jimnoneill/paper-to-field-training huggingface dataset:
Characterisation of glutathione transferase from Arabidopsis thaliana

Glutathione transferases (GSTs) are soluble enzymes with activity towards a wide range of xenobiotic and endogenous compounds. The Arabidopsis genome encoded 54 GSTs, which have been classified into eight classes including Tau and Phi. Members of these Tau and Phi clades are strongly upregulated in response to abiotic stresses such as xenobiotics and biotic stresses including pathogen attack. The most characterised activity of GSTs is the transfer of glutathione to an electrophilic centre to form a polar glutathionylated conjugate. However, increasing number of research demonstrated a non-catalytic activity plants GSTs, especially in the transportation of flavonoids from the cytosol to the vacuole. Despite the wealth of investigations into GSTs, and probably as a result of overlapping substrate specificities, the endogenous roles for the vast majority of these plant GSTs remains unknown.&#13;\nHere, the binding interaction of camalexin, indole-3-aldehyde, quercetrin and quercetin to GSTF2 in a non-catalytic fashion was observed in three different sites; two identical sites of L1 and one L2 from the X-ray crystallography data. Mutagenesis of the active residues, Q73L, H77A, Y97A and R154A were performed and using isothermal calorimetry (ITC) techniques, lower binding affinities were observed for all mutants towards all ligands except for Y97A and Q73L which showed higher binding affinities with indole-3-aldehyde. This unexpected finding was likely due to the conformational change of the mutant compared to the wild type, as observed in the structure of mutant Y97A.&#13;\nOn elucidating the catalytic activity of GSTs, the structure of GSTU25 in complex with disulphide glutathione was obtained. The GSTU25 has been recently identified to catalyse the denitration of TNT to form 2-glutathionyl- 4,6-dinitrotoluene, a potentially more amenable product for subsequent degradation. This structure complex provides insights of GSTU25 folding upon substrate binding.&#13;\nThe involvement of GSTU25 in the detoxification of TNT was further analysed using CRISPR/Cas9 technology. Subclades of GSTU25, including GSTU24, GSTU21, GSTU19 were knockout with the aim to remove overlapping substrate specificities and to finally reveal TNT-specific phenotypes. Only gstU25 Cas9 segregated Arabidopsis were obtained from the experiment that could potentially be optimised in the future study.

Topic: Glutathione Transferases and Polymorphisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
A novel synthetic route toward controlling the structures of thioether-bridged mesoporous organosilicas

The thioether-bridged mesoporous organosilicas with different mesostructures could be controllably synthesized by simply tuning molar ratio of the two precursors in Si-P123-NaAc-HAc-ethanol-H2O-systems. Mesophase transformation from highly ordered 2-D hexagonal structure to mesostructured cellular foam with vesicle-like structure as an intermediate phase is clearly observed when the molar ratio of bis[3-(triethoxysily)propyl]tetrasulfide (TESPTS)/tetramethoxysilane(TMOS) is successively increased.Because of the low hydrolysis and condensation rate of TESPTES under buffer solution, TESPTES can act both as aswelling for p123 surfactant micelles and co-agent for the formation of microemulsion with p123 syrfactant micelles. Our synthetic metnod provides a novel mild synthetic method for the controllable synthesis of mesoprous organosilicas with different mesostructure.

Topic: Mesoporous Materials and Catalysis
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Increased expression of intercellular adhesion molecules in biliary atresia.

The expression of the inflammatory adhesion molecules intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and endothelial leukocyte adhesion molecule-1, was studied in six infants with biliary atresia using an immunoperoxidase technique on frozen sections. Controls consisted of five patients with various conditions including total parenteral nutrition-induced cholestasis, choledochal cyst, viral hepatitis, metastatic carcinoma, and thrombotic thrombocytopenic purpura. None of the patients were in liver failure. Bile ducts from the control subjects did not express any of the inflammatory adhesion molecules on ductal epithelium. In marked contrast, all of the biliary atresia specimens demonstrated strong intercellular adhesion molecule-1 expression and occasional vascular cell adhesion molecule-1 staining on epithelial cell membranes of both intra- and extrahepatic ductal structures. Hepatocytes and sinusoidal lining cells including Kupffer cells showed a pattern of intense intercellular adhesion molecule-1 and vascular cell adhesion molecule-1 expression in all specimens with active inflammation that could not differentiate the biliary atresia cases from the control group. Lymphocyte function-associated antigen-1 intensely stained the inflammatory cell infiltrate in the biliary atresia and inflamed control specimens. The strong expression of intercellular adhesion molecule-1 on biliary ductal epithelium in patients with biliary atresia suggests a potential role for this adhesion molecule in the pathogenesis of this devastating neonatal hepatic disorder.

Topic: Pediatric Hepatobiliary Diseases and Treatments
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
The use of the dialectical method as a theory for understanding social change in the philosophy of global constitutionalism

This article is devoted to the conceptual analysis of the dialectical method for understanding social change in the philosophy of global constitutionalism. The purpose of the research: from the position of socio-philosophical methods of cognition of social reality and ideas reflecting it, to analyze the dialectic model in the doctrine of social changes in the philosophy of global constitutionalism. An analysis of the dialectical method as a theory for understanding social change in the philosophical concept of global constitutionalism has shown that: in the process of its formation, the Hegelian concept of dialectical development and the dialectical materialism of the Marxist-Leninist type, including its basic laws; it is aimed at developing a system of arguments to justify the natural evolutionary nature of the origin of the world capitalist system; the process of removing the qualitatively heterogeneous opposites accumulated in the process of social development is also subordinate to the general logic of the development of the world capitalist system.

Topic: Political Economy and Marxism
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Almost Excellent Extensions and the FP-Homological Property

Let R be a ring and S an almost excellent extension of R. In this paper, we discussed the homological properties of FP-projective modules and FP-injective modules under the extension of rings, which mainly including almost excellent extensions, Polynomial extensions, Morita equivalences and localizations.

Topic: Rings, Modules, and Algebras
Subfield: Algebra and Number Theory
Field: Mathematics
Domain: Physical Sciences
Brief murine myocardial I/R induces chemokines in a TNF-α-independent manner: role of oxygen radicals

Early chemokine induction in the area at risk of an ischemic-reperfused (I/R) myocardium is first seen in the venular endothelium. Reperfusion is associated with several induction mechanisms including increased extracellular tumor necrosis factor (TNF)-α, reactive oxygen intermediate (ROI) species formation, and adhesion of leukocytes to the venular endothelium. To test the hypothesis that chemokine induction in cardiac venules can occur by ROIs in a TNF-α-independent manner, and in the absence of leukocyte accumulation, we utilized wild-type (WT) and TNF-α double-receptor knockout mice (DKO) in a closed-chest mouse model of myocardial ischemia (15 min) and reperfusion (3 h), in which there is no infarction. We demonstrate that a single brief period of I/R induces significant upregulation of the chemokines macrophage inflammatory protein (MIP) -1α, -1β, and -2 at both the mRNA and protein levels. This induction was independent of TNF-α, whereas levels of these chemokines were increased in both WT and DKO mice. Chemokine induction was seen predominantly in the endothelium of small veins and was accompanied by nuclear translocation of nuclear factor-κB and c-Jun (AP-1) in venular endothelium. Intravenous infusion of the oxygen radical scavenger N-2-mercaptopropionyl glycine (MPG) initiated 15 min before ischemia and maintained throughout reperfusion obviated chemokine induction, but MPG administration after reperfusion had begun had no effect. The results suggest that ROI generation in the reperfused myocardium rapidly induces C-C and C-X-C chemokines in the venular endothelium in the absence of infarction or irreversible cellular injury.

Topic: Immune Response and Inflammation
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Monitoring of respiratory tract infection bacteria in ICU and analysis of its risk factors

Objective To monitor the multiple drugs resistance(MDR) bacteria in ICU and to analyze the risk factors for MDR bacteria infection.Methods 137 strains of bacteria,which were isolated from patients confirmed with respiratory tract infection,were analyzed by KB drug sensitive test to observe their drug resistance.Results The main infective bacteria in our hospital was Gram-negative bacteria,which showed different degrees of drug resistance.The high risk factors of MDR strain infection were age,duration of hospital stay,hospitalized times,history of COPD,tracheotomy,central venous catheters,use of antibiotics,and gastric intubation.Conclusion Gram negative bacteria is the main infective bacteria in ICU in our hospital.It is very important for respiratory tract infection reduction to detect MDR and pay attention to the risk factors of MDR strain infection.

Topic: Pneumonia and Respiratory Infections
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Learning and transfer of calorie information

Summary This study compared generating information about food to viewing and verbally producing that information for learning and transfer. Specifically, during training, a list of food items was shown, and some participants generated either real calories (Experiment 1) or fabricated prices (Experiment 2) associated with those foods with feedback provided (seeding), some viewed and read aloud values provided (viewing), and others read aloud the names of the items with no values provided (control). All participants were tested immediately and 1 week later on both old and new foods. In both experiments, the seeding and viewing conditions showed more learning than the control condition, and only the experimental conditions showed transfer of learning from old to new foods, with advantages found for seeding over viewing only in some cases. The results are discussed in terms of the seeding, testing, generation, and production effects, as well as their applications to health and policy.

Topic: Child and Animal Learning Development
Subfield: Developmental and Educational Psychology
Field: Psychology
Domain: Social Sciences
Sudden hearing loss: a ten-year outpatient experience.

The aim of this study was to determine the effects of various treatment modalities employed for patients with sudden sensorineural hearing loss (SHL). We retrospectively evaluated the records of patients treated in the sudden hearing loss section of the Otolaryngology Department at Clinic Hospital, School of Medicine, University of São Paulo, Brazil, between 1996 and 2006. Our study included patients with SHL of sudden onset (occurring over a 72-hour period) at equal to or greater than 30 dB at three consecutive frequencies. We divided patients into five groups by profile and treated them with dextran, dexamethasone, acyclovir, nicotinic acid, and papaverine hydrochloride (with or without vitamin A). We performed audiometry at baseline and on days 30, 90, 120, and 180 of treatment. We determined outcome as the difference between day-0 and day-180 pure-tone averages (PTAs). Among the 139 patients evaluated, baseline PTA was similar in all groups. We observed significant improvements in PTAs after 180 days of treatment and noted a significant linear correlation between time from SHL onset to initial visit and recovery. However, no significant difference was evident among the treatment groups. In the treatment of SHL, dextran provided no more benefit than did dexamethasone or acyclovir. Earlier initiation of treatment improves the prognosis for patients with SHL.

Topic: Vestibular and auditory disorders
Subfield: Neurology
Field: Neuroscience
Domain: Life Sciences
Functional significance of TRIM35 In haematopoietic and hepatic homeostasis

The tumour suppressor, TRIM35, is an E3 ubiquitin ligase initially Identified for Its role in regulating haemopoietic cells but<br/>also implicated in Inflammation and metabolism and recently identified as a key biomarker for liver cancer. Data presented In<br/>this thesis show that TRIM35 can regulate several components of the TGFbsignaling pathway, important In cell growth and<br/>proliferation and often deregulated in cancer. A TRIM35 knockout mouse model demonstrated that TRIM35 is important In<br/>maintaining homeostasis within the haemopoielic stem cell compartment and, In the context of oncogenesis, deleting TRIM35<br/>influenced obesity, Inflammation and liver fibrosis, key precursors to liver cancer.

Topic: interferon and immune responses
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Ethidium Bromide-Resistant Mutant of <i>Bacillus subtilis</i>

An ethidium bromide-resistant mutant (EB8) derived from a Marburg strain of Bacillus subtilis was found to be conditionally resistant to 10 μg of ethidium bromide per ml. Expression of resistance is complete only during vegetative growth at incubation temperatures above 30 C in complex medium or minimal medium supplemented with Casamino Acids. Strain EB8 is cross-resistant to acriflavine and proflavine. The ethidium bromide resistance marker is co-transduced with hisA1 at a frequency of 6% and is located to the right of hisA1 on the B. subtilis chromosome as it is usually represented on the map. Incorporation of [ 5 - 3 H ] uridine by strain EB8 showed that ribonucleic acid synthesis in both whole cells and protoplasts is ethidium bromide-resistant.

Topic: Bacterial Genetics and Biotechnology
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Gold-Catalyzed [3 + 2] Annulation, Carbenoid Transfer, and C–H Insertion Cascade: Elucidation of Annulation Mechanisms via Benzopyrylium Intermediates

It has been established that a cationic gold(I)/PCy3 complex catalyzes the intramolecular cascade reaction of enediyne-carbonyls via benzopyrylium intermediates giving pentacyclic compounds, bearing five or six stereocenters with high yields and diastereoselectivity. In this cascade reaction, [3 + 2] annulation, carbenoid transfer, and C–H insertion proceed in one-pot. The DFT calculation revealed that both the [3 + 2] and [4 + 2] annulations proceed via the same gold(I) carbenoid, produced by the [3 + 2] cycloaddition, and the reaction between the gold(I) carbenoid and the additional alkyne unit promotes the present cascade reaction.

Topic: Catalytic Alkyne Reactions
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Host vs. pathogen evolutionary arms race: Effects of exposure history on individual response to a genetically diverse pathogen

Introduction Throughout their range, bighorn sheep ( Ovis canadensis ) populations have seen significant disease-associated declines. Unfortunately, understanding of the underlying epidemiological processes driving the disease dynamics in this species has hindered conservation efforts aimed at improving the health and long-term viability of these populations. Individual response to pathogen exposure emerges from dynamic interactions between competing evolutionary processes within the host and pathogen. The host’s adaptive immune system recognizes pathogens and mounts a defensive response. Pathogens have evolved strategies to overcome adaptive immune defenses including maintaining high genetic diversity through rapid evolution. The outcomes of this evolutionary warfare determine the success of pathogen invasion of the host and ultimately the success of conservation efforts. Methods During an epizootic dominated by a single strain, we explore these host-pathogen dynamics by examining the variation in effects of pathogen invasion on captive bighorn sheep with differing histories of exposure to genetically diverse strains of Mycoplasma ovipneumoniae (Movi). We monitored clinical signs of disease and sampled animals and their environment to detect spread of Movi among 37 bighorn sheep separated into nine pens based on known exposure histories. Results We documented Movi transmission within and across pens and we detected Movi DNA in air, water, and invertebrate samples. Higher levels of antibody to Movi prior to the epizootic were associated with a lower likelihood of presenting clinical signs of pneumonia. Nonetheless, higher antibody levels in symptomatic individuals were associated with more severe progressive disease, increased probability and speed of pneumonia-induced mortality, and reduced likelihood of returning to a healthy state. Bighorn sheep with previous exposure to a strain other than the predominant epizootic strain were more likely to recover. Discussion Our results indicate that Movi-strain variability was sufficient to overwhelm the adaptive host immunological defenses. This outcome indicates, in free-ranging herds, past exposure is likely insufficient to protect bighorn sheep from infection by new Movi strains, although it influences the progression of disease and recovery within the herd. Therefore, given Movi-strain variability and the lack of immunological protection from past exposure, focusing management efforts on minimizing the introduction of Movi into bighorn herds, through separation of domestic and bighorn sheep and avoidance of management activities that create commingling of bighorn sheep carrying differing Movi strains, will likely be the most effective approach for reducing the effects of disease and achieving bighorn sheep conservation goals.

Topic: Microbial infections and disease research
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
Biocontrol of &lt;I&gt;Rhizoctonia solani&lt;/I&gt; Root Rot of Chilli by &lt;I&gt;Bacillus subtilis&lt;/I&gt; formulations under Pot Conditions

The chilli crop suffers massive yield loss due to root rot caused by &lt;em&gt;Rhizoctonia solani&lt;/em&gt;. An increase of 10 × 10&lt;sup&gt;5&lt;/sup&gt; root colonizing units/cm was obtained as a result of &lt;em&gt;Bacillus subtilis&lt;/em&gt; in vitro root colonisation assay post germination. Shelf life studies of the formulations revealed stable population level of the biocontrol agent upto 180&lt;sup&gt;th&lt;/sup&gt; day (30°C - 1.6 × 10&lt;sup&gt;8&lt;/sup&gt;; 4°C - 1.9 × 10&lt;sup&gt;8&lt;/sup&gt;) in talc and upto 150&lt;sup&gt;th&lt;/sup&gt; day in lignite (30°C - 1.5 × 10&lt;sup&gt;8&lt;/sup&gt;; 4°C - 1.3 × 10&lt;sup&gt;8&lt;/sup&gt;). Soil, seed, foliar spray and dip treatment methods of &lt;em&gt;B. subtilis&lt;/em&gt; and chlorothalonil brought about a considerable enhancement of all biometric parameters and reduced disease incidence compared to the untreated control. In comparison to the untreated control (50 g and 21 g fresh and dry weight, respectively), highest plant fresh weight (76.84 g) and dry weight (34.17 g) was achieved by the Seed application method. Comparison of plant height revealed maximum values 70 cm (soil application) and 77 cm (dip treatment) with &lt;em&gt;B. subtilis&lt;/em&gt; application which was analogous to chlorothalonil treatment (56.5 cm with soil application and 70.33 cm with dip treatment) which was considerably superior to the untreated control (58.2 cm with dip treatment and 61 cm with soil application, respectively). Root dip treatment showed considerable increase in root length with &lt;em&gt;B. subtilis&lt;/em&gt; (33 cm) and chlorothalonil (28.5 cm) when compared to untreated control (15 cm). Growth promotion was better with Root dip application while disease control was achieved better with seed application. A 66% and 84% reduction in incitation of disease was noticed with soil and seed application methods, respectively.

Topic: Plant-Microbe Interactions and Immunity
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Utopia, Domestication and Special Status: Marriage and Family in the Stoic Tradition

The family was a prominent aspect of early imperial ideology arid enjoyed an increased status in Roman society of the period. Since Panaetius, Stoic thought provided rational support for this status by means of its oikeiosis doctrine. Roman Stoics, far from ignoring the prominence of family in their society, imbued the space of marriage with fresh content but did not agree on the issue of whether the philosopher should be exempted from this responsibility. Ambiguity on whether the sage should many can be traced back to the Stoic founder. The scantily transmitted material on Zeno suggests a double focus in early Stoic thought, on the one hand utopian constructions of the ideal sate and ideal sage (where marriage is abolished) and on the other, ordinary reality (where the Stoic sage should marry and procreate). The abolition of property and marriage (having women and children in common) occurs frequently in so-called high Utopias of the classical era, but this aspect of Stoicism diminished since the middle Stoa, together with receding expectations regarding the Stoic wise man. The Roman Stoics Musonius and Epictetus relate differently to their own tradition. Musonius pays no attention to utopia or the ideal sage, but incorporates utopian vocabulary in his defence of marriage for the philosopher, thus 'domesticating' utopia. This results in an emphasis on the marriage partnership as small-scale communism based on friendship. Epictetus retains the distinction between the ideal community of the wise and reality as is. Marriage is an essential part of the latter, but the Cynic, to whom Epictetus assigns the special status of messenger and scout of Zeus, is exempted from the responsibilities accompanying family life.

Topic: Classical Antiquity Studies
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences