jimnoneill/paper-to-field-training huggingface dataset:
Cholesterol in Class C GPCRs: Role, Relevance, and Localization

G-protein coupled receptors (GPCRs), one of the largest superfamilies of cell-surface receptors, are heptahelical integral membrane proteins that play critical roles in virtually every organ system. G-protein-coupled receptors operate in membranes rich in cholesterol, with an imbalance in cholesterol level within the vicinity of GPCR transmembrane domains affecting the structure and/or function of many GPCRs, a phenomenon that has been linked to several diseases. These effects of cholesterol could result in indirect changes by altering the mechanical properties of the lipid environment or direct changes by binding to specific sites on the protein. There are a number of studies and reviews on how cholesterol modulates class A GPCRs, however, this area of study is yet to be explored for class C GPCRs, which are characterized by a large extracellular region and often form constitutive dimers. This review highlights specific sites of interaction, functions, and structural dynamics involved in the cholesterol recognition of the class C GPCRs. We summarize recent data from some typical family members to explain the effects of membrane cholesterol on the structural features and functions of Class C GPCRs and speculate on their corresponding therapeutic potential.

Topic: Receptor Mechanisms and Signaling
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Recovery of sterols as fatty acid steryl esters from waste material after purification of tocopherols

Abstract Tocopherols are purified industrially from soybean oil deodorizer distillate by a process comprising distillation and ethanol fractionation. The waste material after ethanol fractionation (TC waste) contains 75% sterols, but a purification process has not yet been developed. We thus attempted to purify sterols by a process including a lipase‐catalyzed reaction. Candida rugosa lipase efficiently esterified sterols in TC waste with oleic acid (OA). After studying several factors affecting esterification, the reaction conditions were determined as follows: ratio of TC waste/OA, 1∶2 (wt/wt); water content, 30%; amount of lipase, 120 U/g‐reaction mixture; temperature, 40°C. Under these conditions, the degree of esterification reached 82.7% after 24 h. FA steryl esters (steryl esters) in the oil layer were purified successfully by short‐path distillation (purity, 94.9%; recovery, 73.1%). When sterols in TC waste were esterified with FFA originating from olive, soybean, rapeseed, safflower, sunflower, and linseed oils, the FA compositions of the steryl esters differed somewhat from those of the original oils: The content of saturated FA was lower and that of unsaturated FA was higher. The m.p. of the steryl esters synthesized (21.7–36.5°C) were remarkably low compared with those of the steryl esters purified from high‐b.p. soybean oil deodorizer distillate substances (56.5°C; JAOCS 80 , 341–346, 2003). The low‐m.p. steryl esters were soluble in rapeseed oil even at a final concentration of 10%.

Topic: Cholesterol and Lipid Metabolism
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Insulin-like Growth Factor-1 Influences Prostate Cancer Cell Growth and Invasion through an Integrin α3, α5, αV, and β1 Dependent Mechanism

Insulin-like growth factor-1 (IGF-1)-related signaling is associated with prostate cancer progression. Links were explored between IGF-1 and expression of integrin adhesion receptors to evaluate relevance for growth and migration. Androgen-resistant PC3 and DU145 and androgen-sensitive LNCaP and VCaP prostate cancer cells were stimulated with IGF-1 and tumor growth (all cell lines), adhesion and chemotaxis (PC3, DU145) were determined. Evaluation of Akt/mTOR-related proteins, focal adhesion kinase (FAK) and integrin α and β subtype expression followed. Akt knock-down was used to investigate its influence on integrin expression, while FAK blockade served to evaluate its influence on mTOR signaling. Integrin knock-down served to investigate its influence on tumor growth and chemotaxis. Stimulation with IGF-1 activated growth in PC3, DU145, and VCaP cells, and altered adhesion and chemotactic properties of DU145 and PC3 cells. This was associated with time-dependent alterations of the integrins α3, α5, αV, and β1, FAK phosphorylation and Akt/mTOR signaling. Integrin blockade or integrin knock-down in DU145 and PC3 cells altered tumor growth, adhesion, and chemotaxis. Akt knock-down (DU145 cells) cancelled the effect of IGF-1 on α3, α5, and αV integrins, whereas FAK blockade cancelled the effect of IGF-1 on mTOR signaling (DU145 cells). Prostate cancer growth and invasion are thus controlled by a fine-tuned network between IGF-1 driven integrin-FAK signaling and the Akt-mTOR pathway. Concerted targeting of integrin subtypes along with Akt-mTOR signaling could, therefore, open options to prevent progressive dissemination of prostate cancer.

Topic: Prostate Cancer Treatment and Research
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Lung deposition of two bronchodilators in subjects with (COPD) when administered via standard jet nebulizer or Handihaler® using functional respiratory imaging (FRI)

<b>Background:</b> FRI is a non-invasive quantitative imaging methodology that provides detailed measurements of the lungs and airways. FRI uses HRCT scans and quantitative imaging technology based on computational fluid dynamics (CFD) to model airflow in the respiratory system and provide quantifiable measures of drug deposition. <b>Aims:</b> To use FRI to determine the deposition patterns for revefenacin administered via a Pari LC® Sprint® Nebulizer (Neb) and tiotropium administered using the Handihaler® dry powder inhaler (DPI). <b>Methods:</b> 10 COPD subjects in silico (5 males, 5 females; age: 64.7; height: 169 cm; FEV1: 41% predicted) were examined. CFD simulations examined particles past the inhaler: Oropharynx, trachea, extrathoracic and intrathoracic airways including central (&gt;1-2mm, 7-10th generation) and peripheral (&lt;1-2mm, &gt;10th generation). Particle characteristics were taken from published literature. <b>Results:</b> Intrathoracic and peripheral deposition for Neb was 3-fold higher than the DPI device (34.6% ± 8.53 vs. 10.9% ± 5.67 of delivered dose) and (18.2% ± 4.30 vs. 5.8% ± 2.73 of delivered dose) respectively. The central-to-peripheral (C/P) ratio of the nebulizer is very similar to the DPI, even though the MMAD is higher. C/P ratio decreased after bronchodilation, suggesting better deposition in the peripheral region during neb delivery. <b>Conclusions:</b> FRI data suggest more efficient intrathoracic and peripheral drug deposition from a standard jet nebulizer than a Handihaler® DPI. FRI imaging supports using nebulized bronchodilators for those patients who cannot optimally use a DPI or those who remain symptomatic.

Topic: Inhalation and Respiratory Drug Delivery
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Murine Schistosomiasis mansoni: anti‐schistosomula antibodies and the IgG subclasses involved in the complement‐ and eosinophilmediated killing of schistosomula in vitro

Summary Protein A‐sepharose affinity chromatography was used to isolate IgG subclasses from the serum of CBA mice chronically infected with Schistosoma mansoni. The subclasses were tested for the presence of two antibodies which are responsible for the death of young schistosomula in vitro; ‘lethal antibody’ (LA), which kills schistosomula in co‐operation with complement and ‘eosinophil adherence antibody’ (EAA) which causes the death of schistosomula by promoting the adherence of eosinophils to the parasite. LA and EAA were detected only in the IgG fraction of the serum. LA was concentrated in the IgG 2a fraction and EAA in the IgG 1 fraction. The development of IgG subclasses specific for schistosomula was followed in mice exposed to twenty cercariae by the fluorescent antibody technique. IgG 1 , IgG 2a and IgG 2b antibodies were detected 2 weeks after infection and their titres rose steadily to reach high levels by weeks 12 or 14. IgM antibody was not detected until week 6 and IgA until week 10; both were present at lower concentrations than the IgG 1 antibodies.

Topic: Parasites and Host Interactions
Subfield: Parasitology
Field: Immunology and Microbiology
Domain: Life Sciences
“I Am Still a Refugee!” Displacement and Transnational Activism

Abstract This chapter explores the trajectory and experience of a refugee profoundly shaped by the interplay between human agency and shifting geopolitical configurations and refugee/migration regimes in various historical contexts. Drawing upon materials from a life history project about Father Nguyễn Văn Hùng, this chapter centres on his personal journey as one of the Vietnamese “boat people” in the late 1970s, who later became a migrant rights advocate in Taiwan for over three decades. Father Nguyễn’s life history serves as a testimony to the impact of colonialism, the entanglement of the civil war and the Cold War, and the subsequent era of globalisation on the lives of ordinary Vietnamese. Simultaneously, it demonstrates his enduring aspiration for freedom and his identity as both a Vietnamese refugee and a dedicated human rights advocate. Through a nuanced analysis of Father Nguyễn’s life history, this chapter sheds light on the politics of humanitarianism and the varied approaches adopted by different countries, such as Japan, Australia, and Taiwan, in addressing Vietnamese refugees. Moreover, it provides valuable insights into the multifaceted forms of Vietnamese community building and transnational activism that have emerged and evolved in response to the changing patterns and dynamics of migration.

Topic: Migration, Refugees, and Integration
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
&lt;title&gt;Distributed surveillance network utilizes neural networks for stolen vehicle detection&lt;/title&gt;

Real-time automated surveillance for counteracting automobile larceny (RASCAL) is envisioned to be an automated monitoring and vehicle identification system that utilizes neural network technology to provide a non-intrusive detection system for identifying stolen vehicles on the nation's highways. Specific facets of the system that are presented include automatic scene analysis, vehicle classification, and a potential commercial off the shelf license plate reader for plate identification. The general approach is envisioned to include the generation of a target vehicle profile that can be downloaded to each of the remote video surveillance sites on the highway. The profile will be a predefined characterization containing the make, model, year, color and license plate of the target vehicle. The intelligent video processor, located at each remote camera site, will utilize the stolen vehicle profile and advanced neural network classification techniques to search the visual scene for a potential candidate of the stolen vehicle. An automated license plate reading system is used to confirm the identification of the vehicle. Once a potential stolen vehicle has been identified a snapshot of the vehicle, along with the vehicle profile, is transmitted back to the central control facility where law enforcement officials can take appropriate action. For this effort, a three sensor distributed configuration is envisioned.

Topic: Vehicle License Plate Recognition
Subfield: Media Technology
Field: Engineering
Domain: Physical Sciences
Additional file 2: Table S2. of VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

NCBI accession numbers for prokaryotic host and viral genomes used in the training and evaluation of VirFinder.Â (XLSX 2752Â kb)

Topic: Bacteriophages and microbial interactions
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Computational Electrochemistry: The Aqueous Ru<sup>3+</sup>|Ru<sup>2+</sup> Reduction Potential

We present results of density functional calculations for the standard reduction potential of the Ru 3+ |Ru 2+ couple in aqueous solution. The metal cations are modeled as [Ru(H2O)n] q+ surrounded by continuum solvent (q = 2, 3; n = 6, 18). The continuum model includes bulk electrostatic polarization as well as atomic surface tensions accounting for the deviation of the second or third hydration shell from the bulk. After consideration of 37 density functionals with 5 different basis sets it has been found that hybrid and hybrid meta functionals provide the most accurate predictions for the [Ru(H2O)n] q+ geometries and for the corresponding reduction potential in comparison with available experimental data. The gas-phase ionization potentials of [Ru(H2O)n] 2+ calculated by density functional theory are also compared to results of ab initio computations using second order Møller-Plesset perturbation theory. The difference in solvation free energies of Ru 3+ and Ru 2+ varies from −10.56 eV to −10.99 eV for n = 6 and from –6.83 eV to –7.45 eV for n = 18, depending on the density functional and basis set quality. The aqueous standard reduction potential is overestimated when only the first solvation shell is treated explicitly and it is underestimated when the first and second solvation shells are treated explicitly.

Topic: Electrochemical Analysis and Applications
Subfield: Electrochemistry
Field: Chemistry
Domain: Physical Sciences
The real problem is the biomedical ignorance of statisticians

Heath’s review supports a book that gives a “devastating dissection of the statistical illiteracy of doctors,”1 when the real problem is the devastating biomedical ignorance of statisticians.

Why should a doctor need to know how to calculate the chance of breast cancer in a patient with a positive screening mammogram, given …

Topic: Global Cancer Incidence and Screening
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Color difference of four esthetic restorative materials by the illuminant.

In curves of spectral reflectance, the curves were in the similar range of reflectance (%) except glass ionomer. Changes in lightness were low (0.42-1.27), and changes in chroma were 0.26-2.23 for both conditions. These values were different by the kind of materials. The magnitude of the changes in hue angle was the most prominent in both conditions and was significantly different by the illuminants of A and F2 (P< 0.05). The range of color difference was 1.13-3.02 in both conditions.

Topic: Dental materials and restorations
Subfield: Orthodontics
Field: Dentistry
Domain: Health Sciences
Re: Fourteen Babies Born after Round Spermatid Injection into Human Oocytes

Previous studies showed that, compared with men with late maturation arrest (MA), men diagnosed with early MA had a decreased sperm recovery rates by testicular sperm extraction (TESE).In this study, the authors classified patients with non-obstructive azoospermia (NOA) as either early or late, and focal or diffuse and compare sperm recovery rates by a single surgeon using micro TESE operation technique.Early MA was defined in patients whose pathology results showed spermatogenetic arrest at the spermatogonia or spermatocyte stage; and late MA in those arrest occurred at spermatid stage.On biopsy, MA may also vary in its heterogeneity from focal to diffuse pattern in whole seminiferous tubule of the pathology sample.The authors concluded that men with late and focal MA have a higher sperm recovery rate as compared to men with early and diffuse MA.In the presence of MA pathology, a high level of follicle-stimulating hormone (FSH) may predict heterogeneity of testicular tissue.The authors advise the clinicians to be aware of those men with normal FSH and normal testicular volume, with NOA, may have particularly poor sperm recovery rate.

Topic: Reproductive Biology and Fertility
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Towards the Creation of Londra: A Virtual Expressive Animated Dog

We aim to create a virtual dog head capable of displaying and animating facial expressions. The literature on virtual pets and facial animation in animals shows no work using anatomically based simulation and most existing systems attempt to give the animals human-like expressions. We will use a layered model for Londra’s head and connect it to a virtual dog body to enhance expressions with body posture. We have identified anatomical features that will provide a method of parameterization and we propose an anatomically based coding system to organise these parameters. We have developed an object oriented display program which we will use to visualise the model.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Psychiatric Aspects of Somatic Disease

This chapter contains sections titled: Psychological and Psychosocial Factors in Development of Somatic Disease Role of Somatic Disease in Increasing the Risk of Psychiatric Illness Non-categorical Illness, Child- and Family-Related Factors Increasing Risk of Psychiatric Disorder Specific Conditions Presentation of Psychiatric Disorders in the Form of Somatic Symptoms Conclusions References

Topic: Psychosomatic Disorders and Their Treatments
Subfield: Psychiatry and Mental health
Field: Medicine
Domain: Health Sciences
Detention of Children for the Purpose of Educational Supervision

The contribution deals with a specific type of deprivation of liberty of children, namely, their detention in institutions for the purpose of educational supervision, as explicitly permitted by Article 5(1)(d) European Convention on Human Rights (ECHR). This contribution addresses the issue of whether this special exception to the right to personal liberty of children and the respective jurisprudence of the European Court of Human Rights (ECtHR) is still appropriate today. After a short introduction to the interrelation between the human rights to personal liberty and personal integrity, the jurisprudence of the ECtHR is analysed and critically reviewed. While the European Court accepts the detention of children in such institutions even for a period of a few years as long as children receive proper education, Article 37(b) of the United Nations (UN) Convention on the Rights of the Child (CRC) allows the detention of children only as a measure of last resort and for the shortest appropriate period of time. This fairly strict standard led to a general trend towards deinstitutionalisation worldwide, and in Central and Eastern Europe in particular. This trend is reaffirmed by the UN Global Study on Children Deprived of Liberty, which calls for urgent measures by states to stop or at least drastically reduce the detention of children in institutions, including institutions for the purpose of educational supervision. In conclusion, this contribution recommends that the ECtHR revisit its jurisprudence on Article 5(1)(d) ECHR by reaffirming the ECHR as a ‘living instrument’ and thereby properly taking the higher standards of the CRC into account, which has been ratified by all Member States of the Council of Europe (CoE). The recent publication of the Global Study might provide a welcome occasion for stimulating such a change of jurisprudence.

Topic: Legal Rights and Human Rights
Subfield: Law
Field: Social Sciences
Domain: Social Sciences
30-Day Emergency Department Visits After Primary Lumbar Fusion

Our objective was to describe the incidence, causes, risk factors, and costs associated with 30-day emergency department (ED) visits after primary lumbar fusion. A national insurance database was retrospectively analyzed to study patients with primary lumbar fusions performed for degenerative pathology of the spine between 2007 and Q3-2015. Risk factors for ED visits, and ED to hospital transfer were studied using multiple-variable logistic regression analysis. Our cohort included 37,559 patients with a mean age of 66.0±10.0 years. A total of 4806 (12.8%) patients had 10,281 ED visits within 30 days after surgery. Of these, 945 (19.9%) had multiple (≥3) visits, and 1466 (30.5%) were admitted to the hospital for management. Common causes for presentation in the ED were cardiorespiratory complaints (49.4%, n=2377), and back and/or leg pain (47.7%, n=2294). Risk factors for all ED visits, multiple ED visits, and hospital admission from the ED have been identified. The overall ED cost burden was nearly two-thirds as much as hospital readmissions within 30 days ($6,994,260 vs. $10,880,999). There is a sizable subset of patients that present to the ED for acute care but do not require hospitalization. Causes and risk factors for presentation in patients with multiple ED visits are somewhat different than patients requiring hospital readmission.

Topic: Spine and Intervertebral Disc Pathology
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
Capital flow constrained lot sizing problem with loss of goodwill and loan

We introduce capital flow constraints, loss of good will and loan to the lot sizing problem. Capital flow constraint is different from traditional capacity constraints: when a manufacturer launches production, its present capital should not be less than its present total production cost; otherwise, it must decrease production quantity or suspend production. Unsatisfied demand in one period may cause customer's demand to shrink in the next period considering loss of goodwill. Fixed loan can be adopted in the starting period for production. A mixed integer model for a deterministic single-item problem is constructed. Based on the analysis about the structure of optimal solutions, we approximate it to a traveling salesman problem, and divide it into sub-linear programming problems without integer variables. A forward recursive algorithm with heuristic adjustments is proposed to solve it. When unit variable production costs are equal and goodwill loss rate is zero, the algorithm can obtain optimal solutions. Under other situations, numerical comparisons with CPLEX 12.6.2 show our algorithm can reach optimal in most cases and has computation time advantage for large-size problems. Numerical tests also demonstrate that initial capital availability as well as loan interest rate can substantially affect the manufacturer's optimal lot sizing decisions.

Topic: 14-3-3 protein interactions
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Development of high-performance transparent conducting oxides and their impact on the performance of CdS/CdTe solar cells

This paper begins with a review of the modeled performance of transparent conducting oxides (TCOs) as a function of their free-carrier concentration, mobility, and film thickness. It is shown that it is vital to make a film with high mobility to minimize the width and height of the free-carrier absorption band, and to optimize the optical properties. The free-carrier concentration must be kept sufficiently small that the absorption band does not extend into that part of the spectrum to which the solar cell responds. Despite this consideration, a high electrical conductivity is essential to minimize series resistance losses. Hence, a high mobility is vital for these materials. The fabrication of thin-films of cadmium stannate is then discussed, and their performance is compared with that of tin oxide, both optically and as these materials influence the performance of CdTe solar cells.

Topic: Chalcogenide Semiconductor Thin Films
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences