jimnoneill/paper-to-field-training huggingface dataset:
Comprehensive Ontology of Fibroproliferative Diseases: Protocol for a Semantic Technology Study (Preprint)

Field: Computer Science (Physical Sciences)

BACKGROUND

Fibroproliferative or fibrotic diseases (FDs), which represent a significant proportion of age-related pathologies and account for over 40% of mortality in developed nations, are often underrepresented in focused research. Typically, these conditions are studied individually, such as chronic obstructive pulmonary disease or idiopathic pulmonary fibrosis (IPF), rather than as a collective entity, thereby limiting the holistic understanding and development of effective treatments. To address this, we propose creating and publicizing a comprehensive fibroproliferative disease ontology (FDO) to unify the understanding of FDs.

OBJECTIVE

This paper aims to delineate the study protocol for the creation of the FDO, foster transparency and high quality standards during its development, and subsequently promote its use once it becomes publicly available.

METHODS

We aim to establish an ontology encapsulating the broad spectrum of FDs, constructed in the Web Ontology Language format using the Protégé ontology editor, adhering to ontology development life cycle principles. The modeling process will leverage Protégé in accordance with a methodologically defined process, involving targeted scoping reviews of MEDLINE and PubMed information, expert knowledge, and an ontology development process. A hybrid top-down and bottom-up strategy will guide the identification of core concepts and relations, conducted by a team of domain experts based on systematic iterations of scientific literature reviews.

RESULTS

The result will be an exhaustive FDO accommodating a wide variety of crucial biomedical concepts, augmented with synonyms, definitions, and references. The FDO aims to encapsulate diverse perspectives on the FD domain, including those of clinicians, health informaticians, medical researchers, and public health experts.

CONCLUSIONS

The FDO is expected to stimulate broader and more in-depth FD research by enabling reasoning, inference, and the identification of relationships between concepts for application in multiple contexts, such as developing specialized software, fostering research communities, and enhancing domain comprehension. A common vocabulary and understanding of relationships among medical professionals could potentially expedite scientific progress and the discovery of innovative solutions. The publicly available FDO will form the foundation for future research, technological advancements, and public health initiatives.

INTERNATIONAL REGISTERED REPORT

PRR1-10.2196/48645
Comorbidity and Personality in Body Dysmorphic Disorder

Field: Medicine (Health Sciences)

Comorbidity is common in body dysmorphic disorder (BDD). Major depressive disorder, social anxiety disorder (social phobia), obsessive-compulsive disorder, and substance use disorders are the most frequently co-occurring Axis I conditions. Except for eating disorders (more common in women) and substance use disorders (more common in men), Axis I comorbidity rates in BDD appear similar across genders. Axis I comorbidity is associated with greater functional impairment and morbidity. Rates of comorbid personality disorders in BDD are high. Disorders from cluster C occur most frequently, with avoidant personality disorder the most common. Associated traits include low self-esteem and high levels of neuroticism, introversion, unassertiveness, social anxiety and inhibition, rejection sensitivity, and perfectionism. Research is needed on the relationship between BDD and psychiatric comorbidity, the causes and consequences of comorbidity in BDD, and the relationship between BDD and associated personality traits.
Anti-Keynesian Views: Fiscal and Monetary Guidelines

Field: Economics, Econometrics and Finance (Social Sciences)

In this article, we will cover the main anti-Keynesian views and macroeconomic systems that arose in the post Keynes period as well as their fiscal and monetary policy guidelines. As is known, the early Classical economists introduced a macroeconomic system based on the Quantity Theory and Say’s Law resulting in automatic full-employment equilibrium; and finally after 1929-1934 Great World Depression, the Keynesian System was introduced as a “revolution” (Keynesian Revolution) in theory and practice. As a result of the Keynesian policies implemented, European countries and the United States not only got over the Great World Depression but also in the years following the World War II, they have observed a fast and stable growth for a long time. Moreover, cyclical fluctuations have been controlled to a great extent. Even so, at the stage when the Keynesian System was introduced, anti-Keynesian views and macroeconomic systems were immediately introduced. Intense academic discussions between advocates of these views and the Keynesian economists have continued up until today. Meanwhile, many economists such as J.R. Hicks, R.F. Harrod, N. Kaldor, M. Kalesci, A.W. Philips, A. Hansen, P.A. Samuelson, E. Domar, J. Tobin, R. Solow, A.M. Okun, W. Helier, G. Ackler, F. Modigliani, and R. Musgrave and many others have developed and defended the Keynesian System from different aspects. We can characterize significant anti-Keynesian views and macroeconomic systems as the “Counter-Revolution”.
EFFECT OF IONIZING RADIATION ON SOIL MICROORGANISMS

Field: Environmental Science (Physical Sciences)

The effects of neutron and gamma radiation on soil bacteria, actinomycetes, and fungi, and on nitrifying bacteria, nitrogen fixation, and CO/ sub 2/ evolution were studied. Soil samples from alfalfa and ammonia-treated soils at two moisture levels were exposed at a dosage of 4.13 x 10/sup 12/ neutrons per cm/sup 2/ and a mean gamma dosage of 3.4 x 10/sup 12/ ergs per g. Similar studies were made on soil samples taken at varying distances from the reactor after a run of 735 megawatt hours of operation, which gave a cumulative mixed neutron and gamma dosage ranging from over 100000 rems at 100 feet to 9000 rems at 700 feet. The results of the investigation may be summarized as follows: The bacteria and actinomycetes were reduced by about two-thirds in the irradiated soil samples taken from the alfalfa and ammonium-fertilized plots; the total fungi increased two-fold in the irradiated soil from the alfalfa plot, but a consistent effect was not obtained on fungi in the irradiated soil obtained from the plot fertilized with ammonium carriers; soil moisture content did not influence the radiation effects; irradiation reduced the rate of nitrification by two-thirds after 2 weeks of incubation and by one-halfmore » after 4 weeks of incubation; irradiation increased the amount of nitrogen mineralized in the soils studied; the irradiated alfalfa soil was sterile with respect to R. meliloti; carbon dioxide evolution from the irradiated alfalfa soil did not differ from the nonirradiated; soil microflora in the vicinity of the reactor was more related to the environmental conditions of that immediate area than to the total radiation dosage; nitrification in soil near the reactor was not related to the total radiation dosage; and Lespedeza Rhizobia present in soil increased as the distance from the reactor increased. From these results, it is concluded that the nitrogen-fixing bacteria are more susceptible to radiation than the other groups of soil microorganisms studied, and the lethal levels of radiation required for the groups of soil microorganisms studied are relatively high when protected by several inches of soil. (auth)« less
Vertical Semicircular Canal Function: A Study in Patients with Benign Paroxysmal Positional Vertigo

Field: Medicine (Health Sciences)

A pendular rotation test in a head-tilted position (60 degrees backwards and rotated 45 degrees to either the right or left) was performed in 7 patients with benign paroxysmal positional vertigo (BPPV). Patients were rotated 360 degrees at a frequency of 0.1 Hz (maximum speed 114 degrees/s). The excitability of vertical semicircular canals was evaluated using this test procedure. Using an infrared CCD camera and a PC, evoked nystagmus was analyzed in order to determine the morbidity of BPPV. A statistically significant difference (p < 0.05) was found in the maximal slow-phase eye velocity between nystagmus from the anterior semicircular canal and nystagmus from the posterior semicircular canal. The excitability of the posterior semicircular canal in the affected ear was lower than that of the anterior semicircular canal. However, when vertigo and nystagmus disappeared, the difference in excitability was improved. The present results indicate some functional deterioration of the posterior semicircular canal in BPPV cases, suggesting the participation of both mechanical (dumping by mass) and organic (peripheral end organ) factors in causing morbidity.
A method of multi-channel SAR moving target detection and imaging based on complex CNN

Field: Computer Science (Physical Sciences)

Abstract Aiming at the problem of the detecting difficulty and imaging the moving target submerged in clutter, a multi-channel Synthetic Aperture Radar (SAR) moving target detection and imaging method based on complex Convolutional Neural Network (CNN) is proposed. First, using Range Doppler algorithm (RDA) to image SAR data to obtain images with clutter, noise and defocused moving targets. Then, the SAR image is used as the input of complex CNN. A SAR image with the clutter and noise eliminated, and the moving target in focus is obtained after processing by neural network. The simulation experiment results show this method is effectiveness.
Preterm Delivery: a Review of the Evidence-based Literature

Field: Medicine (Health Sciences)

The etiology of higher rates of premature labor in multiple pregnancy is unknown. Some argue, rather simplistically, that it is primarily due to overdistension of the uterus and this in itself is the major cause. However, this is an observation, which is unfounded in any credible scientific basis. Sociologic and epidemiologic factors are also thought to be implicated in the etiology of premature labor, but the vast majority of studies concern singleton pregnancies, and it is widely assumed that such factors also apply to multiple gestation. Numerous epidemiologic studies show that socioeconomic deprivation, smoking, low body mass index (BMI < 19kg/m2) before pregnancy and young maternal age are associated with preterm delivery. Each of these variables carries a relative risk of 1.5-2.0, and attempts to predict risk of premature labor based on such factors alone yield low sensitivity and specificity1. The single most effective predictor of preterm delivery is previous preterm delivery (relative risk 2.3), but this is unhelpful in primigravidae.
Draft Genome Sequence of Idiomarina sp. Strain 5.13, a Highly Stress-Resistant Bacterium Isolated from the Southwest Indian Ridge

Field: Immunology and Microbiology (Life Sciences)

ABSTRACT Idiomarina sp. strain 5.13, able to produce biopolymer and exopolysaccharide, was isolated from a sediment sample collected from the Southwest Indian Ridge, Indian Ocean. Analysis of its draft genome sequence provides insights into its remarkable stress tolerance and offers the genetic basis for harnessing the biotechnological potential of this strain.
High Performance Skiing

Field: Health Professions (Health Sciences)

High-Performance Skiing combines the latest in expert instruction, technique and conditioning with breakthroughs in equipment technology that help skiers negotiate the most difficult runs. Completely new chapters on racing, conditioning, and technique make this the up-to-the-minute information source for alpine skiers. This book offers an up-front, how-to approach for skiers interested in revving up their skiing and racing, replete with timely tips on how to handle a variety of skiing situations. High-Performance Skiing promises to further explore high performance techniques and skills that lead to: - more consistent performance, - less fatigue and more endurance, - increased strength and flexibility, - greater versatility, - more confidence while skiing in all conditions, and - the incentive and know-how to jump into advanced recreational racing. More than 100 photos and illustrations take readers step-by-step through the techniques to tackle steep-slope skiing, moguls, powder skiing and racing.
Curative effect observation of rivaroxaban for the prevention of deep vein thrombosis after hip replacement surgery

Field: Medicine (Health Sciences)

Objective To explore the clinical effect of rivaroxaban for the prevention of deep vein thrombosis after total hip replacement surgery. Methods All patients after hip surgery, oral Rivaroxaban 10mg in 6 hours after the operation began, 1 times per day, for 10 days. Results All Rivaroxaban total hip replacement in patients with and without swelling of the affected limb, postoperative pain, activity limitations, by postoperative color Doppler detection, no 1 cases of lower extremity deep vein thrombosis. Conclusion Rivaroxaban is a highly selective inhibition of blood coagulation factor Xa oral anticoagulant drug, postoperative early use, with good safety and efficacy, clinical use, results are obvious.
Creating a pressure ulcer prevention algorithm: systematic review and face validation.

Field: Health Professions (Health Sciences)

Pressure ulcer (PU) prevention is a care imperative supported by substantive evidence, but translating that knowledge into clinical decision-making at the point of care remains challenging. The purpose of this study was to create a succinct, evidence-based algorithm for inclusion in an existing industry-sponsored, evidence-based wound care program that will: 1) help clinicians assess and document overall patient PU risk; 2) help clinicians assess and address modifiable PU risk factors; and 3) guide clinicians toward an evidence-based protocol of care for patients with impaired skin integrity. First, using a systematic literature review and the Strength of Recommendation Taxonomy (SORT), a one-page algorithm containing 26 distinct decision points/steps was developed with study quality ratings for all publications identified. Second, based on the quality-of-evidence ratings, the strength of each recommendation was obtained for each decision point/ step. Lastly, face validation and subsequent instrument revision based on analytic input occurred. Twelve (12) wound care experts were asked to review each decision step and rate its appropriateness/relevance on a 4-point Likert scale, where 1 = not relevant/appropriate and 4 = very relevant and appropriate. Average scores and a content validity index (CVI) were calculated for the algorithm and each individual component. Two components, the use of high-quality foam and medical grade sheepskin for at-risk patients, had sufficient evidence to receive an A strength of recommendation. However, the latter had a very low CVI (0.18). One other step, frequency of assessment for current or recent history of limited mobility (B strength of recommendation), had a low CVI (0.7). The overall literature-based level of evidence was good, but overall evidence gaps remain. The overall mean score was 3.6 (SD 0.8) with a CVI of 0.89 (out of 1). Both scores indicate strong face validity. This is the first PU prevention algorithm based on systematic literature review and face validation. Future content and construct validation is needed to refine the algorithm.
Selected topics in heavy flavour physics

Field: Physics and Astronomy (Physical Sciences)

We review the status of flavour physics in spring 2014. The numerous accurate\nnew measurements of flavour experiments have enabled us to test our theoretical\nunderstanding of flavour processes with an unprecedented precision. At first\nsight the dominant amount of measurements seems to be standard model like.\nHaving a closer look one finds, however, that in most of the observables there\nis still some considerable space for new effects. In addition many\ndiscrepancies are still not settled yet. For further investigations and\ndefinite conclusions an improvement of the theoretical precision as well as the\nexperimental one is mandatory.\n
Clinical observation of cyclosporin A in treatment of severe ulcerative colitis

Field: Medicine (Health Sciences)

Objective The therapeutic effect of cyclosporin A on the patients with severe ulcerative colitis who had no better effect with glucocorticoid therapy was evaluated.Methods Seven patients with severe ulcerative colitis were treated by cyclosporin A because dissatisfactory therapeutic effect on them was required by use of glucocorticoid.The therapeutic effect was accessed by Southerland index.Cyclosporin A was applied by oral or intravenous route with a daily dose of 4-6 mg/kg.The serum concentration of cyclosporin A,liver function and renal function were monitored.Results After one week and two weeks treatment with cyclosporine A,the Sutherland indexes of these patients,compared with those at the beginning of their hospitalization and after one and two weeks of conventional treatment,were improved significantly(P0.05).The symptom of the patients disappeared basically.When the serum concentration of cyclosporin A was at 200-300 μg/L,better therapeutic efficacy and less adverse effect were observed.Six patients were followed up from 6 to 22 months.One patient took cyclosporin A for 5 months.Five patients had recurrence,one patient had operation.Conclusion Cyclosporin A was effective in treatment of patients with severe ulcerative colitis who had no better effect by glucocorticoid therapy.Cyclosporin A could be applied by both oral and intravenous routes.It is meaningful for clinical medication to monitor the serum concentration of the drug.
Determinations of soverign ratings: an empirical analysis on Turkey and EU countries

Field: Economics, Econometrics and Finance (Social Sciences)

Country credit rating explains the notes andopinions given by credit rating agencies about how much acountry discharge its financial responsibilities. In this study, firstly Credit Rating Agency (CRA) is emphasized and lastly thedeterminants ofcountry credit notes are analyzed. As country credit rating, the determinants of the notes given to Turkey and EU (17) countries by Moody’s Credit RatingAgency, which is one of the International Credit Rating Agencies, have been analyzed. The determinants of the country credit rating are chosen in accordance with theory and literature; and five different determinants havebeen discoursed.According to the results of the analysis conducted with panel regression model in2002-2014, it is concluded thatthe growth rate ofeconomic growth affects the country credit rating positively and balance of foreign trade affects the creditscore negatively.
Correlation of metallothionein-2A, E-cadherin and cyclin E with biochemical recurrence in prostate cancer

Field: Medicine (Health Sciences)

Objective
To investigate the expressions of metallothionein-2A (MT-2A), E-cadherin, interleukin-6 (IL-6), cyclin E, proliferating cell nuclear antigen (PCNA) and bcl-2 in prostate cancer tissues and their correlation with biochemical recurrence of prostate cancer.

Methods
Tissue specimens from 128 cases of prostate cancer who underwent radical prostatectomy in Shanxi Dayi Hospital from October 2012 to October 2017 were processed and transferred into tissue microarrays, the clinicopathological parameters of patients were also recorded. The expression levels of MT-2A, E-cadherin, IL-6, cyclin E, PCNA and bcl-2 were detected by immunohistochemical avidin-biotin complex (ABC) staining. The correlation between different molecular markers and biochemical recurrence of prostate cancer was analyzed.

Results
The biochemical recurrence rate of 128 patients with prostate cancer was 30.5% (39/128). The biochemical recurrence rates of low-risk, intermediate-risk and high-risk prostate cancer patients were 14.8% (8/54), 38.7% (24/62) and 58.3% (7/12), respectively. The risk classification and pathological T stage of patients with prostate cancer were associated with the expressions of MT-2A, cyclin E, IL-6 and E-cadherin (all P < 0.05). Multivariate Cox risk model showed that the high risk classification (HR=1.81, 95% CI 1.56-2.19, P=0.042), MT-2A positive expression (HR=2.01, 95% CI 1.08-3.15, P=0.005), cyclin E positive expression (HR=1.79, 95% CI 1.08-2.21, P=0.042) and E-cadherin negative expression (HR=1.92, 95% CI 1.22-2.45, P=0.020) were the independent risk factors for biochemical recurrence of prostate cancer.

Conclusion
The expression of MT-2A, cyclin E and E-cadherin may serve as independent predictors for biochemical recurrence of prostate cancer.

Key words:
Prostatic neoplasms; Metallothionein 2A; Cadherins; Cyclin E; Biochemical recurrence; Microchip analytical procedures
Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

Field: Chemistry (Physical Sciences)

The principles underlying water reorganization around simple nonpolar solutes are well understood and provide the framework for the classical hydrophobic effect, whereby water molecules structure themselves around solutes so that they maintain favorable energetic contacts with both the solute and the other water molecules. However, for certain solute surface topographies, water molecules, due to their geometry and size, are unable to simultaneously maintain favorable energetic contacts with both the surface and neighboring water molecules. In this study, we analyze the solvation of ligand-binding sites for six structurally diverse proteins using hydration site analysis and measures of local water structure, in order to identify surfaces at which water molecules are unable to structure themselves in a way that maintains favorable enthalpy relative to bulk water. These surfaces are characterized by a high degree of enclosure, weak solute-water interactions, and surface constraints that induce unfavorable pair interactions between neighboring water molecules. Additionally, we find that the solvation of charged side chains in an active site generally results in favorable enthalpy but can also lead to pair interactions between neighboring water molecules that are significantly unfavorable relative to bulk water. We find that frustrated local structure can occur not only in apolar and weakly polar pockets, where overall enthalpy tends to be unfavorable, but also in charged pockets, where overall water enthalpy tends to be favorable. The characterization of local water structure in these terms may prove useful for evaluating the displacement of water from diverse protein active-site environments.
Poultry genetic heritage cryopreservation and reconstruction: advancement and future challenges

Field: Agricultural and Biological Sciences (Life Sciences)

Poultry genetics resources, including commercial selected lines, indigenous breeds, and experimental lines, are now being irreversibly lost at an alarming rate due to multiple reasons, which further threats the future livelihood and academic purpose. Collections of germplasm may reduce the risk of catastrophic loss of genetic diversity by guaranteeing that a pool of genetic variability is available to ensure the reintroduction and replenishment of the genetic stocks. The setting up of biobanks for poultry is challenging because the high sensitiveness of spermatozoa to freezing-thawing process, inability to cryopreserve the egg or embryo, coupled with the females being heterogametic sex. The progress in cryobiology and biotechnologies have made possible the extension of the range of germplasm for poultry species available in cryobanks, including semen, primordial germ cells, somatic cells and gonads. In this review, we introduce the state-of-the-art technologies for avian genetic resource conservation and breed reconstruction, and discuss the potential challenges for future study and further extending of these technologies to ongoing and future conservation efforts.