Miracle-dz/UniFAR-FTUs huggingface dataset:
Mining of candidate genes involved in the biosynthesis of dextrorotatory borneol in Cinnamomum burmannii by transcriptomic analysis on three chemotypes

Background Dextrorotatory borneol (D-borneol), a cyclic monoterpene, is widely used in traditional Chinese medicine as an efficient topical analgesic drug. Fresh leaves of Cinnamomum trees, e.g., C. burmannii and C. camphor, are the main sources from which D-borneol is extracted by steam distillation, yet with low yields. Insufficient supply of D-borneol has hampered its clinical use and production of patent remedies for a long time. Biological synthesis of D-borneol offers an additional approach; however, mechanisms of D-borneol biosynthesis remain mostly unresolved. Hence, it is important and necessary to elucidate the biosynthetic pathway of D-borneol. Results Comparative analysis on the gene expression patterns of different D-borneol production C. burmannii samples facilitates elucidation on the underlying biosynthetic pathway of D-borneol. Herein, we collected three different chemotypes of C. burmannii, which harbor different contents of D-borneol.A total of 100,218 unigenes with an N50 of 1,128 bp were assembled de novo using Trinity from a total of 21.21 Gb clean bases. We used BLASTx analysis against several public databases to annotate 45,485 unigenes (45.38%) to at least one database, among which 82 unigenes were assigned to terpenoid biosynthesis pathways by KEGG annotation. In addition, we defined 8,860 unigenes as differentially expressed genes (DEGs), among which 13 DEGs were associated with terpenoid biosynthesis pathways. One 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and two monoterpene synthase, designated as CbDXS9, CbTPS2 and CbTPS3, were up-regulated in the high-borneol group compared to the low-borneol and borneol-free groups, and might be vital to biosynthesis of D-borneol in C. burmannii. In addition, we identified one WRKY, two BHLH, one AP2/ERF and three MYB candidate genes, which exhibited the same expression patterns as CbTPS2 and CbTPS3, suggesting that these transcription factors might potentially regulate D-borneol biosynthesis. Finally, quantitative real-time PCR was conducted to detect the actual expression level of those candidate genes related to the D-borneol biosynthesis pathway, and the result showed that the expression patterns of the candidate genes related to D-borneol biosynthesis were basically consistent with those revealed by transcriptome analysis. Conclusions We used transcriptome sequencing to analyze three different chemotypes of C. burmannii, identifying three candidate structural genes (one DXS, two monoterpene synthases) and seven potential transcription factor candidates (one WRKY, two BHLH, one AP2/ERF and three MYB) involved in D-borneol biosynthesis. These results provide new insight into our understanding of the production and accumulation of D-borneol in C. burmannii.
COVID‐19 and Ethnic Inequalities in England and Wales*

Abstract The economic and public health crisis created by the COVID‐19 pandemic has exposed existing inequalities between ethnic groups in England and Wales, as well as creating new ones. We draw on current mortality and case data, alongside pre‐crisis labour force data, to investigate the relative vulnerability of different ethnic groups to adverse health and economic impacts. After accounting for differences in population structure and regional concentration, we show that most minority groups suffered excess mortality compared with the white British majority group. Differences in underlying health conditions such as diabetes may play a role; so too may occupational exposure to the virus, given the very different labour market profiles of ethnic groups. Distinctive patterns of occupational concentration also highlight the vulnerability of some groups to the economic consequences of social distancing measures, with Bangladeshi and Pakistani men particularly likely to be employed in occupations directly affected by the UK's ‘lockdown’. We show that differences in household structures and inequalities in access to savings mean that a number of minority groups are also less able to weather short‐term shocks to their income. Documenting these immediate consequences of the crisis reveals the potential for inequalities to become entrenched in the longer term.
DIPPING SOLUTIONS OF NISIN AND BUFFERED SODIUM CITRATE SUPPLEMENTED WITH SODIUM DIACETATE FAIL TO PREVENT GROWTH OF LISTERIA MONOCYTOGENES ON VACUUM PACKAGED BEEF FRANKFURTERS STORED AT 4 AND 10°C UNDER MODEL CONDITIONS

This study evaluated commercially available dip solutions of nisin alone, buffered sodium citrate combined with sodium diacetate (BSCSD), and combined solution of the three antimicrobials for potential to control growth of surface-inoculated Listeria monocytogenes during vacuum packaged refrigerated storage of model beef frankfurters. None of the treatments prevented growth of L. monocytogenes during Frankfurter storage. The combined treatments slowed growth of L. monocytogenes better than individual treatments. Failure to completely eliminate L. monocytogenes on frankfurters or inhibit outgrowth during storage might be attributed to high initial L. monocytogenes inoculum levels, insufficient quantities of antimicrobials to interact with all the target cells, low nisin activity at high pH, or presence of resistant subpopulations, such as nisin-resistant strains. The model conditions used in the experimental setup, such as elimination of natural microbiota from frankfurters and nutrient-rich diluent used for Listeria introduction on the surface, could also contributed to enhanced survival and growth of the pathogen.
Studies on the adult and metacercaria of Holostephanus lühei Szidat, 1936

The metacercaria of Holostephanus lühei Szidat (1936) is described together with comments on both its linear and tissue distribution within the host (Gasterosteus aculeatus L.), host-parasite reaction and numbers of cysts in relation to the size of the fish. The adult of Holostephanus lühei Szidat (1936) (syn. H. bursiformis Szidat, 1936) obtained experimentally from the duck and pigeon, is re-described in detail. It is noted that this species is amphitypic and it is suggested that H. dubius (Szidat, 1936) (syn. Cyanocotyloides Dubius, Szidat, 1936) should be reduced to synonymy with H. lühei. Grateful acknowledgement is expressed to Dr G. Dubois for his interest, advice and valuable opinions given in connexion with this study.
Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region

It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion.
Prevalence of Oral Microbes in the Saliva of Oncological Patients

This study examined the prevalence of oral microbes in the saliva of oncological patients and healthy subjects. PCR was used to assess the frequency of oral microbes including 3 cariogenic bacteria, 5 periodontopathic bacteria and 4 Candida species in the saliva of 104 oncological patients and 52 healthy subjects. Among these microorganims, Streptococcus mutans, Fusobacterium nucleatum and Candida albicans were most frequently detected in both groups. There were no significant differences in the prevalence of cariogenic bacteria between the patient and healthy groups, whereas significant differences in the frequency of Porphyromonas gingivalis and Tannerella forsythia were observed between the two groups (p ＜ 0.05). The prevalence of all five periodontopathogens was higher in the healthy group than in the patient group. The prevalence of C. albicans in patients was significantly higher than that of healthy group (p ＜ 0.05). In conclusion, there were significant differences in the prevalence of P. gingivalis, T. forsythia and C. albicans between the oncological patient group and healthy group.
Current Status and Trends in Muskegon Lake, Michigan

ABSTRACT A long-term monitoring program was initiated in 2003 to determine the ecological status of Muskegon Lake, a Great Lakes Area of Concern. This paper presents data generated from the first 3 years of the monitoring program, discusses how the data are being used to establish and justify lake restoration targets, and assesses how water quality conditions have changed over time. Between 1972 and 2005, lake-wide averages of total phosphorus and soluble reactive phosphorus from the water surface have declined from 68 to 27 μg/L and from 20 to 5 μg/L, respectively. In addition, average chlorophyll α concentrations have declined from 25 to 6 μg/L over this period, while Secchi disk depths have increased from 1.5 to 2.2 m. Wastewater diversion, and perhaps dreissenid filtering activity, is most likely responsible for these changes. However, nitrate concentrations have increased from 70 to 270 μg/L over the same time period. During 2003–2005, phytoplankton abundance and fish catch were lower in the spring compared to the summer and fall. Microcystis was the most abundant phytoplankton genus; the fish community generally was dominated by round goby (Neogobius melanostomus) in spring and summer, and sunfishes (Centrarchidae) in the fall. Dreissenid abundance was highly variable over time, but densities were low relative to Saginaw Bay. Approximately 65% of the Muskegon Lake shoreline has been hardened (i.e., physically altered). Overall, the water quality of Muskegon Lake has improved over the past 30 years, but environmental challenges still exist, including contaminated sediments, loss of natural habitat, and invasive species.
Prevalence and Associated Factors of Thinness among Adolescent Students in Finote Selam Town, Northwest Ethiopia

Even if adolescence is a window of opportunity to break the intergenerational cycle of malnutrition, adolescents are the neglected age groups. Hence, information regarding the nutritional status of adolescents is lacking, making creating and implementing intervention programs difficult. This study aimed to assess the prevalence and determinants of thinness among school adolescents in Finote Selam Town, Northwest Ethiopia. A school-based cross-sectional study among adolescent students aged 10–19 in public primary and secondary schools was carried out in Finote Selam Town from February 05 to March 27, 2018. Stratified and simple random sampling techniques were employed to select study subjects. A total of 397 adolescent students were included in the study. Pretested structured questionnaires were used to collect the data. Data were entered using Epi Info version 7 and analyzed using SPSS version 20 and WHO AnthroPlus software. A multivariable binary logistic regression analysis was employed to identify factors associated with thinness. Crude and adjusted odds ratios with 95% level significance were used to measure the strength of association, and statistical significance was declared at p value less than 0.05. The prevalence of thinness among adolescents was 14.9%. Early adolescent stage (AOR = 4.81; 95% CI : 1.23, 18.51), being male adolescent students (AOR = 2.33; 95% CI : 1.60, 3.40), having less than 1000 birr family monthly income (AOR = 6.54; 95% CI : 3 : 82, 14.89), having 1000–2000 birr family monthly income (AOR = 3.47; 95% CI : 1.15, 7.45), and using well water (AOR = 3.82; 95% CI : 1.46, 10.04) were significantly associated with thinness at 95% confidence interval. The study revealed that prevalence of thinness was high in the study area. Sex, place of residence, and family monthly income were found to be important factors associated with thinness among the respondents.
Spatial Instabilities within the Diffusive Lotka-Volterra System: Individual-Based Simulation Results

Abstract A predator-prey system is studied via an individual-based simulation technique involving discrete Lotka-Volterra-type predator and prey individuals occupying a two-dimensional lattice of up to 256 sites by 256 sites, encompassing up to 65,536 predators and 65,536 prey. Spatial instabilities are found that break the system into "asynchronous regions" that can stabilize the "global" populations. These spatial heterogeneities are determined to be the result of discretizing space, time, and the population. Agreement is found with analytic results for the non-spatial Lotka-Volterra model and the spatial Lolka-Volterra model with diffusion when the discretizations are scaled to zero. It is argued from an individual-based modelling perspective, however, that this limiting procedure is biologically untenable. The conclusion is that under an individual-based model formulation of the Lotka-Volterra system, spatially heterogeneous population distributions are allowed. The specific form of these spatial distributions are shown to be strongly dependent on the prey diffusion rate and the specifics of implementing individual stochasticity.
Altered levels of primary metabolites in response to exogenous indole-3-acetic acid in wild type and auxin signaling mutants of Arabidopsis thaliana: A capillary electrophoresis-mass spectrometry analysis

A comprehensive analysis of the levels of primary metabolites in wild type (WT) and several auxin-signaling mutants namely, tir1, slr and arf7 arf19 of Arabidopsis thaliana has been performed using CE-MS, a technique particularly sensitive for the measurement of polar compounds. We first measured the levels of primary metabolites in shoots and roots, most of the analyzed metabolites were found to be quantitatively and qualitatively comparable in WT and three kinds of mutants (tir1, slr and arf7 arf19). Some amino acids such as GABA, Arg, Orn, Val, Thr, Leu and Ile exhibited a unique pattern of distribution between shoots and roots in both WT and the mutants. On the other hand, the mutant slr showed a quite different pattern of metabolites measured in the present study. Subsequently, the responses of primary metabolites to a short-term (60 min) application of exogenous IAA (10−7, 10−8 M) in WT and the mutants were characterized. Due to IAA treatments, some amino acids such as GABA in WT roots and Gly and Ala in WT shoots were altered, but not in the mutants. Gln was altered in slr shoots by 10−7 M IAA treatment. Levels of G6P from the glycolic pathway were altered in WT roots and those of 2PG, 3PG were altered in tir1 shoots in response to IAA treatments. The levels of succinate in TCA cycle were altered by IAA treatments in WT shoots but not in the mutants. IAA treatment inhibited the respiration in WT roots. The suppression of respiration might account for the IAA-dependent alteration of some metabolites. Difference of auxin responses between WT and auxin-signaling mutants suggests that some metabolic processes are under IAA control.
Factors affecting the genotypic and genetic diversity of the dioecious clonal plant Cirsium arvense at the metapopulation level

In many clonal species, seedling establishment is restricted to early successional stages when recruitment is still possible. Then, one expects that adapted genotypes become dominant and genotypic and genetic diversity should decrease with time. We investigated genotypic and genetic diversity within recently founded and established populations of the common weed Cirsium arvense. We used highly polymorphic AFLP markers. All populations were multiclonal and highly diverse (proportion of distinguishable genotypes was 0.73 ± 0.25 (mean ± SD)). Clonal evenness was variable and ranged from 0.2 to 1. Independent of successional stage, we found on the small geographic scale of our study (< 5 km) a considerable differentiation between populations (Φsc = 0.63). This amount of differentiation was similar between founder and established populations and could result from selection in the early stage of selection, as well as founder effects. Contrary to the general expectation, genotypic and genetic diversity were maintained through time, and molecular variance did not differ between successional stages (1.9 ± 0.89 versus 2.5 ± 1.41). We suggest that this pattern is a consequence of the particular reproductive system of C. arvense that combines clonality with dioecy. The combination of clonal reproduction with recruitment of sexually outcrossed seedlings in the first years allows the species to perform efficient colonisation even with founder effects, to undergo selection without loss of diversity, and to persist locally. This strategy appears to be very efficient in C. arvense and may have contributed to the worldwide success of this species.
The Water Economy of Salamanders: Evaporative Water Loss

these behavioral techniques, one must be able to predict the rate at which water will evaporate from the skin surface under various circumstances and the effect that the behavior will have on that loss rate. This communication will report experiments exploring the relationship between the size of an amphibian and the rate at which it loses water by evaporation. Initially, it might be postulated that the evaporative loss of water from the skin of a salamander into a particular environment will be proportional to the surface area of that salamander. In other words, it might be predicted that, on a large and a small salamander sitting side by side, areas of equal size would be losing water at the same rate. However, water loss from small free-water surfaces is not directly proportional to the area of the surfaces (Sleight, 1917); likewise, water loss from snails is not directly proportional to the surface they expose to the air (Machin, 1964). These observations of Sleight and Machin suggest a second hypothesis: Otherwise identical areas of skin on salamanders differing in size may lose water at different rates, per unit of surface, and the rate of loss would be a function of the size of the salamanders. A test differentiating these two hypotheses will require a measure of the surface area of the salamanders. The surface of a body is proportional to the twothirds' power of the weight (W0'67), and an acceptable approximation for most tetrapods is: surface area = 10(body weight)"67, as suggested by Benedict (1932). This formula incorporates the assumption that the constant K' (here equal to 10) does not change during the growth of the animal. If this assumption is correct, within the limits of the accuracy of the measurement of surface area, then the first hypothesis can be stated as E = kWo.67, where E is the rate of evaporation and k is equal to K'. The hypothesis can be rejected if the slope of a regression line between experimentally determined values of log E and various values of log W is significantly different from 0.67. Whitford and Hutchison (1967) have measured the surface area of specimens of several species of salamanders and report that their data can be described with the relationship: surface area in cm2 = 8.42(weight in grams)0.694. The value 0.694 is not significantly different from 0.67; the differences reflect both the uncertainty of the measurements and actual ontogenetic changes in body shape. The lack of a significant difference between 1Present address: Department of Zodlogy, University of Washington, Seattle, Washington 98105.
Comparison of Human to Macaque Uterosacral–Cardinal Ligament Complex and Its Relationship to Pelvic Organ Prolapse

The uterosacral–cardinal ligament complex is thought to be the critical structure responsible for uterine and apical vaginal support. It is ill defined and can be difficult to dissect in the cadaver lab and in the operating room. Even less information is available on the analogous structures in the monkey model. We present this report to bring together what little is known to aid in studying this model and pelvic organ prolapse (POP), and to point out the need for critical assessment of this hormone-responsive tissue in the process of drug development. Competing Interests: This article was sponsored by Covance Inc. and Schering-Plough. The authors did not declare any other competing interests.
An Efficient Sampling Survey Design to Estimate Pink Shrimp Population Abundance in Biscayne Bay, Florida

Abstract We developed an efficient sampling design-based approach using fishery-independent surveys to estimate population abundance of pink shrimp Penaeus duorarum over time in Biscayne Bay, Florida. We initially implemented quarterly stratified random sampling (StRS) using nine habitat strata and determined that average pink shrimp density (numbers/m2) was highest in late fall and lowest in spring and late summer. Coefficient of variation of the quarterly surveys, expressed as percent standard error/mean density, ranged from 5.8% to 14.3%. We found StRS to be more efficient (i.e., with lower variance) than simple random sampling (SRS) in most seasons. Statistical analyses suggested that pink shrimp densities were dependent on the biophysical habitat variables of bottom substrate, depth, and salinity. We also noted ontogenetic shifts in these relationships that were particularly pronounced at the onset of sexual maturation. Poststratification analysis was used to further evaluate several alternative habi.
Analysis of Seedling Vigour in Bacteriologically Treated Sewage Water

The study was concerned about the effect of the sewage water in the agricultural fields as an irrigation perspective. In vitro experiment was done where the seeds of Cicer arientinum and Vigna radiata were treated with the different concentrations of untreated and bacterial consortium treated sewage water. The effect of sewage water on seedling growth was suitable in the lower concentration (25%), whereas the higher concentration (50, 75 and 100%) was inhibitory in untreated. The sewage water after treatment was found to be of improved quality and showed good germination and seedling growth.