jimnoneill/paper-to-field-training huggingface dataset:
Identification of MAP3K15 as a Potential Prognostic Biomarker and Correlation with Immune Infiltrates in Osteosarcoma

Abstract Background: Osteosarcoma (OS) is a type of primary malignant tumor, and increasing amounts of evidence show the clinical benefits of immunotherapy in treating OS. However, the lack of comprehensive studies on the complex OS immune microenvironment hinders the application of immunotherapy. Thus, we aimed to systematically study the immune characteristics of OS and identify novel biomarkers for OS treatment. Methods: We systematically studied the immune score and proportion of infiltrating immune cells in OS in the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) and Gene Expression Omnibus (GEO) databases using the ESTIMATE and CIBERSORT algorithms. Differential expression and functional analyses were used to identify dysregulated genes and explore their functions. Survival and Cox regression analyses were applied to establish an immune-related prognostic signature. The expression of MAP3K15 was performed by qPCR assay and immunohistochemistry. We divided 48 patients into high expression and low expression groups according to MAP3K15 expression. Results: A total of 103 differentially expressed immune genes (DEIGs) were found in the TARGET-OS and GSE39058 databases, and these DEIGs were mainly enriched in leukocyte proliferation, leukocyte differentiation, osteoclast differentiation, natural killer (NK) cell-mediated cytotoxicity and the adaptive immune system. A predictive signature was constructed based on the survival analysis, with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.65. Moreover, we found that mitogen-activated protein kinase kinase kinase 15 (MAP3K15) can predict the prognosis of patients with OS and is closely related to CD4 T cells, M0 macrophages, and M1 macrophages. We found that patients with high MAP3K15 expression had a significantly poorer prognosis Conclusions: Our study found that MAP3K15, whose expression level is closely related to immune activity in tumors, was a critical immune-related biomarker and may provide a basis for OS immunotherapy. Clinical Trial Registration Not applicable.

Topic: Melanoma and MAPK Pathways
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Fuzzy Logic Classification of Imaging Laser Desorption Fourier Transform Mass Spectrometry Data

A fuzzy logic based classification engine has been developed for classifying mass spectra obtained with an imaging internal source Fourier transform mass spectrometer (I^2LD-FTMS). Traditionally, an operator uses the relative abundance of ions with specific mass-to-charge (m/z) ratios to categorize spectra. An operator does this by comparing the spectrum of m/z versus abundance of an unknown sample against a library of spectra from known samples. Automated positioning and acquisition allow I^2LD-FTMS to acquire data from very large grids, this would require classification of up to 3600 spectrum per hour to keep pace with the acquisition. The tedious job of classifying numerous spectra generated in an I^2LD-FTMS imaging application can be replaced by a fuzzy rule base if the cues an operator uses can be encapsulated. We present the translation of linguistic rules to a fuzzy classifier for mineral phases in basalt. This paper also describes a method for gathering statistics on ions, which are not currently used in the rule base, but which may be candidates for making the rule base more accurate and complete or to form new rule bases based on data obtained from known samples. A spatial method for classifying spectra with low membership values, based on neighboring sample classifications, is also presented.

Topic: Metabolomics and Mass Spectrometry Studies
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Pyrimidine Glycosides

Pyrimidine glycosides of greatest concern are vicine and convicine. The glycosides appear to occur only in the seed portion of the plant and not in other parts of the plant including the seed coat or the testa. Dry milling of dehulled faba beans yields protein-rich and starch-rich fractions with high and low concentrations, respectively, of total glycosides. Rats appear to be insensitive to orally administered glycosides even when they were sensitized by factors that inhibit GSH synthesis, such as prefeeding a diet deficient in riboflavin, tocopherol, and selenium or pretreatment with buthionine sulfoximine. However, they are sensitive to the glycosides and their aglycones when injected intraperitoneally or intravenously. Presumably the glycosides were transported to the intestine where they were hydrolyzed and reabsorbed as their aglycones. Successive injections of subacute amounts of vicine and convicine over several days caused a decrease in liver size and an increase in spleen size.

Topic: Botanical Research and Chemistry
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Expression of biologically active recombinant rat IgE-binding protein in Escherichia coli.

IgE-binding protein (epsilon BP) is a protein which has affinity for IgE and was originally identified in rat basophilic leukemia (RBL) cells. Subsequently, it was found to be the rat homolog of CBP35, a murine beta-galactoside-specific lectin. This protein is also designated as L-34 and RL-29 and studied independently by several laboratories. More recently, CBP35 (epsilon BP) was found to be equivalent to Mac-2, a surface marker on activated macrophages. Using rat epsilon BP cDNA, we have succeeded in expressing recombinant epsilon BP in Escherichia coli. Milligram quantities of homogeneous epsilon BP could be obtained from bacterial lysate in a one-step affinity purification procedure utilizing lactosyl-Sepharose 4B and elution with a lactose gradient. The recombinant epsilon BP (r epsilon BP) binds mouse IgE and retains reactivity to anti-peptide antibodies specific for a sequence within rat epsilon BP. The purified r epsilon BP exhibits binding activity to various saccharides, with affinity for N-acetyllactosamine greater than thiodigalactoside greater than lactose much greater than D-galactose greater than L-arabinose, an order identical to that exhibited by native epsilon BP isolated from RBL cells. The recombinant lectin displayed hemagglutination activity when tested with rabbit erythrocytes. Although epsilon BP shares sequence homology to other lectins containing S-type (thiol-dependent) carbohydrate-recognition domains, r epsilon BP is resistant to air oxidation and does not require reducing agents for maintaining its activity. Furthermore, the single cysteine residue appears to be unexposed and can be alkylated only when the protein is denatured in 5.6 M guanidinium hydrochloride. The availability of a source for a large quantity of epsilon BP should facilitate the analysis of biological function(s) and structure-activity relationships of this lectin.

Topic: Glycosylation and Glycoproteins Research
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Stratigraphy, Chronology, and Social Context of David Malo's Kalepolepo Church Site from the Island of Maui

This paper examines data from the Kalepolepo Church Site on the island of Maui, a mid-19th century pondfield and church site. A series of pondfield layers were identified that precede the construction of the church, separated by regular flood intervals. A variety of material culture was recovered, including burnt charcoal, shell midden, pollen and phytoliths. Radiocarbon evidence indicates that the earliest pondfield floor dates to 1410 BP (table 1). Charcoal concentrations suggest early burning of coastal vegetation, corroborated by the pollen samples which suggest a sudden replacement of indigenous coastal vegetation by coastal grasses and shrubs. Extremely high concentrations of shell midden were recovered from the same contexts as the earlier pondfield layers and suggests the discarding of food debris. These data suggest very early human activity in and around Kalepolepo which may have included clearing and burning of local vegetation, and pondfield agriculture.

Topic: Pacific and Southeast Asian Studies
Subfield: Geography, Planning and Development
Field: Social Sciences
Domain: Social Sciences
Comparing the Care of Pediatric Hospitalists With That of General Pediatricians

Mariam Krikorian Atkinson, PhD; Mark A. Schuster, MD, PhD; Jeremy Y. Feng, MD; Temilola Akinola, MBBS, MPH; Kathryn L. Clark, BA; Benjamin D. Sommers, MD, PhD

Topic: Hospital Admissions and Outcomes
Subfield: Emergency Medicine
Field: Medicine
Domain: Health Sciences
Beyond the Basics of Executive Compensation: Researching What Corporate Executives Are Really Worth

This article explores two academically underserved areas on the subject of executive compensation: change in control payments and perquisites. These figures, although readily available through public filings, have been excluded from mainstream company-based resources and left to sporadically released topical reports. The article provides thorough background for these payments, the parameters for which they are allocated, and where to find the information using freely-available resources. Additionally, the article provides a review of paid resources that publish reports with this type of information.

Topic: Corporate Finance and Governance
Subfield: Accounting
Field: Business, Management and Accounting
Domain: Social Sciences
3M Touchscreen Monitor Driver CD

An ISO image of the driver CD that came with 3M touchscreen monitors. Touch Solutions CD, Version 2.8, April 2003 Copyright 1991-2003 3M All rights reserved. __________________________________________________________________ PRODUCT SUMMARY This CD contains 3M Touch Systems: * Software * Touch screen drivers * Utilities * Technical documentation The touch screen software enables users to select, launch, and drag objects using 3M Touch Systems touch screens. CONTENTS Current software: * TouchWare for Windows XP, 2000, NT 4.0, 9x, and Me including a Japanese version * Near Field Imaging Software for Windows XP and 2000 * Near Field Imaging Software for other versions of Windows * SC3/SC4 Software for Windows Utilities: * Bar code linearization process instructions and utility * Microcal 7.3 Documentation: * Touch Screens * Monitors * Controllers * Software * Adobe Acrobat Reader Archived Software: * TouchWare for Windows NT 3.51 * TouchWare for Windows 3.1x and DOS * TouchWare for OS/2 * TouchWare for Macintosh * TouchWare for Macintosh (USB) * SC3 Software for DOS, DOS Windows, Windows 9X, Windows NT, Utilities * SC4 Software for DOS, Windows 9X, Windows NT Some documents are available in languages other than English. Where available, you may click on the flag under the title of the document to view the document in that country's language. You may use F1 to get help at any time during the CD's presentation. KNOWN ANOMALIES When you launch the "Near Field Imaging (NFI) for other versions of Windows" software, two buttons appear to "view" related documentation. These buttons do not work -- please go to the documentation section of this CD to download the appropriate guides.

Topic: Magnetic confinement fusion research
Subfield: Nuclear and High Energy Physics
Field: Physics and Astronomy
Domain: Physical Sciences
INTERACTION BETWEEN CHOLINERGIC AND OPIOID SYSTEMS IN ALCOHOL SEEKING BEHAVIOR

Objective: To confirm the interaction between cholinergic and opioid systems in alcohol seeking behavior using an animal model. Methods: Experiments were conducted using Conditioned Place Preference(CPP) paradigm. Mice were conditioned with alcohol, nicotine and combination of both. They were then subjected to postconditioning test, in which their preference scores were measured. Following a period of drug abstinence, they were reinstated by morphine at doses of 5, 10, 20 and 40 mg/kg BW to induce relapse. Acetylcholinesterase (AChE) activity measurements were performed at the end of the behavioral tests using Ellman’s method. Results: Priming dose of morphine of10mg/kg, 20mg/kgand40mg/kg BW increased significantly the preference score during relapse to alcohol compared with the score in post conditioning test. AChE activity in animal at the time of relapse was significantly different compared to saline treated group. The highest enzyme activity was shown after priming dose of 20 mg/kg BW in group conditioned with alcohol and nicotine. There was no significant differences between the activity of AChE in groups receiving 5 mg/kg, 10 mg/kg, 20 mg/kg and 40 mg/kg BW of morphine challenge. Conclusion: Result of the present study indicated that morphine challenge in alcohol dependent animals during drug abstinence induces relapse to alcohol dependence. This is accompanied by increased AChE activity suggesting cholinergic-opioid system interaction

Topic: Cholinesterase and Neurodegenerative Diseases
Subfield: Pharmacology
Field: Medicine
Domain: Health Sciences
Eye Movement Dynamics in the Dogfish

ABSTRACT A method is described of obtaining the relationship between electrical stimulation of the abducens nerve and horizontal eye movement in the dogfish. The stump of the Vlth nerve was stimulated intracranially in a fish in which the brain had been removed, but in which the circulation remained intact, and the gills were perfused with sea water. Horizontal rotation of the eye was monitored with an opto-electronic movement detector. Eye rotation was linearly related to stimulus frequency in the 0–20 Hz range, and was maximal at frequencies above 40 Hz. Stimulation of the Vlth nerve, with a pulse train whose frequency was modulated sinusoidally between 0 and 20 Hz, produced sinusoidal eye movements. The frequency response of the system approximates a first order low pass filter with a characteristic frequency of 0·23 Hz, and an additional phase lag equivalent to a time delay of approximately 50 ms.

Topic: Photoreceptor and optogenetics research
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
Programming with intention: fostering positive youth development through recreation

The intent of this project is to create a staff handbook for Northern Star Kids, a non-profit organization in Prince George, BC, that offers free quality recreation opportunities for children living in financial poverty. Research has shown that children living in financial poverty are less likely than their middle class peers to participate in organized recreational opportunities or to remain committed without support. The Northern Star staff handbook will help to address these issues by equipping staff with the tools to deliver a high quality program to the children in the organization's service area. The staff handbook has three main functions: a) to ensure the vision, philosophy, and goals of Northern Star Kids are sustained over time b) to create a culture of consistency in the delivery of programs and staff interactions with youth and c) to articulate a program focused on the unique needs of youth living in financial poverty.

Topic: Youth Development and Social Support
Subfield: Safety Research
Field: Social Sciences
Domain: Social Sciences
“Pirates of Our Spirituality”

Maya spirituality serves as a locus of enunciation for the ongoing negotiation between local expressive culture and a changing globalized society. In recent years the Mayas of Guatemala have subversively used the global market provided by tourism to survive economically, recover their cultural property, and reclaim their heritage. Lacking voice and representation in an environment that has historically threatened their way of life, they assert their heritage in order to valorize their culture. They employ public knowledge and experience of natural disasters to demonstrate not just the accuracy of the 2012 prophecies of change at the end of the Maya calendar’s long count, but also the value of the knowledge systems that produced them. La espiritualidad maya sirve como un lugar de enunciación de la negociación en curso entre la cultura local expresiva y la sociedad cambiante y globalizada. En los últimos años los mayas de Guatemala han utilizado subversivamente el mercado global provisto por el turismo para sobrevivir económicamente, recuperar su patrimonio cultural, y recuperar su patrimonio. Careciendo de voz y representación en un ambiente que históricamente ha amenazado su modo de vida, han afirmado su patrimonio con el fin de valorar su cultura. Ellos emplean el conocimiento público y la experiencia de los desastres naturales para demostrar no sólo la exactitud de las profecías del 2012 del cambio al final de la cuenta larga del calendario maya, sino también el valor de los sistemas de conocimiento que los produjo.

Topic: Diverse Aspects of Tourism Research
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Finding “Health” and “Meaning” in Texas-Sized Turnover: Application of Seminal Management Principles for Administration and Research in U.S. Public Child Welfare Agencies

Public child welfare agencies in the United States have struggled with high turnover rates, especially among caseworkers. Research has explored turnover in terms of negative organizational outcomes, and efforts have been developed to reduce overall turnover rates. However, there has been little change in turnover rates in the last 30 years. The public child welfare system is inclined to higher turnover due to the unique nature of the work. Efforts to reduce the overall turnover rate fail to recognize the heterogeneity and healthy aspects of turnover unique to public child welfare organizations, which present challenges for both practice and research. By critically questioning how turnover is socially constructed, measured, and addressed, and integrating seminal management principles, a more meaningful metric can be developed. These challenges are explored, and recommendations are proposed for administration and research that include reconstructing and applying a new perspective on turnover to inform and evaluate initiatives that can reduce the impact of dysfunctional turnover within public child welfare organizations.

Topic: Social Work Education and Practice
Subfield: Public Administration
Field: Social Sciences
Domain: Social Sciences
Current Research on the Structure and Function of the Growth Hormone Releasing Hormone Receptor

Growth hormone releasing hormone receptor (GHRH-R) is a family B1 G-protein coupled receptor found predominantly on pituitary somatotrophs.In the adults it is required for the normal synthesis and release of growth hormone (GH) from the pituitary.During development it is required for the normal proliferation and maturation of somatotrophs within the pituitary.Mutations of this receptor in mouse and man are associated with GH deficiency, short stature and pituitary hypoplasia.This signaling system plays important roles in growth and development, metabolism of muscle and fat, and is implicated in the regulation of cardiac and immune function, wound healing, tumor growth and the aging process.Current areas of active research discussed here include: studiesof the structure of the receptor binding site and its interaction with GHRH, alternative splice variants of the GHRH-R which appear to promote tumor proliferation, truncated receptor isoforms that act as dominant negative inhibitors of wild type receptor, and the unclear physiologic role of the GHRH system in birds and fishes.(

Topic: Growth Hormone and Insulin-like Growth Factors
Subfield: Endocrinology, Diabetes and Metabolism
Field: Medicine
Domain: Health Sciences
Life in the trees: the ecology and life history of <i>Kentropyx striatus</i> (Teiidae) in the lavrado area of Roraima, Brazil, with comments on the life histories of tropical teiid lizards

The ecology and life history of the tropical teiid lizard Kentropyx striatus were studied in a grassland of northern Brazil, the lavrado area. The area, located nearly at the equator, experiences a prolonged dry season with a wet season extending from May to September. Total annual rainfall averages 1750 mm. Lizards were nonrandomly distributed among habitat patches and microhabitats. Most individuals were in trees and shrubs surrounding temporary and permanent water. Most individuals were observed active during late morning, the time period during which feeding and social interactions were observed. Lizards bask to achieve active body temperatures averaging 35.7 ± 0.23 °C. Body temperature is correlated with both substrate and air temperatures; foraging lizards maintained higher temperatures than basking lizards regardless of whether they were in sun, and lizards sampled when there was cloud cover had lower body temperatures than those sampled when sun was available. Females reach sexual maturity at 74 mm snout–vent length (SVL), produce 3–9 eggs per clutch, reproduce more than once per season, and commence reproduction during the wet season. Lizards hatch from eggs at 31 mm SVL. Maturity appears to be reached in 1 year or less. Overall, female reproductive characteristics are similar to those of other tropical teiid lizards that have been studied, with body size explaining much of the variance in reproductive characteristics across species. There is pronounced sexual dimorphism, with males larger in body size as well as certain other characteristics independent of body size. Sexual dimorphism appears to be a consequence of sexual selection. The diet is varied, but is dominated volumetrically by frogs, eruciform larvae, and spiders. Lizard body size accounted for only 5.5% of the variance in prey size and there was no difference in prey size due to sex. The occurrence of frogs and lizards in K. striatus stomachs suggests that teiid lizards may influence the structure of lizard and frog assemblages. The similarity of K. striatus to other studied tropical teiids in reproductive characteristics, morphology, activity period, activity temperatures, and diet underscore the conservative nature of the ecology of teiid lizards, presumably a consequence of their mode of prey acquisition.

Topic: Amphibian and Reptile Biology
Subfield: Global and Planetary Change
Field: Environmental Science
Domain: Physical Sciences
Research and Publication and Teaching in the Promotion of University Academic Staff

Research and publication and teaching are among the criteria used for considering academics for promotion at institutions of higher education. 300 faculty at the University of Transkei were asked to indicate which one of the two was more important for promotion. While some indicated that teaching was more important, others indicated that both should be considered, implying perhaps they were equally important. Such results are contrary to the common practice of highly valuing research and publication for purposes of promotion in many institutions of higher education.

Topic: Higher Education Learning Practices
Subfield: Education
Field: Social Sciences
Domain: Social Sciences