Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of mounding, drainage and fertilization on CH4 fluxes and methane-cycling functional genes in waterlogged forest stands

Site preparation techniques including mounding, drainage and nitrogen (N) fertilization can enhance seedling survival and site productivity, particularly in waterlogged, low-productivity forest stands. However, practices that alter soil conditions and site hydrology can lead to the unintended alteration of biogeochemical process rates, such as CH4 fluxes. This study sought to measure CH4 fluxes measured using static closed chambers at a sub-boreal spruce site and a coastal cedar-hemlock site that underwent mounding and drainage, respectively, to manipulate water table depth relative to planted seedlings, as well as fertilization. The abundance of methyl coenzyme M reductase (mcrA) gene found in methanogenic archaea and the particulate methane monooxygenase (pmoA) gene found in methane-oxidizing bacteria (MOB) were examined. The use of sulphate as a potential method to stimulate sulphate-reducing bacteria (SRB) and reduce methanogen activity was also investigated using the dissimilatory sulfite reductase β-subunit (dsrB) gene. qPCR was used to link mcrA,pmoA and dsrB gene abundance to soil factors and GHG fluxes. Mounding created hot-spots of CH4 emissions at the spruce site. Drainage improved soil aeration at the coastal cedar-hemlock site and reduced CH4 emission rates. Fertilization did not affect CH4 emissions from either site. CH4 rates were influenced by soil water content and mcrA abundance. Measurements of microbial functional genes can elucidate the effects of site preparation on GHG fluxes in waterlogged forest stands.
Clinical and therapeutic implications of sex steroid hormone receptor status in urothelial bladder cancer

Studies on the clinical profile of urothelial bladder cancer (UBC) have shown significant gender differences, namely, higher occurrence in males (male-to-female ratio of 3.5:1) and an advanced stage of disease at the time of diagnosis with rapid progression of the disease after initial diagnosis seen more commonly in females. The relationship between gender and UBC is complex and probably influenced by biological and epidemiological factors. Potential contributory factors such as sex steroid hormone pathway, gender difference in environmental carcinogen exposure, metabolic enzyme activity, and disparities in the intensity of diagnostic evaluation could probably explain the demographic trends in UBC. This comprehensive review of Medline publications during the period 2009–2019 attempts to identify the possible role of sex hormone receptors in gender variation and sexual dimorphism in the occurrence and progression of UBC. The clinical implications of identifying sex steroid receptors on factors such as disease prognostication and the therapeutic role of anti-androgens in the prevention and progression of UBC are critically reviewed. There is now significant evidence in literature to suggest the possible role of sex steroid hormone receptor-mediated signals in the genesis and progression of UBC. These receptors include androgen receptors, estrogen receptors, progesterone receptors, and various other orphan receptors. Excessive or reduced expression of these receptors, as well as alterations in their upstream or downstream pathways, correlate well with the clinical and therapeutic outcomes of UBC.
Peptide Extracts from Native Lactic Acid Bacteria Generate Ghost Cells and Spheroplasts upon Interaction with Salmonella enterica, as Promising Food Antimicrobials

Protecting foods from contamination applying peptides produced by lactic acid bacteria is a promising strategy to increase the food quality and safety. Interacting with the pathogen membranes might produce visible changes in shape or cell wall damage. Previously, we showed that the peptides produced by Lactobacillus plantarum UTNGt2, Lactobacillus plantarum UTNCys5-4, and Lactococcus lactis subsp. lactis UTNGt28 exhibit a broad spectrum of antibacterial activity against several foodborne pathogens in vitro. In this study, their possible mode of action against the commensal microorganism Salmonella enterica subsp. enterica ATCC51741 was investigated. The target membrane permeability was determined by detection of beta-galactosidase release from ONPG (o-nitro-phenyl-L-D-galactoside) substrate and changes in the whole protein profile indicating that the peptide extracts destroy the membrane integrity and may induce breaks in membrane proteins to some extent. The release of aromatic molecules such as DNA/RNA was detected after the interaction of Salmonella with the peptide extract. Transmission electronic microscopy (TEM) micrographs depicted at least four simultaneous secondary events after the peptide extract treatment underlying their antimicrobial actions, including morphological alterations of the membrane. Spheroplast and filament formation, vacuolation, and DNA relaxation were identified as the principal events from the Gt2 and Cys5-4 peptide extracts, while Gt28 induced the formation of ghost cells by release of cytoplasmic content, filaments, and separation of cell envelope layers. Gel retarding assays indicate that the Gt2 and Gt28 peptide extracts are clearly binding the Salmonella DNA, while Cys5-4 partially interacted with Salmonella genomic DNA. These results increased our knowledge about the inhibitory mechanism employed by several peptide extracts from native lactic acid bacteria against Salmonella. Further, we shall develop peptide-based formulation and evaluate their biocontrol effect in the food chains.
MithraDetective: A System for Cherry-picked Trendlines Detection

Given a data set, misleading conclusions can be drawn from it by cherry-picking selected samples. One important class of conclusions is a trend derived from a data set of values over time. Our goal is to evaluate whether the 'trends' described by the extracted samples are representative of the true situation represented in the data. We demonstrate MithraDetective, a system to compute a support score to indicate how cherry-picked a statement is; that is, whether the reported trend is well-supported by the data. The system can also be used to discover more supported alternatives. MithraDetective provides an interactive visual interface for both tasks.
The Cross-Sectional Investigation Of The Association Between Adipokines Omentin-1, Vaspin, And Retinol Binding Protein-4 With Body Composition Indices And Metabolic Status Of Women

S Background: The adipokines omentin-1, vaspin, and retinol binding protein-4 (RBP-4) are mediators of body composition and adipose tissue that contribute to metabolic changes caused by obesity. The aim of this study was to determine the association between serum levels of these adipokines with body composition indices and metabolic status in different phenotypes of body size. Methods: In the present cross-sectional study, a total of 350 women, including 127 metabolically healthy (MH) subjects and 223 metabolically unhealthy (MUH) subjects participated. The subjects were considered as MH in the presence of at least 4 of the five following metabolic indices: TG ≤ 1.70 mmol/L, LDL-C≤ 2.60 mmol /L, TC≤ 5.20 mmol /L, HDL-C≥1.30, and HOMA-IR≤ 1.95; otherwise subjects were considered as MUH. Results: The results showed that serum levels of omentin-1 have a significant positive association with MHS (OR = 1.04, p <0.0001). Even after controlling the confounding factors of age, sex and weight, this relationship was still significant. Plasma levels of vaspin and RBP-4 were not significantly related to MHS. Furthermore, there was a significant correlation between omentin-1 and body mass index (r = 0.31, p = 0.02) and body fat percentage (r = 0.32, P = 0.02) in MH subjects. In the healthy group, serum levels of RBP-4 were positively correlated with fat percentage (r = 0.68, p <0.0001) and body fat mass (r = 0.74, P <0.0001) and were negatively correlated with fat-free mass (r = -0.74, P <0.0001) and total body water (r = -0.76, P <0.0001). There was no statistically significant correlation between serum vaspin levels and body composition indices in both groups. Conclusion: Serum levels of adipokines may be an appropriate predictor for metabolically healthy status. Further studies in this field can reveal possible mechanisms.
Nicotine Induces An Increase In Excitatory Junctional Potential Amplitude At The Crayfish Neuromuscular Junction And Desensitization After Prolonged Nicotine Exposure

The objective of our study was to establish the relationship between nicotine exposure and excitatory junctional potential (EJP) amplitude at the crayfish neuromuscular junction (NMJ). We isolated crayfish dorsal lateral tail extensor muscles and recorded the EJP amplitude in standard crayfish ringers solution and ringers solution containing nicotine. We found that applications of 6 and 12 mM nicotine to the crayfish NMJ were sufficient to enhance EJP amplitude. We also found evidence for desensitization after prior exposure to nicotine. These results suggest the short term effects of nicotine enhance EJP amplitude, whereas the long-term effects are desensitizing.
A disease resistance and high yielding Rehmannia glutinosa Libosch. ex Steud. cultivar ‘Tokang’

A new Rehmannia glutinosa cultivar ‘Tokang’ was derived from ‘Jihwang 1’ seedlings by medicinal crop breeding team of National Institute of Horticulture and Herbal Science, RDA in 2009. It has pink flower, dark brown seed coat, light yellow root cortex. The plant type was some rising from the ground. The content of catalpol and extract were higher than the ‘Jihwang 1’(check variety). The content of catalpol was 4.55% and the extract was 71.2%. It showed stronger resistance to root rot compare with the ‘Jihwang 1’. The regional yield trials were conducted at three different locations from 2007 to 2009. The average yield of ‘Tokang’ was 21.1ton/ha, which was 12% more than the ‘Jihwang 1’. This cultivar is adaptable to the whole of Korea except for mountain areas. (Registration No. 4725)
Mechanism of Replication-Coupled DNA Interstrand Crosslink Repair

DNA interstrand crosslinks (ICLs) can be induced by multiple crosslinking agents and are a severe form of DNA damage that prevents strand separation during DNA replication and transcription. Failure to repair endogenous ICLs in S phase is thought to underlie the bone marrow failure syndrome Fanconi anemia, and up-regulation of ICL repair is one of the causes of tumor chemoresistance against widely used cancer drugs. In metazoans, a major pathway of ICL repair is coupled to DNA replication and requires the Fanconi anemia pathway. In most current models, collision of a single DNA replication fork with an ICL is sufficient to initiate repair. In contrast, we show that in Xenopus egg extracts, two DNA replication forks must converge on an ICL to trigger repair. When only one fork reaches the ICL, the replicative DNA helicase, CMG, fails to unload from the stalled fork, and repair is blocked. Arrival of a second fork, even when substantially delayed, rescues repair. We conclude that ICL repair requires a replication-induced X-shaped DNA structure surrounding the lesion, and we speculate how this requirement helps maintain genomic stability in S phase. Next, we focus on how psoralen-induced ICLs are repaired. Although psoralen-ICL repair still requires replication fork convergence, downstream repair events are completely different. Unlike cisplatin-ICLs, which are resolved via incisions in the parental strands with formation of doublestrand breaks (DSBs), psoralen-ICLs are resolved via cleavage of a N-glycosyl bond that forms part of the ICL. Unlike cisplatin-ICL repair, psoralen-ICL repair does not require CMG helicase unloading or FANCI-FANCD2. When N-glycosyl bond cleavage is inhibited, the psoralen-ICL is repaired via FANCI-FANCD2-dependent incisions. Our work identifies a novel S phase ICL repair mechanism that is independent of the Fanconi anemia pathway and avoids DSBs.
BuShen HuoXue Decoction Promotes Decidual Stromal Cell Proliferation via the PI3K/AKT Pathway in Unexplained Recurrent Spontaneous Abortion

BuShen HuoXue decoction (BSHXD) has been used to treat patients with unexplained recurrent spontaneous abortion (URSA). However, the chemical compounds and mechanism by which BSHXD exerts its therapeutic and systemic effects to promote the proliferation of decidual stromal cells (DSCs) has not been elucidated. This work sought to elucidate the cellular and molecular mechanism of BSHXD in terms of inflammatory factors IL-17A in DSCs in vitro because of the critical roles of inflammation, apoptosis, and immunity in the development and progression of pregnancy loss. Twelve migratory chemical compounds from BSHXD extract were qualitatively analyzed by high-performance liquid chromatography (HPLC). DSCs were collected from normal early pregnancy (NEP) and URSA to determine whether BSHXD affects IL-17A/IL17RA via the PI3K/AKT pathway. Abnormal apoptosis and activated p-AKT were observed in URSA DSCs. RhIL-17 A, LY294002 (a PI3K pathway inhibitor), and BSHXD were individually or simultaneously administered in NEP DSCs, suggesting that BSHXD restored cell proliferation without excessive stimulation and IL-17A promotes proliferation via the PI3K/AKT pathway. Using the same intervention in URSA DSCs, qRT-PCR measured the upregulated mRNA levels of IL-17 A/IL-17RA, PI3K, AKT, p-AKT, PTEN, Bcl-2, and Bcl-xL and downregulated mRNA levels of BAD and ACT1 after treatment with BSHXD. We demonstrated that BSHXD affected IL-17A/IL-17R via PI3K/AKT pathway to promote the proliferative activity of DSCs in URSA. These results provide a new insight to further clarify the relationship between inflammation and apoptosis and the mechanism of imbalance in the dynamic equilibrium between Th17/Treg immune cells at the maternal-fetal interface.
Fragmented host distribution and trombiculid parasitic load: Eutrombicula araucanensis and Liolaemus pictus in Chile

Habitat fragmentation produced by human impacts can generate changes in the distribution and abundance of populations across their geographic ranges. The chigger mites are ectoparasites that are widely distributed on a wide range of species. The distribution depends of the characteristics of the host and of the habitat where said species is found. As the host distribution is highly dependent on environmental factors, chigger mites are good study models to test geographical distribution patterns. The main objective of this study was to determine variation in abundance of Eutrombicula araucanensis, parasite on Liolaemus pictus, by testing three hypotheses: abundant centre hypothesis, abundance optimum hypothesis and latitudinal distribution pattern. For this purpose, mites from 147 individuals from 23 localities along the distribution of L. pictus were extracted. The three distribution models evaluated in the present study were not adequate to represent the geographical structure of parasitic mites on L. pictus. No association between the distance from the area of greatest species abundance and relative intensity, or association with the distance to the mite’s distribution centre was observed. In addition, no latitudinal distribution pattern was observed. Temperate forest fragmentation may influence the population density of mites, with each forest patch having different optimal conditions for development. The heterogeneity makes it difficult to find a clear distribution pattern.
Example-Driven Intent Prediction with Observers

A key challenge of dialog systems research is to effectively and efficiently adapt to new domains. A scalable paradigm for adaptation necessitates the development of generalizable models that perform well in few-shot settings. In this paper, we focus on the intent classification problem which aims to identify user intents given utterances addressed to the dialog system. We propose two approaches for improving the generalizability of utterance classification models: (1) observers and (2) example-driven training. Prior work has shown that BERT-like models tend to attribute a significant amount of attention to the [CLS] token, which we hypothesize results in diluted representations. Observers are tokens that are not attended to, and are an alternative to the [CLS] token as a semantic representation of utterances. Example-driven training learns to classify utterances by comparing to examples, thereby using the underlying encoder as a sentence similarity model. These methods are complementary; improving the representation through observers allows the example-driven model to better measure sentence similarities. When combined, the proposed methods attain state-of-the-art results on three intent prediction datasets (banking77, clinc150, hwu64) in both the full data and few-shot (10 examples per intent) settings. Furthermore, we demonstrate that the proposed approach can transfer to new intents and across datasets without any additional training.
Potato Plant Gene Expression and Physiology During Three-Way Interactions with Mycorrhizal Fungi and Lepidopteran Larvae

53 Introduction. 54 Methods. Growth Conditions and Glomus intraradices Inoculation Insect Herbivory Plant Physiology Measurements Plant Biomass and Glomus intraradices Root Colonization Statistical Analysis 58 Results. Mycorrhiza Increases Shoot Growth in Undamaged Potato Plants 60
Holistic View on Health: Two Protective Layers of Biodiversity

The western world has witnessed a rising epidemic of chronic inflammatory disorders, such as allergies and asthma. This epidemic is expected to spread also to the rest of the world, where allergies have to date been practically absent, along with adoption of western lifestyle. In parallel, biological diversity is globally declining. This inspired Ilkka Hanski, together with medical doctors, to formulate the biodiversity hypothesis of allergic disease. This hypothesis proposes that reduced contact with natural environments, including natural microbial diversity, is associated with unhealthy human microbiota, less able to educate the immune system. Contact with beneficial bacteria, particularly early in life, seems to be instrumental to the normal development of immune responses. Changes in lifestyle and diet, destruction of natural environments, and urbanisation threaten our natural exposure to these beneficial bacteria and thus also reduce their impact on our physiology. To ensure a healthy life, we need to preserve biodiversity in the environment and make sure it finds a favourable home in us. In this review, we will focus on the role of commensal microbiota in human health and wellbeing, as well as the interaction between our microbiota and environmental microbiota, highlighting the contribution of Ilkka Hanski.
Influence of the addition of post-extraction rapeseed meal on the sensoric quality of poultry meat

Complete feed mixtures, very often enriched by the addition of various probiotic preparations, oils, extract, essential oils, mouldings, pollards etc., that are often added as a replacement for animal meals, antibiotic preparations, coccidiostats respectively, are used for feeding of chickens. In addition to the positive effects of these supplements, the final quality of meat may be adversely affected by the accumulation of certain components. The aim of the work was to monitor the influence of adding post -extraction rapeseed meal (PRM) to a broiler feed mixture on the sensory quality of breast and thigh muscle. The experience includes two hybrid combinations of broilers, ROSS 308 and COBB 500. Samples of breast and thigh muscle of broilers fed by a feed mixture with the addition of 10% post -extraction rapeseed meal were compared, using sensory analysis, with a control sample where the broilers were fed by a standard feed mixture without the addition of PRM. It has been found that the addition of post -extraction rapeseed meal to the broilers' feed mixture had a positive effect ( p <0.05) on the sensory quality of hybrid ROSS 308, both on the breast and thigh muscle. For COBB 500 hybrid, the quality of both breath and thigh muscle has not been shown to be significantly affected. The addition of 10% PRM affected positively especially the texture properties of ROSS 308, hybrid breast muscle, whereas they were deteriorated in COBB 500. In sensory evaluation, by adding 10% of PRM to the feed mixture, thigh muscle was affected less than breath muscle. Adding 10% PRM to the feed has almost no effect on descriptors of the intensity and pleasantness of smell and the intensity and pleasantness of taste, both in the negative and positive sense, both in breath and thigh muscle. The evaluation of the overall quality of both breath and thigh muscle has turned out more positive for ROSS 308 hybrid, although only slightly. The addition of rapeseed extracted meal to feed hybrids ROSS COBB 308 and 500 had no significant effect on the sensory quality of breast and thigh muscle.
Observational studies assessing the pharmacological treatment of obstructive lung disease: strengths, challenges and considerations for study design

Randomised controlled trials (RCTs) are the gold standard for evaluating treatment efficacy in patients with obstructive lung disease. However, due to strict inclusion criteria and the conditions required for ascertaining statistical significance, the patients included typically represent as little as 5% of the general obstructive lung disease population. Thus, studies in broader patient populations are becoming increasingly important. These can be randomised effectiveness trials or observational studies providing data on real-world treatment effectiveness and safety data that complement efficacy RCTs. In this review we describe the features associated with the diagnosis of asthma and chronic obstructive pulmonary disease (COPD) in the real-world clinical practice setting. We also discuss how RCTs and observational studies have reported opposing outcomes with several treatments and inhaler devices due to differences in study design and the variations in patients recruited by different study types. Whilst observational studies are not without weaknesses, we outline recently developed tools for defining markers of quality of observational studies. We also examine how observational studies are capable of providing valuable insights into disease mechanisms and management and how they are a vital component of research into obstructive lung disease. As we move into an era of personalised medicine, recent observational studies, such as the NOVEL observational longiTudinal studY (NOVELTY), have the capacity to provide a greater understanding of the value of a personalised healthcare approach in patients in clinical practice by focussing on standardised outcome measures of patient-reported outcomes, physician assessments, airway physiology, and blood and airway biomarkers across both primary and specialist care. Observational studies can support RCTs in influencing clinical practice in the field of obstructive lung disease https://bit.ly/36YWu0W