Miracle-dz/UniFAR-FTUs huggingface dataset:
Therapeutic Effect of Berberine on Insomnia Rats by ErbB Signaling Pathway

Background Insomnia seriously affects people’s health and quality of life. Short-term use of Western drugs may also be harmful. Traditional Chinese medicine has been widely used to treat diseases in world. Therefore, this paper aims to study the therapeutic effect of berberine based on the insomnious rat model. Material/Methods The insomnia rat model was established by intragastric administration of caffeine and parachlorophenylalanine (PCPA). Berberine and diazepam were used to treat the established insomnia rats. Then, the pathological changes of insomnia rats were detected. In addition, transcriptome sequencing and data analysis were carried out using rat hippocampus. The expression of key genes was verified by quantitative polymerase chain reaction and western blot. Results After 7 days of intragastric administration of berberine, the body weight, memory, and sleep quality of insomnia rats were significantly improved. The key roles of Erbb4, Erbb2, Ar, and Grin2a in berberine treatment were identified. Through the analysis of biological functions and signaling pathways, berberine was shown to play a salutary role through nervous system development and ErbB signaling pathway. Gene-set enrichment analysis (GSEA) results showed that berberine treatment affected more metabolic pathways. Compared with diazepam, berberine can play a faster role, and also improve the overall health level of insomnia rats. Conclusions These results suggest that berberine can alleviate insomnia in rats through a neuroprotective effect and improved metabolic level. Berberine has great potential in treatment of insomnia and might have better clinical significance.
A Personality Trait-Based Network of Boredom, Spontaneous and Deliberate Mind-Wandering

This article reports the translation into German and validation of two self-report measures of mind-wandering and boredom (the Spontaneous and Deliberate Mind-Wandering Scales and the Short Boredom Proneness Scale). Confirmatory factor analyses provided support for the original conceptualization of the constructs. To evaluate measurement invariance across samples, data were collected in a German-speaking sample (n = 418) and an English-speaking sample (n = 364). The results indicated weak measurement invariance. To explore the interplay between mind-wandering and boredom, we performed an exploratory graph analysis in the entire sample (N = 782), which revealed the structure of relationships between boredom and the two facets of mind-wandering. The results are discussed in the context of theoretical accounts of boredom and mind-wandering.
Occurrence of aflatoxin M1 in UHT milk in Erzurum-Turkey.

Summary In this study, 150 UHT milk samples were analyzed for aflatoxin M1. They were obtained from supermarkets in Erzurum city. The occurrence and concentration range of AFM1 in the samples were investigated by ELISA method. Fifty-nine percent of the UHT milk samples contained AFM1. AFM1 levels in 16 (10.7%) UHT milk samples exceeded the maximum tolerable limit of the European Community and the Turkish Food Codex. It was concluded that high AFM1 level is an important problem threatening the public health in Turkey.
Acetylcholinesterase inhibitors in the context of therapeutic strategies to combat Alzheimer’s disease

Acetylcholinesterase inhibitors (AChEIs) are a class of drugs useful in the treatment of Alzheimer’s disease (AD) as a result of their indirect cholinomimetic effect. In this review, patents claiming AChEIs that have appeared from the late 1990s (after the marketing of second generation compounds) to the present day will be discussed. The patents filed in this period fall into two categories of AChEIs, new products and combinations of drugs. Most of the new compounds are modifications of known drugs, although some novel structures have been claimed. The association of AChEIs with other pharmacological agents is hoped to improve efficacy of treatment by combining effects from the different pharmacological mechanisms of action. To put this discussion of AChEIs into perspective, some observations on the clinical uses of the anticholinesterases are also briefly summarised.
Structural factor equation models for causal network construction via directed acyclic mixed graphs

Directed acyclic mixed graphs (DAMGs) provide a useful representation of network topology with both directed and undirected edges subject to the restriction of no directed cycles in the graph. This graphical framework may arise in many biomedical studies, for example, when a directed acyclic graph (DAG) of interest is contaminated with undirected edges induced by some unobserved confounding factors (eg, unmeasured environmental factors). Directed edges in a DAG are widely used to evaluate causal relationships among variables in a network, but detecting them is challenging when the underlying causality is obscured by some shared latent factors. The objective of this paper is to develop an effective structural equation model (SEM) method to extract reliable causal relationships from a DAMG. The proposed approach, termed structural factor equation model (SFEM), uses the SEM to capture the network topology of the DAG while accounting for the undirected edges in the graph with a factor analysis model. The latent factors in the SFEM enable the identification and removal of undirected edges, leading to a simpler and more interpretable causal network. The proposed method is evaluated and compared to existing methods through extensive simulation studies, and illustrated through the construction of gene regulatory networks related to breast cancer.
Catalytic arylative endo cyclization of gold acetylides: access to 3,4-diphenyl isoquinoline, 2,3-diphenyl indole, and mesoionic normal NHC-gold complex.

3,4-Diphenyl isoquinoline and 2,3-diphenyl indole are readily accessed by catalytic selective bis-arylative endo cyclization of gold acetylides. The synthetic approach could be also extended to prepare six-membered mesoionic NHC complex, which could further undergo deprotonation/complexation to afford 1,3-N-heterocyclic dicarbene (NHDCs) Au 2 and Au/Ag complexes. The key vicinal diaurated alkene intermediates have been isolated and the studies on their reactivities towards coupling partners confirm the proposed mechanisms.
The value of estuarine and coastal ecosystem services

The global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat–fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat–fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land–sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options.
The equatorial Pacific Ocean: Grazer-controlled phytoplankton populations in an iron-limited ecosystem1

Experiments were conducted in the equatorial Pacific Ocean to assess the role of Fe and grazing in regulating use of N03- by the phytoplankton community. Nitrate uptake rates in situ were slow because NH,+ concentrations were inhibitory and because phytoplankton biomass was kept low by grazing. When feeding of grazers was artificially suppressed, phytoplankton net growth rate increased, biomass accumulated, and NO, - was consumed. Rapid rates of Fe uptake [40 pmol Fe (g Chl a)-’ h-l] decreased by an order of magnitude in l-2 d after Fe was added, demonstrating that these rates were under physiological regulation and were elevated in response to low Fe concentrations. Addition of Fe increased carbon uptake and the short-term N-specific NO,- uptake rate by 2-9 times. These physiological stimulations were confined to large phytoplankton (> 3 pm), which thus must have been Fe-limited in situ. N03- uptake rate and biomass of small phytoplankton were unaffected by Fe enrichment. The results thus suggest that the low biomass, N03- -rich condition of the equatorial Pacific Ocean exists because low Fe concentrations limit use of N03- by large phytoplankton and favor growth of small phytoplankton that are grazed efficiently and use NH,+ preferentially.
Clonal plant research: proliferation, integration, but not much evolution

The vast majority of plants are modular i.e., made up of reiterated pieces. Plant pieces also tend to be highly totipotent. You can regenerate a whole plant from just a tiny fragment of tissue. The ultimate elaboration of modularity and totipotency is clonal growth: one plant gives rise to another gives rise to another gives rise to another with no sex in between. A large proportion of plants possesses the capacity for clonal growth and, as a group, plants clone themselves in an intriguing variety of ways. Much of the recent fascination with clonal plants among botanists grew out of work by John Harper and colleagues in the 1970s (reviewed by Harper and White, 1974; Harper, 1978). During the decade that followed, other biologists joined Harper & co. in exploring the consequences of modularity for the ecology, and evolution of clonal plants, and animals (reviewed in Jackson, Buss,
Digital Image Correlation of Forescatter Detector Images for Simultaneous Strain and Orientation Mapping

Abstract Improved plasticity models require simultaneous experimental local strain and microstructural evolution data. Microscopy tools, such as electron backscatter diffraction (EBSD), that can monitor transformation at the relevant length-scale, are often incompatible with digital image correlation (DIC) techniques required to determine local deformation. In this paper, the viability of forescatter detector (FSD) images as the basis for the DIC study is investigated. Standard FSD and an integrated EBSD/FSD approach (Pattern Region of Interest Analysis System: PRIAS™) are analyzed. Simultaneous strain and microstructure maps are obtained for tensile deformation of Q&P 1180 steel up to ~14% strain. Tests on an undeformed sample that is simply shifted indicate a standard deviation of error in strain of around 0.4% without additional complications from a deformed surface. The method resolves strain bands at ~2 μm spacing but does not provide significant sub-grain strain resolution. Similar resolution was obtained for mechanically polished and electropolished samples, despite electropolished surfaces presenting a smoother, simpler topography. While the resolution of the PRIAS approach depends upon the EBSD step size, the 80 nm step size used provides seemingly similar resolution as 8,000× (22.7 nm) FSD images. Surface feature evolution prevents DIC analysis across large strain steps (>6% strain), but restarting DIC, using an FSD reference image from an interim strain step, allows reasonable DIC across the stress–strain curve. Furthermore, the data are obtained easily and provide complementary information for EBSD analysis.
Multinomial logistic regression with missing outcome data: An application to cancer subtypes

Many diseases such as cancer and heart diseases are heterogeneous and it is of great interest to study the disease risk specific to the subtypes in relation to genetic and environmental risk factors. However, due to logistic and cost reasons, the subtype information for the disease is missing for some subjects. In this article, we investigate methods for multinomial logistic regression with missing outcome data, including a bootstrap hot deck multiple imputation (BHMI), simple inverse probability weighted (SIPW), augmented inverse probability weighted (AIPW), and expected estimating equation (EEE) estimators. These methods are important approaches for missing data regression. The BHMI modifies the standard hot deck multiple imputation method such that it can provide valid confidence interval estimation. Under the situation when the covariates are discrete, the SIPW, AIPW, and EEE estimators are numerically identical. When the covariates are continuous, nonparametric smoothers can be applied to estimate the selection probabilities and the estimating scores. These methods perform similarly. Extensive simulations show that all of these methods yield unbiased estimators while the complete‐case (CC) analysis can be biased if the missingness depends on the observed data. Our simulations also demonstrate that these methods can gain substantial efficiency compared with the CC analysis. The methods are applied to a colorectal cancer study in which cancer subtype data are missing among some study individuals.
mRNA and Translation

I. INTRODUCTION The process of gene expression, during which the nucleotide sequence of a gene is converted to the amino acid sequence of a protein, is long and tortuous. An expressed gene must be transcribed, its pre-mRNA must be capped, polyadenylated, spliced, and transported to the cytoplasm, and the mature mRNA must be loaded onto polysomes and faithfully translated. In principle, gene expression can be regulated by modulating any of these molecularly complex steps. Indeed, examples of biological regulation occurring at each of these steps have been described in various organisms. We focus in this chapter on translation and translational regulation in Caenorhabditis elegans. Recent work with several C. elegans genes demonstrates that the level, timing, and pattern of gene expression can be regulated at the level of translation by elements contained within a messenger RNA’s 3′-untranslated region (3′ UTR). We also review the genetic and molecular effects of mutations that affect the translational apparatus itself. By altering the mechanics of translation, such mutations can influence the phenotypic consequences of mutations in many different genes. II. THE TRANSLATIONAL APPARATUS A. Cytoplasmic Translation Many components of the translational apparatus have been identified and studied, including ribosomal RNAs and the ribosomal DNA repeat (Sulston and Brenner 1974; Files and Hirsh 1981; Albertson 1984a; Ellis et al. 1986); 5S rRNA and the 5S rDNA repeat (Kumazaki et al. 1982; Nelson and Honda 1985, 1986); ribosomal proteins L29, L21, L35, L37, S9, and S16 (Bektesh et al. 1988; Wilson et al. 1994; Zorio et.
Factors affecting Bittern Botaurus stellaris distribution in a Mediterranean wetland

The habitat requirements of a resident population of Bittern Botaurus stellaris were investigated during the breeding season in a Mediterranean upland wetland, with particular reference to the area's isolation from other wetlands, its small size and hydrological conditions. Vegetation structure and water-level were described and associated with booming male and nesting female distribution within the marsh. A logistic regression model showed that water-level was the only significant factor affecting the distribution of booming males, which occupied areas seasonally flooded with shallower water (< 1 m). Females nested in seasonally flooded zones, while vegetation density appeared an important variable for nesting-site choice. Management of the wet area is discussed and the importance of a better understanding of the temporal dynamics of vegetation cover and spatial and temporal variations in water-level, and their possible effects on prey distribution, is highlighted.
FORAGING STRATEGIES OF SYMPATRIC KILLER WHALE (ORCINUS ORCA) POPULATIONS IN PRINCE WILLIAM SOUND, ALASKA

Killer whales (Orcinus orca) feed on a wide variety of fish, cephalopods, and marine mammals throughout their cosmopolitan range; however, the dietary breadth that characterizes the species is not reflected in all populations. Here, we present the findings of a 14-yr study of the diet and feeding habits of killer whales in Prince William Sound, Alaska. Two non-associating forms of killer whale, termed resident and transient (Bigg et al. 1987), were identified. All prey seen taken by transients were marine mammals, including harbor seals (Phoca vitulina), Dall's porpoises (Phocoenoides dalli), Steller sea lions (Eumetopias jubatus), and harbor porpoises (Phocoena phocoena). Resident killer whales appeared to prey principally on salmon (Oncorhynchus spp.), preferring coho salmon (O. kisutch) over other, more abundant salmon species. Pacific herring (Clupea pallasi) and Pacific halibut (Hippocampus stenolepis) were also taken. Resident killer whales frequently were seen to interact in non-predatory ways with Steller sea lions and Dall's porpoises, while transients were not. Differences in the social organization and behavior of the resident and transient killer whales in Prince William Sound are discussed in the light of the dietary differences documented here.
Phylogenetic and gene trees of Synechococcus: choice of the right marker to evaluate the population diversity in the Tucuruí Hydroelectric Power Station Reservoir in Brazilian Amazonia

LEONARDO T. DALL’AGNOL1, RUBENS GHILARDI-JUNIOR2, JOHN A. MCCULLOCH1, HORACIO SCHNEIDER3, MARIA P. C. SCHNEIDER1 AND ARTUR SILVA1* 1 LABORATORIO DE POLIMORFISMO DE DNA, INSTITUTO DE CIENCIAS BIOLOGICAS, UNIVERSIDADE FEDERAL DO PARA, RUA AUGUSTO CORREA, 01, 66075-900 BELEM, PA, BRAZIL, CENTRAIS ELETRICAS DO NORTE DO BRASIL S/A, BRASILIA, DF, BRAZIL AND INSTITUTO DE ESTUDOS COSTEIROS, UNIVERSIDADE FEDERAL DO PARA, BRAGANCA, PA, BRAZIL
The Expression of CYP19a Gene at Two Temperature Levels During the Thermosensitive Period of the Nile Tilapia (Oreochromis niloticus)

The gene expression of ovarian aromatase is regulated according to the period of exposure to different post-fertilization temperatures. Previous studies show that high temperatures regulate aromatase gene expression, or transcription factors responsible for gene expression during sex differentiation in fish. The fact that this enzyme is part of the reproductive hormone estrogen synthesis pathway, leads researchers to study how the differential expression of this gene can influence the proportion of males and females in the process of sexual reversion. The objective of this study was to evaluate the effect of temperatures at 25? and 35? on the expression of ovarian aromatase during the period of sexual reversion in Supreme strain of the Nile Tilapia ( Oreochromis niloticus ). We conducted two times the same experiment under the same conditions and at an interval of 12 months between both. We used 1500 larvae three days after hatching, in the final phase of resorption of the yolk sac per experiment maintained in water in a closed recirculatory system. For each experiment we used eight experimental units, each containing 93 larvae that were separated into two groups of four repetitions for each temperature treatment. Treatments lasted a total period of 30 days, with a 12L:12D photoperiod. Total RNA was extracted from a sample of four larvae that was collected every week from each treatment using a Quick-RNATM MiniPrep (R1054) extraction kit. The synthesis of cDNA was performed using 10ng of RNA with the GoScript™ Reverse Transcription System kit. We were not able to completely block the expression of aromatase in the 35? treatments in the Supreme strain since we found a variation in the responses to the expression of aromatase. Gene expression was detected during the thermosensitive period (TSP) in both treatments. We suggest that the bands that present low levels of expression in the treatment at 35°C probably belong to male individuals, while the high intensity bands in the 25? treatment are most probably females.
A global relationship between the heterotrophic and autotrophic components of soil respiration?

Soil surface CO2 flux (RS) is overwhelmingly the product of respiration by roots (autotrophic respiration, RA) and soil organisms (heterotrophic respiration, RH). Many studies have attempted to partition RS into these two components, with highly variable results. This study analyzes published data encompassing 54 forest sites and shows that RA and RH are each strongly (R2>0.8) correlated to annual RS across a wide range of forest ecosystems. Monte Carlo simulation showed that these correlations were significantly stronger than any correlation introduced as an artefact of measurement method. Biome type, measurement method, mean annual temperature, soil drainage, and leaf habit were not significant. For sites with available data, there was a significant (R2=0.56) correlation between total detritus input and RH, while RA was unrelated to net primary production. We discuss why RA and RH might be related to each other on large scales, as both ultimately depend on forest carbon balance and photosynthate supply. Limited data suggest that these or similar relationships have broad applicability in other ecosystem types. Site‐specific measurements are always more desirable than the application of inferred broad relationships, but belowground measurements are difficult and expensive, while measuring RS is straightforward and commonly done. Thus the relationships presented here provide a useful method that can help constrain estimates of terrestrial carbon budgets.
Proximate Composition, Biochemical and Microbiological Changes Associated with Fermenting African Oil Bean (Pentaclethra macrophylla Benth) Seeds

The proximate composition, biochemical changes and microbiology of fermenting Pentaclethra macrophylla (Ugba) seeds were evaluated. Studies were carried out to screen for microorganisms associated with the natural fermentation of the oil bean seeds. Bacterial isolates obtained include species of Bacillus, Streptococcus, Salmonella, Micrococcus, Lactobacillus and Proteus. Fungal isolates include Yeast, species of Penicillium, Aspergillus, Fusarium and Rhizopus. Total aerobic counts (TAC) ranged from 1.5 x 106 to 2.5 x 106 cfu/g, while total coliform counts (TCC) ranged from 1.7 x 103 to 7.2 x 103 cfu/g. More so, total lactic acid bacterial counts ranged from 2.6 x 105 to 4.6 x 105 cfu/g. Among the various bacterial isolates obtained from the fermenting Ugba, Bacillus and lactic acid bacteria were dominant from the beginning to the end of the fermentation the oil bean seeds. The proximate composition of the fermenting seeds showed the presence of protein, fats, fibre, carbohydrates, and ash. Temperature variations in oil bean seed fermentation showed higher temperatures in the purchased Ugba compared to the laboratory Ugba after 72 hours fermentation. There were significant reduction in pH and titratable acidity as the fermentation time progressed, showing that temperature, pH and titratable acidity of fermenting African oil bean seeds were affected by the metabolic activities of resident microorganisms.