jimnoneill/paper-to-field-training huggingface dataset:
Anti-Hinge Antibodies Recognize IgG Subclass– and Protease-Restricted Neoepitopes

Field: Immunology and Microbiology (Life Sciences)

Abstract Anti-hinge Abs (AHAs) target neoepitopes exposed after proteolytic cleavage of IgG. In this study, we explored the diversity of protease- and IgG subclass–restricted AHAs and their potential as immunological markers in healthy donors (HDs) and patients with rheumatoid arthritis (RA) or systemic lupus erythematosus (SLE). AHA reactivity against IgG-degrading enzyme of Streptococcus pyogenes (IdeS)– or pepsin-generated F(ab′)2 fragments of all four human IgG subclasses was determined. AHA reactivity against one or more out of eight F(ab′)2 targets was found in 68% (68 of 100) of HDs, 69% (68 of 99) of SLE patients, and 81% (79 of 97) of RA patients. Specific recognition of hinge epitopes was dependent on IgG subclass and protease used to create the F(ab′)2 targets, as confirmed by inhibition experiments with F(ab′)2 fragments and hinge peptides. Reactivity against IdeS-generated F(ab′)2 targets was found most frequently, whereas reactivity against pepsin-generated F(ab′)2 targets better discriminated between RA and HDs or SLE, with significantly higher AHA levels against IgG1/3/4. In contrast, AHA levels against pepsin-cleaved IgG2 were comparable. No reactivity against IdeS-generated IgG2-F(ab′)2s was detected. The most discriminatory AHA reactivity in RA was against pepsin-cleaved IgG4, with a 35% prevalence, ≥5.8-fold higher than in HDs/SLE, and significantly higher levels (p &lt; 0.0001). Cross-reactivity for F(ab′)2s generated from different IgG subclasses was only observed for subclasses having homologous F(ab′)2 C termini (IgG1/3/4). For IgG2, two pepsin cleavage sites were identified; anti-hinge reactivity was restricted to only one of these. In conclusion, AHAs specifically recognize IgG subclass– and protease-restricted hinge neoepitopes. Their protease-restricted specificity suggests that different AHA responses developed under distinct inflammatory or infectious conditions and may be markers of, and participants in, such processes.
Cryophilic Isotomidae (Collembola) of the Northwestern Rocky Mountains, U. S. A.

Field: Agricultural and Biological Sciences (Life Sciences)

Fjellberg, Arne (2010): Cryophilic Isotomidae (Collembola) of the Northwestern Rocky Mountains, U. S. A. Zootaxa 2513: 27-49, DOI: 10.5281/zenodo.196078
Transformation-optics antenna lens design using complex coordinate transformation

Field: Physics and Astronomy (Physical Sciences)

In this paper, we present an effective approach to design antenna lenses for controlling the far-field patterns, which only uses a single electromagnetic source or antenna feed located outside the lens. By employing a complex coordinate transformation, a spatial distribution of gain and/or loss can be introduced into the lens. Consequently, the proposed approach offers an extra degree of freedom that allows for controlling not only the phase distribution of the electromagnetic field inside the lens but also its amplitude distribution. Several full-wave simulated lens examples and corresponding linear antenna array calculations are presented, showing the capability of complex transformation optics for far-field pattern manipulation and near-field amplitude tapering across the lens aperture.
Improved Mechanical Properties and Bioactivity of Silicate Based Bioceramics Reinforced Poly(ether-ether-ketone) Nanocomposites for Prosthetic Dental Implantology

Field: Materials Science (Physical Sciences)

Polyether-ether-ketone (PEEK) biomaterial has been increasingly employed for orthopedic, trauma, spinal, and dental implants due to its biocompatibility and in vivo stability. However, a lack of bioactivity and binding ability to natural bone tissue has significantly limited PEEK for many challenging dental implant applications. In this work, nanocomposites based on PEEK reinforced with bioactive silicate-based bioceramics (forsterite or bioglass) as nanofillers were prepared using high energy ball milling followed by melt blending and compression molding. The influence of nanofillers type and content (10, 20 and 30 wt.%) on the crystalline structure, morphology, surface roughness, hydrophilicity, microhardness, elastic compression modulus, and flexural strength of the nanocomposites was investigated. The scanning electron microscopy images of the nanocomposites with low nanofillers content showed a homogenous surface with uniform dispersion within the PEEK matrix with no agglomerates. All nanocomposites showed an increased surface roughness compared to pristine PEEK. It was found that the incorporation of 20 wt.% forsterite was the most effective in the nanocomposite formulation compared with bioglass-based nanocomposites; it has significantly improved the elastic modulus, flexural strength, and microhardness. In vitro bioactivity evaluation, which used biomimetic simulated body fluid indicated the ability of PEEK nanocomposites loaded with forsterite or bioglass nanofillers to precipitate calcium and phosphate bone minerals on its surface. These nanocomposites are expected to be used in long-term load-bearing implant applications and could be recommended as a promising alternative to titanium and zirconia when used as a dental implant material.
Serum YKL-40 levels as a novel marker of inflammation in patients with endometriosis

Field: Medicine (Health Sciences)

This is the first study evaluating serum YKL-40 levels in endometriosis. The present results indicate that YKL-40 levels were increased in patients with endometriosis compared to controls. The authors propose that circulating YKL-40 levels could be a novel biomarker for diagnosis and follow-up of endometriosis.
New Thermodynamics: Rethinking the Science of Climate Change

Field: Environmental Science (Physical Sciences)

Statistical analysis shows that climate change is due to human activities. The accepted reason being the greenhouse effect, which is based on the erroneous assumption that homonuclear gases are opaque to thermal energy. The reality is that all polyatomic gases absorb and then radially radiate thermal energy, as proven by their heat capacities. The greenhouse effect, then becomes secondary. Thermal energy generated by human activities is part of Earth’s anthroposphere which is where climate change is measured. Such human-generated thermal energy is absorbed by all our atmosphere’s polyatomic gases, which is then radially radiated by those very gases. Therefore, our whole atmosphere forms Earth’s thermal blanket, and human’s activities becomes the root cause of climate change. Our Sun’s influx starts outside of Earth’s thermal blanket, with much of its visible light reaching Earth’s surface. However, the majority of the Sun’s insolation is at thermal wavelengths, which are readily absorbed by Earth’s atmosphere, and whose energy are then radially radiated by its polyatomic gases.
The future of anaesthesia robotics and artificial Intelligence: Will computers take over from doctors?

Field: Health Professions (Health Sciences)

Discussions concerning technology's inventive potential are becoming increasingly mainstream as it continues to develop at an exponential rate. This pattern is also present in medicine and the practise of anaesthesia. Among both current and aspiring professionals, discussions about artificial intelligence (AI) provoke a range of emotions, from enthusiasm about its potential to improve patient care to worry about the effect that it could have on future generations of the profession. Despite these mixed reactions, practically everyone can agree that the field of anesthesiology will be affected by future technological developments.
Ecological characterization of supina bluegrass (Poa supina Schrad.) germplasm from the Italian Alps

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract A collection was carried out in the Italian Alps to gather local genetic resources and acquire information on the ecological adaptation of supina bluegrass ( Poa supina Schrad.), a cool‐season grass native to the Alpine region in Europe. It has potential for pastures and a growing interest for turfs, owing to excellent traffic, shade and cold tolerance. Available germplasm for research and breeding is scant, and extensive collections are needed to enable further development of adapted materials. Alpine germplasm has already proved valuable for breeding at lower altitude in pioneering selection work carried out in Germany. Extensive exploration throughout different environments, mostly above 1600 m elevation, yielded fifty‐five novel populations. Collections largely occurred in environments exposed to heavy disturbance by livestock, but it was also frequently found on very poor substrates along mountain paths and dirt roads, or around buildings. Some populations were present locally in shaded environments. Preliminary ex‐situ observations indicated likely among‐population variation to occur for important traits of breeding relevance such as disease and drought tolerance. Genetic variation for adaptive traits, although unproven, is hypothesized given the diversified habitats where the species was collected across the Italian Alps.
Inferior Vena Cava (IVC) Resections without Reconstruction in Renal Tumors: Two Case Reports

Field: Medicine (Health Sciences)

(1) Background: We aim to present our experience with resection of the inferior vena cava (IVC) without reconstruction in two patients diagnosed with renal tumors. (2) Case Report: The first case was diagnosed with right renal vein sarcoma and the second case was diagnosed with clear cell renal carcinoma; both presented signs of invasion and thrombosis of the IVC at infrarenal and cruoric levels, along with the development of collateral circulation with the help of the paravertebral plexus. In both patients, en bloc right nephrectomy was performed along with the resection of the thrombosed IVC without further reconstruction. In the case of the patient with right vein sarcoma, preservation of the left renal and caval intrahepatic vein was possible, whilst in the second case diagnosed with clear cell renal carcinoma, the associated left renal thrombosis also enforced the resection of the left renal vein. (3) Discussion: Postoperative evolution was favorable in both cases and did not exhibit major complications. Antibiotic therapy, analgesics, and anticoagulant medication were administered at therapeutic doses after surgery in both cases. The histopathological examination of the surgical specimen confirmed the diagnoses of renal vein sarcoma in the first case and clear cell renal carcinoma in the second case. Surgical treatment and adjuvant chemotherapy prolonged survival for two years for the first case and for two months, up until this moment, for the second case. The survival of clear cell renal carcinoma is currently at two months. (4) Conclusions: The resection of the inferior vena cava, without subsequent reconstruction in cases presenting diffused distal thrombosis, can represent an alternative to IVC reconstruction, which might lead to a major ulterior risk of thrombosis. In some cases, this can result in long-term survival.
Data on arbuscular mycorrhizal fungal variables and soil properties from coffee plantations in Colombia

Field: Agricultural and Biological Sciences (Life Sciences)

Data on soil properties from two coffee plantations located in Chachagüí, Nariño, Colombia. Three lots called Albergue (AL), Lajas (LA) and Mataredonda (MA) were sampled three times in May 2015, September 2015 and February 2016. 17, 19 and 20 sampling sites were established within the lots AL, LA and MA, respectively. Data presented here were used to perform discriminant analyses between the three lots with the contribution of the variables arbuscular mycorrhizal colonization percentage, arbuscular mycorrhizal spore density, easily extractable glomalin, bulk density, organic matter, pH, electrical conductivity, total nitrogen, water soluble phosphorus, extractable phosphorus, cation exchange capacity, available iron, phosphatase activity, ammonia monooxygenase activity, β-Glucosidase activity and clay content to the lot classification. Statistical analyses were carried-out with R (StatR, RWizard platform version 2.0). For conducting the multivariate analyses, a dataset for each sampling time was employed separately. When a row had a “not available” value for any of the 16 variables included, the row was excluded from the dataset, resulting in the three files presented here.
Inner Gippsland Children & Youth Area Partnership (IGCYAP)

Field: Social Sciences (Social Sciences)

The Inner Gippsland Children and Youth Area Partnership (IGCYAP) is committed to improving outcomes for vulnerable children and young people from birth to eighteen years in the local government areas of Baw Baw Shire, LaTrobe City, South Gippsland Shire, and Bass Coast Shire.
General relationships between ultrasonic attenuation and dispersion

Field: Physics and Astronomy (Physical Sciences)

General relationships between the ultrasonic attenuation and dispersion are presented. The validity of these nonlocal relationships hinges only on the properties of causality and linearity, and does not depend upon details of the mechanism responsible for the attenuation and dispersion. Approximate, nearly local relationships are presented and are demonstrated to predict accurately the ultrasonic dispersion in solutions of hemoglobin from the resuts of attenuation measurements.
Sustained increases in blood pressure elicited by prolonged face cooling in humans

Field: Medicine (Health Sciences)

We tested the hypothesis that increases in blood pressure are sustained throughout 15 min of face cooling. Two independent trials were carried out. In the Face-Cooling Trial, 10 healthy adults underwent 15 min of face cooling where a 2.5-liter bag of ice water (0 ± 0°C) was placed over their cheeks, eyes, and forehead. The Sham Trial was identical except that the temperature of the water was 34 ± 1°C. Primary dependent variables were forehead temperature, mean arterial pressure, and forearm vascular resistance. The square root of the mean of successive differences in R-R interval (RMSSD) provided an index of cardiac parasympathetic activity. In the Face Cooling Trial, forehead temperature fell from 34.1 ± 0.9°C at baseline to 12.9 ± 3.3°C at the end of face cooling ( P < 0.01). Mean arterial pressure increased from 83 ± 9 mmHg at baseline to 106 ± 13 mmHg at the end of face cooling ( P < 0.01). RMSSD increased from 61 ± 40 ms at baseline to 165 ± 97 ms during the first 2 min of face cooling ( P ≤ 0.05), but returned to baseline levels thereafter (65 ± 49 ms, P ≥ 0.46). Forearm vascular resistance increased from 18.3 ± 4.4 mmHg·ml −1 ·100 g tissue −1 ·min at baseline to 26.6 ± 4.0 mmHg·ml −1 ·100 g tissue −1 ·min at the end of face cooling ( P < 0.01). There were no changes in the Sham Trial. These data indicate that increases in blood pressure are sustained throughout 15 min of face cooling, and face cooling elicits differential time-dependent parasympathetic and likely sympathetic activation.
Urban density and modal split: analysis of two Portuguese medium cities

Field: Social Sciences (Social Sciences)

The influence of urban patterns, mostly urban density, on mobility behaviour has been widely studied in the last two decades. A great number of studies focused essentially on the main conurbations and metropolitan areas. The conclusions of a large number of these studies pointed to that in large urban areas the land use patterns has a moderate to strong influence in the mobility pattern. However few studies analyzed this type of relation in the context of small and medium cities, outside the area of major metropolitan areas. The current study is focused on two Portuguese medium cities, Santarem and Tomar, which have on average about 15.000 inhabitants, and it aims to contribute to the enlightenment of this less studied area. The results of two mobility surveys made in 2003, in the context of two mobility plans are analyzed. Since that in both cities there are no efficient urban public transport systems, a binary logit model is drawn (car use or other modes, essentially walking) for each one of the case studies. In the proposed models, land use variables (urban density, density of public parking supply and accessibility indicators) and socio-economical variables (age, social status, household composition, car availability) are included in order to identify its weight in the modal choice of home based trips. The obtained results, in both models, are compared and discussed, in order to identify the real weight of urban density as an explicative variable of modal split in the context of medium and small cities. For the covering abstract please see ITRD E135207.
Sorghum bicolor (L.) Moench subsp. bicolor (L.) Moench IS 16157

Field: Agricultural and Biological Sciences (Life Sciences)

Plant Genetic Resource.
Taxonomy: Sorghum bicolor (L.) Moench subsp. bicolor (L.) Moench
Common name(s): Sorghum
Other names: 4-1-3-3-A, NSL 84004, IS 16157
Conserved by: International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), India
Local sample unique identifier: IS 16157
Method of creation: Acquisition
Date: 1974-05-10
Other identifiers: n/a,4-1-3-3-A, n/a,NSL 84004
Historical: No
Biological status: Traditional cultivar/landrace
MLS status: Included
Scaffold Repurposing Reveals New Nanomolar Phosphodiesterase Type 5 (PDE5) Inhibitors Based on Pyridopyrazinone Scaffold: Investigation of In Vitro and In Silico Properties

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Inhibition of PDE5 results in elevation of cGMP leading to vascular relaxation and reduction in the systemic blood pressure. Therefore, PDE5 inhibitors are used as antihypertensive and antianginal agents in addition to their major use as male erectile dysfunction treatments. Previously, we developed a novel series of 34 pyridopyrazinone derivatives as anticancer agents (series A–H). Herein, a multi-step in silico approach was preliminary conducted to evaluate the predicted PDE5 inhibitory activity, followed by an in vitro biological evaluation over the enzymatic level and a detailed SAR study. The designed 2D-QSAR model which was carried out to predict the IC50 of the tested compounds revealed series B, D, E and G with nanomolar range of IC50 values (6.00–81.56 nM). A further docking simulation model was performed to investigate the binding modes within the active site of PDE5. Interestingly, most of the tested compounds showed almost the same binding modes of that of reported PDE5 inhibitors. To validate the in silico results, an in vitro enzymatic assay over PDE5 enzyme was performed for a number of the promising candidates with different substitutions. Both series E and G exhibited a potent inhibitory activity (IC50 = 18.13–41.41 nM). Compound 11b (series G, oxadiazole-based derivatives with terminal 4-NO2 substituted phenyl ring and rigid linker) was the most potent analogue with IC50 value of 18.13 nM. Structure–activity relationship (SAR) data attained for various substitutions were rationalized. Furthermore, a molecular dynamic simulation gave insights into the inhibitory activity of the most active compound (11b). Accordingly, this report presents a successful scaffold repurposing approach that reveals compound 11b as a highly potent nanomolar PDE5 inhibitor worthy of further investigation.
Enzyme Induction Studies in Drug Discovery and Development

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Changes in the expression of absorption, distribution, metabolism and excretion (ADME) genes can impact the pharmacokinetics of many small molecule drugs. This chapter aims to provide a broad understanding of the process of induction as well as other phenomenon related to the change in expression levels of ADME genes. Induction of ADME genes is well recognized for its importance in altering the exposure of substrates of the induced enzyme; leading to loss of efficacy and, in some cases, toxicity. There are a number of in vitro and in vivo tools available for preclinical investigations aiming to determine whether or not a drug candidate will be an inducer in vivo. physiologically-based pharmacokinetic modeling and simulation incorporates demographic, genetic, anatomical, physiological, and drug-specific parameters to predict drug concentration-time profiles. Due to the evolutionary divergence of the xenobiotic receptors, the use of animal models has questionable value regarding predictions of outcomes in humans.
Information and other Factors Influencing Treatment Expenditures Incurred by Buruli Ulcer Sufferers in the Nsawam-Adoagyiri Municipality of Ghana

Field: Health Professions (Health Sciences)

We analyzed the factors influencing the treatment expenditures incurred by sufferers of Buruli ulcer disease in the Nsawam-Adoagyiri Municipality in the Eastern Region of Ghana using a random sampling survey. The factors analyzed in the study included the information about the disease available to the sufferers related to time and the stage of the disease that sufferers reported the disease to health clinics and hospitals. We showed that the factors that significantly influenced treatment expenditures included the income of the sufferer, early reporting of the disease to clinics, and the employment status of the sufferer. Higher-income people spent more money to treat the disease than those with lower incomes. People who were unemployed spent relatively money in treating the disease as compared to those who were employed. With increasing incomes, sufferers who reported the disease to clinics in the early stages of the disease, incurred relatively less costs compared to those of similar high-income group of sufferers who reported the disease to clinics at the ulcerative stage of the disease.
[Not Available].

Field: Chemistry (Physical Sciences)

The complexes of iron(II) with violuric acid and 2-thiovioluric acid have been studied by conductimetry, potentiometry, and spectrophotometry at 25 degrees in aqueous medium. The formation of triviolurate [Fe(C(4)H(2)N(3)O(4))(-)(3) and trithioviolurate [Fe(C(4)H(2)N(3)O(3)S)(-)(3)] compounds with iron(II) is confirmed, and their maximum absorptions are at 605 nm and 615 nm respectively. The stability constants of these complexes were determined at ionic strength 0.5M by potentiometry and spectrophotometry. These two methods gave nearly the same results: (4.0 +/- 0.3) x 10(8) and (8.3 +/- 0.7) x 10(8) for the violurate complex and (1.1 +/- 0.5) x 10(9) and (1.45 +/- 0.7) x 10(9) for the thioviolurate complex.