jimnoneill/paper-to-field-training huggingface dataset:
Regulation and Function of Autophagy in Cigarette Smoke-Induced Cellular Stress: Implications for Chronic Obstructive Pulmonary Disease

Field: Medicine (Health Sciences)

Chronic obstructive pulmonary disease (COPD) is characterized by an abnormal inflammatory response to inhalation of noxious agents, particularly cigarette smoke (CS), which leads to a progressive and poorly reversible decline in lung function. Autophagy, a highly conserved adaptive response to cellular stresses, which removes cytoplasmic components such as organelles and long-lived proteins via encapsulation and lysosome-dependant degradation, has also been implicated in cell death pathways. We previously observed autophagy protein induction and autophagosome accumulation in in vivo and in vitro models of experimental COPD, as well as in COPD patients. The regulation and function of autophagy in CS-induced COPD have not been fully elucidated. \nTo delineate the role of autophagy in the response of lung epithelial cells to CS we developed a novel in vitro model of mainstream CS exposure in primary mouse tracheal epithelial cells (MTECs) differentiated at an air-liquid interface (ALI). MTEC cultures in response to CS in vitro recapitulated many features of CS exposure in vivo, including autophagosome accumulation, cilia shortening, misfolded protein aggregation, loss of tight junction integrity and cell death. In vitro we discovered that sublethal doses of CS enhanced selective autophagic flux, while CS-induced cytotoxicity was associated with decreased autophagic activity and autophagosome accumulation. We also discovered that autophagic flux is induced in vivo upon acute exposure, but is not significantly upregulated following chronic 6 month exposure to CS. Both LC3B-/- and Beclin-1+/- mice and MTEC cultures were protected from CS induced injury, indicating that these autophagy proteins promote epithelial cell death. Moreover, we investigated the effects of CS on autophagic substrates. HDAC6 regulates autophagosome-lysosome fusion, autophagic degradation of ubiquitinated protein aggregates, and cilia resorption. Cytotoxicity and protein aggregate accumulation were observed basally in HDAC6-/Y derived MTEC cultures, while CS-exposed mice were more vulnerable to emphysematous changes. Evidence of autophagic degradation of cilia components was also observed following CS treatment. These data indicate that autophagy plays a complex role in COPD pathogenesis, in which CS-induced autophagy both removes deleterious protein aggregates and contributes to apoptosis. \n
Products of Variables in Structural Equation Models

Field: Decision Sciences (Social Sciences)

A general method is introduced in which variables that are products of other variables in the context of a structural equation model (SEM) can be decomposed into the sources of variance due to the multiplicands. The result is a new category of SEM which we call a Products of Variables Model (PoV). Some useful and practical features of PoV models include the estimation of interactions between latent variables, latent variable moderators, manifest moderators with missing values, and manifest or latent squared terms. Expected means and covariances are analytically derived for a simple product of two variables and it is shown that the method reproduces previously published results for this special case. It is shown algebraically that using centered multiplicands results in an unidentified model, but if the multiplicands have non-zero means, the result is identified. The method has been implemented in OpenMx and Ωnyx and is applied in five extensive simulations.
[Transiliacal screw fixation of the sacrum in unstable pelvic ring fractures].

Field: Medicine (Health Sciences)

This article presents our experiences from fixation of the sacrum by transiliacal screw in 13 patients with unstable fractures of the pelvic ring. Early mobilization, with no secondary dislocation or postoperative complications, was achieved in all patients. Sagittal instability in unstable pelvic ring fractures must be acknowledged. The transiliac screw offers the possibility of early mobilization of patients with this fracture. The procedure is demanding and patients selected for this treatment should be referred to hospitals with experience in the treatment of pelvic fractures.
The Timing of Senescence and Response to Pathogens Is Altered in the Ascorbate-Deficient Arabidopsis Mutant vitamin c-1

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract The ozone-sensitive Arabidopsis mutant vitamin c-1 (vtc1) is deficient in l-ascorbic acid (AsA) due to a mutation in GDP-Man pyrophosphorylase (Conklin et al., 1999), an enzyme involved in the AsA biosynthetic pathway (Smirnoff et al., 2001). In this study, the physiology of this AsA deficiency was initially investigated in response to biotic (virulent pathogens) stress and subsequently with regards to the onset of senescence. Infection with either virulent Pseudomonas syringae or Peronospora parasitica resulted in largely reduced bacterial and hyphal growth in the vtc1 mutant in comparison to the wild type. When vitamin c-2 (vtc2), another AsA-deficient mutant, was challenged with P. parasitica, growth of the fungus was also reduced, indicating that the two AsA-deficient mutants are more resistant to these pathogens. Induction of pathogenesis-related proteins PR-1 and PR-5 is significantly higher in vtc1 than in the wild type when challenged with virulent P. syringae. In addition, the vtc1 mutant exhibits elevated levels of some senescence-associated gene (SAG) transcripts as well as heightened salicylic acid levels. Presumably, therefore, low AsA is causing vtc1 to enter at least some stage(s) of senescence prematurely with an accompanying increase in salicylic acid levels that results in a faster induction of defense responses.
SH0946899.10FU

Field: Agricultural and Biological Sciences (Life Sciences)

UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
Competitive exclusion and metabolic dependency among microorganisms structure the cellulose economy of agricultural soil

Field: Environmental Science (Physical Sciences)

Abstract

Many cellulolytic microorganisms degrade cellulose through extracellular processes that yield free intermediates which promote interactions with non-cellulolytic organisms. We hypothesize that these interactions determine the ecological and physiological traits that govern the fate of cellulosic carbon (C) in soil. We evaluated the genomic potential of soil microorganisms that access C from 13 C-labeled cellulose. We used metagenomic-SIP and metaproteomics to evaluate whether cellulolytic and non-cellulolytic microbes that access 13 C from cellulose encode traits indicative of metabolic dependency or competitive exclusion. The most highly 13 C-enriched taxa were cellulolytic Cellvibrio ( Gammaproteobacteria ) and Chaetomium ( Ascomycota ), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. These ruderal taxa were common indicators of soil disturbance in agroecosystems, such as tillage and fertilization. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria , demonstrating differences in dependency among cellulose degraders. Non-cellulolytic taxa that accessed 13 C from cellulose ( Planctomycetales , Verrucomicrobia and Vampirovibrionales ) were highly dependent, as indicated by patterns of auxotrophy and 13 C-labeling (i.e. partial labelling or labeling at later-stages). Major 13 C-labeled cellulolytic microbes ( e.g. Sorangium, Actinomycetales, Rhizobiales and Caulobacteraceae ) possessed adaptations for surface colonization ( e.g. gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposition. These results suggest that access to cellulose was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion. These trade-offs likely influence microbial growth dynamics on particulate organic carbon and reveal that the fate of carbon is governed by a complex economy within the microbial community.
IRF-7, a new interferon regulatory factor associated with Epstein-Barr virus latency.

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

The Epstein-Barr virus (EBV) BamHI Q promoter (Qp) is the only promoter used for the transcription of Epstein-Barr virus nuclear antigen 1 (EBNA-1) mRNA in cells in the most restricted (type I) latent infection state. However, Qp is inactive in type III latency. With the use of the yeast one-hybrid system, a new cellular gene has been identified that encodes proteins which bind to sequence in Qp. The deduced amino acid sequence of the gene has significant homology to the interferon regulatory factors (IRFs). This new gene and products including two splicing variants are designated IRF-7A, IRF-7B, and IRF-7C. The expression of IRF-7 is predominantly in spleen, thymus, and peripheral blood leukocytes (PBL). IRF-7 proteins were identified in primary PBL with specific antiserum against IRF-7B protein. IRF-7s can bind to interferon-stimulated response element (ISRE) sequence and repress transcriptional activation by both interferon and IRF-1. Additionally, a functional viral ISRE sequence, 5'-GCGAAAACGAAAGT-3', has been identified in Qp. Finally, the expression of IRF-7 is consistently high in type III latency cells and almost undetectable in type I latency, corresponding to the activity of endogenous Qp in these latency states and the ability of the IRF-7 proteins to repress Qp-reporter constructs. The identification of a functional viral ISRE and association of IRF-7 with type III latency may be relevant to the mechanism of regulation of Qp.
4-[(5-Hydroxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)phenylmethyl]-5-methyl-2-phenyl-1H-pyrazol-3(2H)-one ethanol hemisolvate

Field: Chemistry (Physical Sciences)

The asymmetric unit of the title compound, C(27)H(24)N(4)O(2)·0.5C(2)H(6)O, comprises two crystallographically independent mol-ecules (A and B) with slightly different conformations, and one ethanol mol-ecule of crystallization. Intra-molecular C-H⋯O and O-H⋯O hydrogen bonds generate six- and eight-membered rings, producing S(6) and S(8) ring motifs, respectively. In mol-ecule A, one of the benzene rings is disordered over two positions, with site-occupancy factors of 0.542 (11) and 0.458 (11). The dihedral angles between the central benzene ring and the two outer benzene rings are 73.88 (9) and 82.6 (2)/88.9 (2)° in mol-ecule A, and 80.81 (8) and 79.38 (8)° in mol-ecule B. In the crystal structure, mol-ecules form infinite one-dimensional chains in the (101) plane. The crystal structure is stabilized by inter-molecular O-H⋯N, N-H⋯N, N-H⋯O and C-H⋯O hydrogen bonds, weak C-H⋯π and π-π [centroid-centroid = 3.5496 (1) Å] inter-actions.
Efficient Synthesis of α-Ketoamides via 2-Acyl-5-aminooxazoles by Reacting Acyl Chlorides and α-Isocyanoacetamides

Field: Chemistry (Physical Sciences)

Acyl chlorides and alpha-isocyanoacetamides undergo an efficient reaction in dichloromethane in the presence of triethylamine to give 2-acyl-5-aminooxazoles. Subsequent acid hydrolysis of the 5-aminooxazole moiety leads to alpha-ketoamides in good overall yields.
P143 Gaviscon double action protects against acid-induced increases in oesophageal mucosal permeability ex vivo

Field: Medicine (Health Sciences)

Introduction

Gastro-oesophageal reflux disease (GORD) is characterised by symptoms (most commonly heartburn) caused by exposure of the oesophageal mucosa to gastric contents. Usually, the macroscopic appearance of the mucosa in GORD is normal (non-erosive reflux disease, NERD). However, the oesophageal mucosa in NERD has microscopic dilated intercellular spaces (where the gaps between epithelial cells are wider), suggestive of impaired barrier function. This increased mucosal permeability is likely to allow permeation of refluxate to deeper layers of the mucosa where it can stimulate nociceptive nerves. Mucosal permeability can be measured by way of transepithelial electric resistance (TER) of biopsies in an Ussing chamber, and increased permeability (reduced TER) is rapidly induced by exposure of the biopsies to acidic solutions. Alginate solutions are used in GORD primarily for their gastric 'raft' forming and antacid properties. However, alginate solutions may also have a therapeutic action via oesophageal mucosal protection properties. We tested the ability of topically applied Gaviscon Double Action to reduce impairment of mucosal integrity caused by reflux-like solutions in an Ussing chamber model.

Methods

24 patients having gastroscopy for clinical reasons were recruited at the Royal London Hospital. From each patient, mucosal biopsies were taken from the distal oesophagus, 3–5 cm above the z-line. The lumen of each biopsy was protected for 5 minutes with Gaviscon Double Action (GDA), or Gaviscon Placebo (GP, a solution of similar viscosity to GDA but without alginates). Protectant was washed off, biopsies were mounted in an Ussing chamber filled with pH7.4 Krebs-Henseleit solution, and baseline TER was measured. Next, the solution in the luminal chamber was replaced with a reflux-like solution of pH2 Krebs-Henseleit solution + 1mM deoxycholic acid + 1mg/mL porcine pepsin for 30mins. Percentage change of TER from baseline at 30mins was analysed by paired t-test.

Results

Acid-induced reduction of TER was less in the GDA group than in the GP group (mean 29.9% ± 16.0% vs 40.4% ± 15.0%; p = 0.0015). Data is represented in figure 1 as% change in oesophageal biopsy TER in response to luminal acid exposure following pre-treatment with test solutions.

Conclusions

When pre-applied to human oesophageal mucosal biopsies, GDA (containing alginate) is more effective than GP (which does not) at preventing the effects of acid exposure on oesophageal epithelial permeability. Penetration of toxic refluxate into the epithelium of the oesophagus is important in both pain perception and inflammation in GORD, via receptor-mediated mechanisms and induction of epithelial cell damage. Mucosal topical protection such as that provided by GDA could as a useful therapeutic tool in the treatment of GORD.
[Dysphagia and emotional distress].

Field: Medicine (Health Sciences)

Swallowing function may be impaired by a number of conditions involving primary or associated emotional distress. When psychogenic dysphagia is suspected, routine investigation using radiological and manometric examination is inappropriate. These cases demand an evaluation of the individual as a whole, comprising the disease as well as the patient's personal problems and concerns. Five cases of patients complaining of swallowing difficulty and showing concurrent emotional distress were studied. Four individuals were anxious and one was depressed. Because of our approach a close medical-patient relationship was established. Afterwards, an explanation about the normal swallowing mechanisms and the role of the emotions was provided. All patients showed improvement of the symptom in the next 24 hours. Dysphagia can be found in anxiety, depression and conversion hysteria, with high incidence in the urban population of the third world countries. However, several professionals are unaware of these disorders. Our results suggest that this simple approach is an useful tool in managing dysphagic patients and its has validity even in individuals bearing dysphagia due to comproved organic disease. The results also emphasize the importance of the medical-patient relationship and the utility of a hollistic evaluation of the disease.
Influence of chitosan on the emulsifying properties of egg yolk hydrolysates: study on creaming, thermal and oxidative stability

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract BACKGROUND Egg yolk, as a natural emulsifier, is widely used in high‐oil‐phase food systems, such as mayonnaise and salad. However, the application of egg yolk in an oil‐in‐water system is still limited due to poor emulsifying stability. To improve the emulsifying capacity of egg yolk, the effect of chitosan addition sequence and concentration on emulsifying properties (creaming stability, thermal tolerance and oxidation resistance) of egg yolk hydrolysates were investigated. RESULTS Stacking sequence of multilayer materials has an influence on properties of composite emulsions. The composite emulsions with egg yolk hydrolysis dominate at the interface (functioning on reducing interfacial tension), and chitosan layered on the surface (providing steric hindrance) displayed better stability. Little chitosan addition (0.5 g × kg −1 , w/w) was unhelpful for the dispersion of emulsion droplets as a result of bridging flocculation. At a chitosan concentration of 2 g kg −1 (w/w), the composite emulsion possesses the best stability. When chitosan concentration was higher than 2 g kg −1 (w/w), depletion flocculation would occur. Hydrolyzed egg yolk prepared composite emulsions possessed better thermal resistance, but with poorer oxidative stability as compared to natural egg yolk. In combination with chitosan it also displayed a negative effect on the oxidative stability of the emulsion system. CONCLUSION The research revealed the effect of chitosan addition on the physical and chemical stability of emulsions prepared with egg yolk hydrolysates. The results could provide guidance on expanding the application of egg yolk as an emulsifier in water‐abundant food systems such as beverages. © 2021 Society of Chemical Industry.
CPA-DF: A Tool for Configurable Interval Analysis to Boost Program Verification

Field: Computer Science (Physical Sciences)

Software verification is challenging, and auxiliary program invariants are used to improve the effectiveness of verification approaches. For instance, the k-induction implementation in CPACHECKER, an award-winning framework for program analysis, uses invariants produced by a configurable data-flow analysis to strengthen induction hypotheses. This invariant generator, CPA-DF, uses arithmetic expressions over intervals as its abstract domain and is able to prove some safe verification tasks alone. After extensively evaluating CPA-DF on SV-Benchmarks, the largest publicly available suite of C safety-verification tasks, we discover that its potential as a stand-alone analysis or a sub-analysis in a parallel portfolio for combined verification approaches has been significantly underestimated: (1) As a stand-alone analysis, CPA-DF finds almost as many proofs as the plain k-induction implementation without auxiliary invariants. (2) As a sub-analysis running in parallel to the plain k-induction implementation, CPA-DF boosts the portfolio verifier to solve a comparable amount of tasks as the heavily-optimized k-induction implementation with invariant injection. Our detailed analysis reveals that dynamic precision adjustment is crucial to the efficiency and effectiveness of CPA-DF. To generalize our results beyond CPACHECKER, we use CoVeriteam,a platform for cooperative verification, to compose three portfolio verifiers that execute CPA-DF and three other software verifiers in parallel, respectively. Surprisingly, running CPA-DF merely in parallel to these state-of-the-art tools further boosts the number of correct results up to more than 20 %. Demonstration video: https://youtu.be/l7UG-vhTL_4
LHD 6-T_U_01 #172768.1 (analyzed)

Field: Physics and Astronomy (Physical Sciences)

Luminance data of the plasma monitor camera. Time variation of the average and maximum luminance within the ROI (Region of Interests) of the plasma images observed by the 6-T port camera, where ROI is (672,10) - (776,86) of the original image of 1920x1080. The luminance value is between 0 and 255 in arbitrary unit.
Incidence of bacteremia after endoscopic laser treatment of stenosing processes in the upper gastrointestinal tract.

Field: Medicine (Health Sciences)

Bacteremia following endoscopic interventions has been repeatedly described. This prospective study was intended to establish the extent to which this condition can occur after endoscopic laser therapy. A total of 32 procedures to treat stenosing processes in the upper gastrointestinal tract had been performed on the 20 patients admitted to the study. The incidence of bacteremia was found to be 34%. Two patients developed sepsis that required antibiotic treatment, despite which, however, one of the patients died. Routine prophylactic antibiotic administration would, at present, appear to represent overtreatment. However, patients with cardiac diseases or artificial heart valves need antibiotic prophylaxis. Should a fever develop in patients undergoing laser therapy, immediate broad-band antibiotic cover is urgently recommended to prevent septic complications.
Supplementary Figure S2 from Preclinical Antitumor Efficacy of BAY 1129980—a Novel Auristatin-Based Anti-C4.4A (LYPD3) Antibody–Drug Conjugate for the Treatment of Non–Small Cell Lung Cancer

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

<p>C4.4A-Ab BAY 1112623 binds domain 1 of C4.4A.</p>
Effect of Narrowband Ultraviolet B on IFN-γ,IL-4 in Serum and Lesions of Psoriasis Patients

Field: Medicine (Health Sciences)

Objective To determine the effect of 311nm narrow band UVB(NB-UVB)on the level of IFN-γ and IL-4 in serum and lesions of patients with psoriasis vulgaris. Methods 40 patients with psoriasis vulgaris were divided randomly into NB-UVB group and control group, and each group contained 20 patients who received phototherapy 3 times per week, and 4 weeks totally, and control group was not given phototherapy. The severity of psoriasis was evaluated by PASI score, and serumal IFN-γ and IL-4 were examined by ELISA, and the expression of IFN-γ and IL-4 in lesions were detected by immunohistochemistry and image-analysis system before and after treatment. Results PASI score decreased significantly after treatment(P0.05)in both groups, and which in NB-UVB group decreased more significant than that in control group. The level of serumal IFN-γ decreased in both groups and the level of serumal IL-4 had no significant change after treatment(P0.05). The level of IFN-γ in lesions decreased significantly after treatment(P0.05), and which in NB-UVB group decreased more than that in control group(P0.05). The level of IL-4 increased significantly after treatment(P0.05), and which in NB-UVB group increased more significantly than that in control group(P0.05).Conclusion NB-UVB has a therapeutic effect on psoriasis vulgaris by regulating the level of IFN-γ in serum and lesions to improve the imbalance of Th1 and Th2.