnel of the facility. Data was analysed using the Statistical Package for Scientific Solutions (SPSS) version 17.0 (statistical software package) for analyses. Ethical considerations were adhered to during this study. Results: Common complaints include transient tinnitus (97.3%), joint pain of varying degrees (83.6%), occasional prickling sensation in the skin (78.1%) and the lowest frequency of health Original Research Article Osakwe; JAMMR, 32(9): 66-72, 2020; Article no.JAMMR. 58224 67 effects was claims of stressful feeling (56.6%). Environmental problems including the destruction of aquatic biodiversity as well as water contamination were reported in this study. Conclusion: This study found experience of several morbidities by the respondents. They also reported observation of certain environmental problems related with oil exploratory activities at the oil and gas installation. It is recommended that a regular review of measures be put in place to prevent these health and environmental problems from occurring in or around oil and gas installation located in Nigeria.
Improved “K” type seven‐level switched capacitor inverter topology with Self‐voltage balancing

This paper proposes an improved “K” type seven‐level switched capacitor inverter topology. The proposed topology consists of eight active switches, one floating capacitor, and two dc‐link capacitors. The floating capacitors are charged and discharged in each half‐cycle to maintain the capacitor voltage with the same value of the input voltage. The floating capacitor voltage is self‐balanced, and the output voltage is 1.5 times higher than the input voltage. To prove the superiority of the proposed topology, it is compared with the existing seven‐level inverters in terms of maximum voltage stress on the switch and required the number of power components. The simulation and experimental validation are carried out for 1.6 kW, 50 Hz using a laboratory‐based setup with a switching frequency of 5 kHz. The results are discussed highlighting the performance of the proposed topology for the dynamic load variations at different modulation indices. Both simulation results and experimental results have good agreement in terms of voltage balancing of flying capacitor.
Application of piezosurgery osteotomy in cervical laminoplasty: prospective, randomized, single-blind, clinical comparison study

Objective: To compare and analyze the clinical efficacy of piezosurgery osteotomy and high-speed drilling respectively in cervical laminoplasty, so as to explore the operability, safety and clinical application value of piezosurgery osteotomy in cervical laminoplasty. Methods: A total of 60 patients with multilevel cervical stenosis from the Inner Mongolia Autonomous Region People's Hospital were randomly divided into two groups (piezosurgery osteotomy group and high-speed drill group) with 30 patients in each group. Operation time, intraoperative blood loss, postoperative drainage, complication rate, Japanese orthopaedic association (JOA) score and JOA improvement rate were compared and analyzed. Results: The operation time in piezosurgery osteotomy group and high-speed drill group was (87 ± 22 min) and (96 ± 35 min), respectively, and the difference between two groups was not statistically significant (P > 0.05). The intraoperative blood loss in the piezosurgery osteotomy group was (121 ± 86 mL) lower than that (172 ± 93 mL) in the high-speed drill group (P 0.05). Dural injury developed 1 patient in high-speed drill group and cerebrospinal fluid leakage occurred after surgery. No serious complications such as spinal cord injury occurred in either group. Conclusion: Piezosurgery osteotomy in cervical laminoplasty is safe and effective, and is superior in operation time, intraoperative blood, and postoperative drainage. Its safety and efficacy are similar to high-speed drill in cervical laminoplasty. Keywords: Cervical laminoplasty; piezosurgery osteotomy; high-speed drill; cervical spondylotic myelopathy; safety; efficacy
Polymerization coupled to oscillating reactions: A mechanistic investigation of acrylonitrile polymerization in the Belousov-Zhabotinsky reaction in a batch reactor.

When acrylonitrile is added to the Belousov−Zhabotinsky reaction, periodic polymerization is observed. (Pojman, J. A.; Leard, D. C.; West, W. W. J. Am. Chem. Soc. 1992, 114, 8298). The polymer's structure and the amount of bromine in the polymer sample were determined by 13C NMR and elemental analysis, respectively. Carbon-13-labeled malonic acid indicates that polymerization of acrylonitrile is initiated by malonyl radical. The bromous radicals are believed to terminate the polymer leaving an alcohol group on the polymer end. Further analysis of the polymer sample confirms that the sample is partially brominated. Numerical simulations based on a modified FKN mechanism are found to be in good agreement with experimental findings. Simulations indicate that periodic termination of the polymer chain by bromine dioxide, not the periodic initiation by malonyl radical, is the dominant cause of the periodic polymerization. Similar results were found in the malonyl-controlled variant of the BZ reaction.
English Language Speaking Anxiety among Students from Two Public Universities in Sarawak

This quantitative research studied the anxiety level of university students towards speaking English as a second language (ESL)to examine whether there is any correlation between the university students’ ESL speaking anxiety and the demographic factors such as the SPM English results, mother tongue, and parents’ academic qualifications. A sample of 592 students was randomly selected from two public universities in Sarawak, Malaysia. Items in the PSCAS questionnaire by Yaikhong and Usaha (2012) were adapted to measure the students’ anxiety level in speaking English. Data were analysed using descriptive statistics to identify the students’ anxiety level in speaking English. Inferential statistics (Pearson correlation) was used to examine the relationship between the university students’ ESL speaking anxiety and demographic factors. The findings indicate that these students experienced a moderate level of speaking anxiety. There was a positive correlation between the university students’ ESL speaking anxiety and SPM English Language results. Nevertheless, there was a low negative correlation between the students’ ESL speaking anxiety and mother tongue as well as parents’ academic qualifications. Findings from this study provide a basis for educators to plan effective teaching strategies to reduce English speaking anxiety among university students.
The effects of different mowing regimes on diversity of grasses in lowland meadows

This study addresses the question of how changing the mowing regime influences the floristic composition and floristic diversity of grasses in an experimental lowland meadow. The study location is Bia? owie? a Forest, NE Poland. To achieve the aim we used phytosociological data from long-term studies in Bia? owie? a Forest on the course of secondary succession. The relationship between the biodiversity of grasses and type of mowing was determined using statistical analysis. Changes in the dominance and frequency of individual grass species have occurred during the last 28 years of observations. The analysis of floristic similarity demonstrated a turnover of species between the individual years of observation. Principal component analysis showed that the change in mowing method resulted in a change of the species composition, cover, and domination. However, differences in the intensity of disturbance level were rather small (one cut yearly by scythe, by sickle bar mower, and by trimmer), and changes in floristic composition were also moderate in most years. During the initial years (1984? 1990), Dactylis glomerata , Agrostis gigantea , and Anthoxanthum odoratum dominated. After 1990, Arrhenatherum elatius and Holcus lanatus spread and took over, with Trisetum flavescens joining them later. Between 2008 and 2012 the cover of Dactylis glomerata increased more than two times. The reasons for the floristic transformations were changes in the management mode, e.g., the transition from mowing by scythe (medium disturbance) to mechanized mowing, first by sickle bar mower (strong disturbance) and then by trimmer (weak disturbance).
Action of thymol, carvacrol and eugenol on Penicillium and Geotrichum isolates resistant to commercial fungicides and causing postharvest citrus decay

Abstract This study aimed to evaluate the antifungal activity of oregano and clove essential oils and their main components (thymol, carvacrol and eugenol) against Penicillium digitatum, as well as against isolates of Penicillium italicum and Geotrichum candidum resistant to imazalil or guazatine, respectively. In vitro tests were conducted by a direct contact method on potato dextrose agar medium. The results indicated that the essential oils and their main components were effective in inhibiting fungal growth, with thymol displaying the highest efficacy. The antifungal activity of thymol was evaluated further on orange fruit infected experimentally with a suspension of spores of P. digitatum, G. candidum or a mixture of both fungi, using isolates resistant to chemical fungicides. Treatment of the oranges with the thymol solutions reduced or totally inhibited the development of fruit decay, depending on the thymol concentration used. These essential oils and their main components demonstrated a strong antifungal effect against Penicillium spp. and G. candidum resistant to chemical fungicides. They may have potential as active compounds for the formulation of natural preparations to use as alternatives to synthetic fungicides for the management of green, blue and sour rot in citrus fruit.
Simple model of evapotranspiration by Eucalyptus plantations for data poor areas and tested using water balance data from a small catchment in Guangxi, China

ABSTRACT Measurements of catchment and stand water balance were made in a small, upland catchment in Guangxi province, China that was covered with a plantation of a Eucalyptus urophylla × Eucalyptus grandis hybrid. These data were used to investigate the relationship between streamflow and the net stand water balance and to test the efficacy of a relationship between the crop factor (ratio of evapotranspiration to potential evaporation) and relative plant available soil water for predicting evapotranspiration. The model was then used to quantify the effect of afforestation with Eucalyptus plantations on the water balance of (1) upland catchments with shallow soils and (2) catchments with deeper soil profiles such as those that can occur in lowland catchments in Guangxi. During the experiment, the plantation experienced a dry year in 2014, when rainfall was 1095 mm, and a year with approximately average rainfall in 2015 (1493 mm). In 2014, plantation evapotranspiration was 779 mm or 71% of rainfall while during 2015 the annual plantation evapotranspiration was 931 mm or 61% of rainfall. Measured streamflow for a full year was only 18 mm (2%) less than the difference between rainfall and estimated evapotranspiration. The relationship between measured streamflow and the net stand water balance was also strong (r2 = 0.8) and unbiased (slope of 1.006). A model that predicted the crop factor as a function of relative plant available soil water explained more than 78% of the variation in observed evapotranspiration and had a model efficiency of 0.73. It also provided an unbiased prediction of monthly evapotranspiration. When used to model the effect of a change from grassland to a plantation of E. urophylla, it predicted an average annual decrease in drainage of 70 mm and a 5% increase in the number of months with zero flow.
Let’s nab fake science news: Predicting scientists’ support for interventions using the influence of presumed media influence model

Fake science news is a type of fake news that can threaten the credibility of the scientific community. Scientists’ attention to fake science news can indirectly influence the way they react to tackling fake science news through socio-psychological factors. Applying the influence of presumed media influence (IPMI), this study examines how scientists’ attention to fake science news indirectly influences their support for initiatives to tackle fake science news through presumed harm of fake science news on other scientists and the general public, as well as their attitude and personal norm towards tackling fake science news. Specifically, this study explicates the behavioural outcome into support for education and support for legislation against fake science news. The results from a survey of 706 Singapore-based scientists supported the relationships posited in the IPMI. Theoretical and practical implications are discussed.
What factors are most important in finding the best model of a psychological process?

Psychology research has become increasingly focused on creating formalized models of psychological processes, which can make exact quantitative predictions about observed data that are the result of some unknown psychological process, allowing a better understanding of how psychological processes may actually operate. However, using models to understand psychological processes comes with an additional challenge: how do we select the best model from a range of potential models that all aim to explain the same psychological process? A recent article by Navarro (2019; Computational Brain & Behavior) provided a detailed discussion on several broad issues within the area of model selection, with Navarro suggesting that “one of the most important functions of a scientific theory is . to encourage directed exploration of new territory” (p.30), that “understanding how the qualitative patterns in the empirical data emerge naturally from a computational model of a psychological process is often more scientifically useful than presenting a quantified measure of its performance” (p.33), and that “quantitative measures of performance are essentially selecting models based on their ancillary assumptions” (p.33). Here, I provide a critique of several of Navarro’s points on these broad issues. In contrast to Navarro, I argue that all possible data should be considered when evaluating a process model (i.e., not just data from novel contexts), that quantitative model selection methods provide a more principled and complete method of selecting between process models than visual assessments of qualitative trends, and that the idea of ancillary assumptions that are not part of the core explanation in the model is a slippery slope to an infinitely flexible model.