jimnoneill/paper-to-field-training huggingface dataset:
Integrated Multi-Omics Analysis to Investigate the Molecular Mechanisms Underlying the Response of Auricularia heimuer to High-Temperature Stress

Field: Agricultural and Biological Sciences (Life Sciences)

High-temperature stress is a key factor that reduces the yields of edible fungi. Auricularia heimuer (A. heimuer) is a nutrient-rich edible fungus that is widely cultivated in China. In this study, we analyzed the physiological, transcriptomic, and metabolomic results of A. heimuer (variety “Hei29”) under high-temperature stress. Our findings revealed that high temperatures (30 °C and 35 °C) significantly reduced hyphal growth, increased malondialdehyde content and antioxidant enzyme activity, and enhanced the accumulation of secondary metabolites, such as phenolic compounds and flavonoids. A total of 15 candidate genes potentially responsive to high-temperature stress were identified through transcriptomic analysis, including those involved in regulating antioxidant defense, heat shock response, sugar metabolism, amino acid metabolism, and accumulating secondary metabolites. Metabolomic analysis identified three candidate metabolites potentially responsive to high-temperature stress, including kinetin, flavonoids, and caffeic acid, as well as several metabolic pathways, including nucleotide metabolism, ABC transporters, and cofactor biosynthesis. These mechanisms help mitigate oxidative damage to cellular structures and energy deficits caused by elevated temperatures, enabling the fungus to maintain cellular stability, metabolic function, and growth under heat stress. This study is the first to explore the molecular mechanism of A. heimuer in response to high-temperature stress. The results provide valuable insights into the molecular mechanisms of heat stress tolerance in A. heimuer, highlighting potential targets for developing heat-tolerant strains for industrial application.
Light-controlled smart nanotubes based on the orthogonal assembly of two homopolymers

Field: Chemistry (Physical Sciences)

Two homopolymers can orthogonally self-assemble into pseudo-copolymer based on terminal host–guest interactions, and these supramolecular copolymers further fabricate one-dimensional nanotubes in water. By applying alternate UV/visible light, the aggregates can reversibly assemble and disassemble by means of the association and disassociation of active connection.
The language of software engineering

Field: Computer Science (Physical Sciences)

The first course in software engineering is the most critical. Education must start from an understanding of the heart of software development, from familiar ground that is common to all software development endeavors. This book is an in-depth introduction to software engineering that uses a systematic, universal kernel to teach the essential elements of all software engineering methods. This kernel, Essence, is a vocabulary for defining methods and practices. Essence was envisioned and originally created by Ivar Jacobson and his colleagues, developed by Software Engineering Method and Theory (SEMAT) and approved by The Object Management Group (OMG) as a standard in 2014. Essence is a practiceindependent framework for thinking and reasoning about the practices we have and the practices we need. Essence establishes a shared and standard understanding of what is at the heart of software development. Essence is agnostic to any particular method, lifecycle independent, programming language independent, concise, scalable, extensible, and formally specified. Essence frees the practices from their method prisons. The first part of the book describes Essence, the essential elements to work with, the essential things to do and the essential competencies you need when developing software. The other three parts describe more and more advanced use cases of Essence. Using real but manageable examples, it covers the fundamentals of Essence and the innovative use of serious games to support software engineering. It also explains how current practices such as user stories, use cases, Scrum, and microservices can be described using Essence, and illustrates how their activities can be represented using the Essence notions of cards and checklists. The fourth part of the book offers a vision how Essence can be scaled to support large, complex systems engineering. Essence is supported by an ecosystem developed and maintained by a community of experienced people worldwide. From this ecosystem, professors and students can select what they need and create their own way of working, thus learning how to create ONE way of working that matches the particular situation and needs.
Antibiotic therapy for pulmonary exacerbations in adults with cystic fibrosis.

Field: Nursing (Health Sciences)

Individuals with CF are living longer but often with chronic lung infections. Effective antibiotic therapy is necessary to treat life-threatening infectious exacerbations. Knowledge of the particular requirements of antibiotic therapy for the patient with CF allows the nurse to anticipate management plans, prepare for inpatient and outpatient care, and assess response to treatment.
Production of .ALPHA.-glucosidase and its role in regulation of amylase production by Bacillus circulans F-2.

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Bacillus circulans F-2 requires a special carbon source or cultural conditions for amylase production. The α-glucosidase production of this bacterium was studied in various cultural conditions with measured glucose concentrations. High amylase production was always accompanied by low α-glucosidase production and the absence of glucose in culture broth. Usually higher α-glucosidase production was observed in cultural conditions where little amylase was produced. In the presence of 1-deoxynojirimycin, an inhibitor of α-glucosidase activity, the bacterium produced significant amounts of amylase even in conditions giving high α-glucosidase production. It was concluded that the special requirement of this bacterium to produce amylase is effected by its high sensitivity to glucose repression and by the production of α-glucosidase which leads to the formation of glucose. Production of α-glucosidase was, like that of amylase, induced by maltooligosaccharides and repressed by glucose, but both its induction and repression are less sensitive to glucose than those of amylase.
Implant Choices, Technique, and Results in Revision Acetabular Surgery: A Review

Field: Medicine (Health Sciences)

Acetabular reconstruction in revision total hip arthroplasty can successfully be achieved with hemispherical components featuring a porous or roughened ingrowth surface and options for placement of multiple screws. Most defects can be reconstructed with large hemispherical or “jumbo” cups. Achieving component stability and sufficient contact area on adequate host bone is mandatory. Defects with greater bony loss or compromised columns require either the use of modular augments combined with a hemispherical shell, reconstruction cages, structural allografts, or custom triflange acetabular components. This paper will detail the necessary pre-operative evaluation, the intra-operative details, and the reported results of these acetabular revisions.
Role of the Lectin Pathway Recognition Molecule Ficolin A in Fighting Pneumococcal Infection

Field: Immunology and Microbiology (Life Sciences)

Complement system is an essential part of innate immune system that plays major role in protection against various pathogens, including Streptococcus pneumoniae. Complement is activated via three pathways; the classical pathway, the alternative pathway and the lectin pathway. Lectin pathway of complement activation is mediated via ficolins, MBL and recently described C-type lectin, CL-11, that recognise a wide range of carbohydrates on microbial surfaces and activate the complement system via MASP-2, the effector enzyme of the lectin pathway of complement activation. A significant role of the lectin pathway has been described previously using MASP-2 deficient mice, with a complete deficiency of the lectin activation pathway specific C3 and C5 converting enzymes C4b2a and C4b2a(3b)n respectively. However, the role of MBL, ficolins and CL-11 in activating lectin pathway against S. pneumoniae has not been fully characterised. \nIn vitro studies demonstrate that ficolin A and CL-11 are the relevant carbohydrate recognition molecules that can activate the lectin pathway of complement on the surface of S. pneumoniae. The protective activity of ficolin A was demonstrated in vivo using ficolin A-/- mice compared to wild-type controls, the ficolin A-/- mice were highly susceptible to pneumococcal infection with higher mortality and higher bacterial burden in both blood and lungs after intranasal infection with S. pneumoniae D39 compared to wild-type controls. These findings imply that the lectin pathway has a significant role in protection against S. pneumoniae infection and highlights the importance of non-MBL mediated lectin pathway activation in the innate host defence against S. pneumoniae. \nThe essential role of the lectin pathway in providing protection against S. pneumoniae was further described by blocking the lectin pathway by i.p. injection of mice with anti-MASP-2 mAb. Mice receiving anti-MASP-2 mAb showed significantly higher mortality after intranasal infection with S. pneumoniae when compared to mice receiving control antibody.
Hypoxia survival variations in male and female mice as functions of chronological and environmental factors.

Field: Neuroscience (Life Sciences)

The inhalation by mice for 20 min of 5.5% oxygen in nitrogen, performed 29 times over 40 months, causes a mortality of 49.81%. Correlation coefficients were calculated between hypoxia mortality and different parameters: environmental--lighting, temperature, hygrometry, barometric pressure, biological--sex, age, body weight; and chronological--circadian, circannual, pluriannual. Partial correlation coefficients eliminate several interrelationships and finally point out the statistical significance of transfer from dark to light (p less than 0.001), of circadian (p less than 0.05), and of circannual (p less than 0.01) hypoxic mortality variations. Moreover, a significant (p less than 0.001) sex-related difference of mortality (males: 56.94%; females : 41.14%) was observed, independently of the environmental and chronological parameters studied.
Reversible Hydrogen-Induced Phase Transformations in La0.7Sr0.3MnO3 Thin Films Characterized by In Situ Neutron Reflectometry

Field: Materials Science (Physical Sciences)

We report on the mechanism for hydrogen-induced topotactic phase transitions in perovskite (PV) oxides using La0.7Sr0.3MnO3 as a prototypical example. Hydrogenation starts with lattice expansion confirmed by X-ray diffraction (XRD). The strain- and oxygen-vacancy-mediated electron-phonon coupling in turn produces electronic structure changes that manifest through the appearance of a metal insulator transition accompanied by a sharp increase in resistivity. The ordering of initially randomly distributed oxygen vacancies produces a PV to brownmillerite phase (La0.7Sr0.3MnO2.5) transition. This phase transformation proceeds by the intercalation of oxygen vacancy planes confirmed by in situ XRD and neutron reflectometry (NR) measurements. Despite the prevailing picture that hydrogenation occurs by reaction with lattice oxygen, NR results are not consistent with deuterium (hydrogen) presence in the La0.7Sr0.3MnO3 lattice at steady state. The film can reach a highly oxygen-deficient La0.7Sr0.3MnO2.1 metastable state that is reversible to the as-grown composition simply by annealing in air. Theoretical calculations confirm that hydrogenation-induced oxygen vacancy formation is energetically favorable in La0.7Sr0.3MnO3. The hydrogenation-driven changes of the oxygen sublattice periodicity and the electrical and magnetic properties similar to interface effects induced by oxygen-deficient cap layers persist despite hydrogen not being present in the lattice.
The fly specimen that awaited a growing barcode community to be dusted off the shelves and given a name

Field: Agricultural and Biological Sciences (Life Sciences)

While it can take an average of 21 years between the discovery and description of a new species1, the challenges of relating known taxa and the scarcity of high-quality specimens make the description of a new genus even more difficult and time-consuming. Our paper recently published in the Biodiversity Data Journal introduced a new fungus gnat genus – <i>Coelosynapha</i> – demonstrating that despite a taxon being shelved for a long time after discovery, strong collaborative networks spanning many countries combined with the power of DNA barcoding are greatly changing the pace at which we catalogue life.
EPLMaoist Guerilla Movement

Field: Social Sciences (Social Sciences)

The Popular Army of Liberation (EPL) was formed by a group of students in 1967 as an armed branch of the Marxist‐Leninist Communist Party of Colombia (PCC‐ML). A Maoist splinter group of the Communist Party of Colombia, it was born out of the differences between the pro‐Soviet and the pro‐China groups. Espousing a Maoist political ideology, it endorsed the concept of a prolonged popular war, with the aim of disposing of the Colombian government and erecting a socialist state.
Bring back order in the polymethine dye medley: Classification, structure and spectra

Field: Chemistry (Physical Sciences)

The term polymethine dyes was introduced by Walter König in 1922 and four years later he created a general classification of polymethine dyes. In current terms polymethine dyes are characterized by a conjugated chain of (2n + 1) sp2-hybridized carbon atoms that connects a terminal π-electron accepting group and a terminal π-electron donating group. The second feature is an odd number 2n + 3 of π-centres and an even number 2n + 4 of π-electrons, where n is equal to the number of –C(R) = C(R′)– groups (usually vinylene groups –CHCH–). These features confer special structure-absorption relationships on the class owing to their strong influence over the nature of possible transitions from the electronic ground state and thus dye absorption spectra. Over the years, the general definition has been divided into sub-classes - in some instances, not systematically - with a great diversity of complete different chemical structures, belonging to the polymethine dyes. Some of these aspects have been forgotten or overlooked or even misunderstood and such mistakes have been propagated in the literature. In this review an attempt is made to bring clarity to the nomenclature of dye sub-classes, the history of the respective terms and to highlight common structural features.
The effect of DuSuQing granule on IL-1,TNF-α,MIP-2 in small intestine of the aged rats with Klebsiella pneumonia

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Objective To study the mechanism of protective effect of DuSuQing on small intestine injury induced by pneumonia in the aged.Methods The model of rats with Klebsiella pneumonia was established.The aged SD rats were randomly divided into control,model,DuSuQing and levofloxacin groups.The pathological changes and water content of small intestine and lung were observed and determined.IL-1,TNF-α and MIP-2 protein expressions were measured by immunohistochemistry.MIP-2mRNA expression was detected by in situ hybridization.Results The rats of model group had obvious intestine injury,the increased water content,but those of DuSuQing and levofloxacin groups had less injury and the decreased water content.The expressions of IL-1,TNF-α,MIP-2 and MIP-2mRNA of model group were significantly higher than those in the control group,while those of DuSuQing and levofloxacin groups were significantly lower than those of model group.Conclusions The intestine injury induced by Klebsiella pneumonia is related to IL-1,TNF-α,MIP-2 and MIP-2mRNA.To decrease the excessive expression of IL-1,TNF-α,MIP-2 and MIP-2mRNA might be the main mechanism of protective effect of DuSuQing on intestine injury.
Comparison of central axis and jet ring coolant supply for turbine disk cooling on a SSME-HPOTP model

Field: Engineering (Physical Sciences)

The test facility, test methods and results are presented for an experimental study modeling the cooling of turbine disks in the blade attachment regions with multiple impinging jets, in a configuration simulating the disk cooling method employed on the Space Shuttle Main Engine oxygen turbopump. The study's objective was to provide a comparison of detailed local convection heat transfer rates obtained for a single center-supply of disk coolant with those obtained with the present flight configuration where disk coolant is supplied through an array of 19 jets located near the disk outer radius. Specially constructed disk models were used in a program designed to evaluate possible benefits and identify any possible detrimental effects involved in employing an alternate disk cooling scheme. The study involved the design, construction and testing of two full scale rotating model disks, one plane and smooth for baseline testing and the second contoured to the present flight configuration, together with the corresponding plane and contoured stator disks. Local heat transfer rates are determined from the color display of encapsulated liquid crystals coated on the disk in conjunction with use of a computer vision system. The test program was composed of a wide variety of disk speeds, flowrates, and geometrical configurations, including testing for the effects of disk boltheads and gas ingestion from the gas path region radially outboard of the disk-cavity.
Phytoecdysteroids in seeds and plants of Rhagodia baccata (Labill.) Moq. (Chenopodiaceae)

Field: Agricultural and Biological Sciences (Life Sciences)

Seeds of Rhagodia baccata afforded, in addition to 20-hydroxyecdysone and polypodine B, a novel phytoecdysteroid, (20R)-22-deoxy-20,21-dihydroxyecdysone, the structure of which was elucidated unequivocally by UV, LSIMS and NMR techniques. This compound possessed agonistic activity in the Drosophila melanogaster BII cell bioassay, with an ED50 value of 2.0 × 10–7M (ED50 value for 20-hydroxyecdysone = 7.5 × 10–9M). The distribution of ecdysteroids in plants of R. baccata has been determined. Highest levels are associated with the youngest aerial tissues and with the roots. Ecdysteroid profiles are qualitatively very similar throughout the plant, with 20-hydroxyecdysone and polypodine B predominating in all plant parts tested. Arch. Insect Biochem. Physiol. 41:18–23, 1999. © 1999 Wiley-Liss, Inc.
Deciphering real estate investment decisions through fuzzy logic systems

Field: Decision Sciences (Social Sciences)

Purpose The purpose of this paper is to explore the application of fuzzy logic in real estate investment in Hong Kong. There have been sufficient debates on the literature, providing the theoretical background on real estate investment decisions but there has been a lack of empirical support in this regard. This paper attempts to fill the gap between theorem and application. Design/methodology/approach The fuzzy logic system is adopted to evaluate the situation of a real estate market with imprecise and vague information. An indicator‐portfolio, rather than a specific indicator/index usually employed by practitioners, is explored to assist investors in risk management. The result derived from this framework is then compared to the property price index. This approach provides a framework in understanding the market without statistical and mathematical models. It tries to stimulate the complex human cognitive process involving decision making. Findings The housing‐indicator portfolio composition produces an outcome value which is able to reflect the complexities of both the real estate market and investors' expectations. An increase of this value implies that the investment condition is becoming more positive. Research limitations/implications The paper reveals that fuzzy logic can provide some insights in an intuitive manner and is capable of obtaining information not found in market data. It is particularly useful to investors without experience in mathematical modeling. Practical implications This paper establishes a basic framework of fuzzy logic for real estate investment on which a base is formed as a reference for practitioners and investors. However, they should make references to the specific housing‐indicator portfolio composition in their own regions. Originality/value This paper has used a fuzzy logic system to assist practitioners as well as investors on decision making in real estate investment with imperfect market information. With the aid of the system, practitioners and investors are able to enhance their investment decision‐making quality by reducing the risk incurred by such uncertainties.
Normal and Aberrant Craniofacial Development and Nutrition in Infancy

Field: Dentistry (Health Sciences)

The oral cavity is the usual portal for nutrition throughout life and any aberrations in its development or function may impact on the capacity of an infant to thrive. The mouth is complex and unique, it is open to the environment, forms the anterior section of the gastrointestinal system and contains tissue derived from ectoderm, mesoderm, and endoderm, including teeth, in the presence of saliva. Any interference with normal development of the face, mouth, and teeth arising in utero and infancy can lead to a wide spectrum of disorders presenting at birth or in infancy. Some malformations are evident at birth, such as cleft lip/palate, Trisomy 21, and Pierre Robin Sequence. Other issues with structure and function of components of the craniofacial complex may not be immediately apparent but can complicate feeding and nutrient intake in the infant which will manifest as failure to thrive.
Assessing the population transmission dynamics of tilapia lake virus in farmed tilapia

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract A novel virus, tilapia lake virus (Ti LV ), has been identified as a key pathogen responsible for disease outbreak and mass mortality of farmed tilapia. We used a deterministic susceptible‐infectious‐mortality ( SIM ) model to derive key disease information appraised with published Ti LV ‐induced cumulative mortality data. The relationship between tilapia mortality and Ti LV exposure dosages was described by the Hill model. Furthermore, a disease control model was proposed to determine the status of controlled Ti LV infection using a parsimonious control reproduction number ( R C )‐control line criterion. Results showed that the key disease determinants of transmission rate and basic reproduction number ( R 0 ) could be derived. The median R 0 estimate was 2.59 in a cohabitation setting with 2.6 × 10 5 TCID 50 fish −1 Ti LV . The present R C ‐control model can be employed to determine whether Ti LV containment is feasible in an outbreak farm by quantifying the current level of transmission. The SIM model can then be applied to predict what additional control is required to manage R C < 1. We offer valuable tools for aquaculture engineers and public health scientists the mechanistic‐based assessment that allows a more rigorous evaluation of different control strategies to reduce waterborne diseases in aquaculture farming systems.