jimnoneill/paper-to-field-training huggingface dataset:
Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC

The emergence of open-source libraries and development tools in the last decade has changed the process of academic software development in many ways. In medical image processing and visualization this change is especially evident, also because open source projects are actively furthered by grant funding institutions. This manuscript presents the use of such development tools and libraries at the UNC Neuro-Image Analysis Laboratory for open source applications and tools. We have also experienced in our research that the development of open source in academics raises the issue of access to unpublished methodology. The strategy at our laboratory is to combine all in-house libraries and applications into a single repository that consists of two parts: a fully open source part that is distributed under a Berkley-style license and a private, closed source part with unpublished tools and methods. Access to the open source part is unrestricted, whereas the private parts can only be downloaded via cvs user login. This setup solved our issues regarding unpublished methodology, as migration from the private to the open source part is very simple. Overall our experience with this development environment within the academic setting is very positive.

Topic: Cell Image Analysis Techniques
Subfield: Biophysics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
A Rhythmic Approach to Geometry

Several authors have used string designs to help students develop and understand mathematical ideas. Different aspects of this activity can be emphasized. First, students can focus on the beauty of the final string design, which in many instances, is related to mirror and rotational symmetries (Pohl 1986). Second, string designs can be used to highlight relations among such numbers as common factors, multiples, and prime numbers (Bennett 1981; Perl 1981). String designs can also give rise to interesting mathematical curves (Millington 1996), such as parabolas, pursuit curves, spirals, cardioids, and many more.

Topic: Art, Technology, and Culture
Subfield: Visual Arts and Performing Arts
Field: Arts and Humanities
Domain: Social Sciences
Myeloma light chains induce epithelial-mesenchymal transition in human renal proximal tubule epithelial cells

To determine the role of epithelial-mesenchymal transition (EMT) as a potential mechanism contributing to the characteristic tubulointerstitial renal fibrosis in multiple myeloma, we examined whether myeloma light chains (LCs) directly induce EMT in human renal proximal tubule epithelial cells (PTECs).As positive controls we used TGF-beta1 and cyclosporine A (CsA), two agents known to induce EMT in PTECs. Human LCs were isolated and purified from the urine of myeloma patients with modest renal insufficiency without evidence of glomerular involvement. HK-2 cells were exposed to kappa LC (25 microM) for periods up to 72 h.LCs induced marked cellular morphological alterations in PTECs, accompanied with increased expression levels of profibrotic TGF-beta1, FSP-1 and extracellular matrix components. Using semiquantitative immunoblotting and RT-PCR, we observed that the expression of E-cadherin decreased after 24 h, while the expression of alpha-SMA increased in PTEC after continuous exposure to kappa-LCs. Human serum albumin (HSA; 160 microM) had less potent effect on the expression of EMT-related molecules. Neutralizing TGF-beta1 antibody blocked CsA-induced EMT but had no effect on LC-exposed cells. LC-induced EMT and the secretions of IL-6 and MCP-1 were, however, markedly attenuated by p38 MAPK interference. The use of bone morphogenetic protein-7 or pituitary adenylate cyclase-activating polypeptide (PACAP) induced the formation of cell aggregates, and the reacquisition of E-cadherin expression and renal proximal tubule epithelial morphology within the confluent cell monolayer during and after LC exposure.These findings demonstrate that LC is a direct stimulus for EMT in PTECs. LC-induced EMT involved multiple cytokines, is modulated by p38 MAPK, but appeared independent of the action of TGF-beta1. LC-induced EMT may be an important mechanism of kidney injury associated with myeloma and may be reversible upon the administration of exogenous PACAP.

Topic: Multiple Myeloma Research and Treatments
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
Organophosphate esters and their metabolites in eggs from Vietnam

Data on the occurrence of organophosphate tri-esters (tri-OPEs) and their metabolites (di-OPEs) in hen’s eggs are scarce. Therefore, 200 egg samples were gathered in 2023 in Hanoi, Vietnam and analysed by UHPLC-Q-Exactive HRMS. The majority of these compounds were detected, with tris(2-ethylhexyl) phosphate (0.10–2.7 ng/g wet weight (ww)) and trihexyl phosphate (0.08–2.3 ng/g ww) being the most prevalent tri-OPEs. Significant differences in tri-OPE profiles were observed in egg samples from battery-cage and free-range farming (<i>p</i> &lt; .05). Despite egg levels ranging from 0.05 to 11.2 ng/g ww, Σdi-OPE accumulation in yolk and egg white was not significantly different in (<i>p</i> &gt; .05). Among di-OPEs, dibutyl phosphate was found at the highest levels in the egg white, while bis(2-ethylhexyl) phosphate had the highest levels in yolk. There was no carcinogenic human health risk associated with OPEs in eggs (HQs &lt;1).

Topic: Pesticide Exposure and Toxicity
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
ChemInform Abstract: Reaction of Oxazolidines with Triethylsilane in the Presence of Dicyclopentadienylzirconium Dichloride

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Topic: Chemical Synthesis and Reactions
Subfield: Organic Chemistry
Field: Chemistry
Domain: Physical Sciences
Evaluation of the effect of background electrolyte composition and independence of parameters in determining binding constants of betulin derivatives to β‐ and dimethyl‐β‐cyclodextrins by affinity capillary electrophoresis

The values of the apparent binding constants for β‐cyclodextrin complexes of betulin derivatives determined by mobility shift affinity capillary electrophoresis were found to be independent of the composition of the two background electrolytes used (tetraborate buffer, pH 9.18, and phosphate buffer, pH 8.00, both of them with 20 mM ionic strength). It has been found that if there is not a constant plateau on the binding curve then four independent parameters can be determined: binding constants (also referred to as stability, association, or formation constants) and ionic mobilities of 1:1 and 1:2 complexes. However, at least 10–12 data points in the binding curve should be used to reliably estimate the parameters. For the first time, the apparent binding constants for complexes of ester betulin derivatives with dimethyl‐β‐cyclodextrin have been determined by mobility shift affinity capillary electrophoresis. The logarithms of the constants for 1:1 and 1:2 complexes at 25°C for betulin 3,28‐diphthalate with a 95% confidence interval are 4.98 (4.95–5.01) and 7.52 (7.26–7.68); for betulin 3,28‐disulfate, the values are 4.97 (4.89–5.03) and 8.24 (6.82–8.52). It has been found that betulin 3,28‐disuccinate forms only a 1:1 complex and the binding constant logarithm is 5.25 ± 0.02.

Topic: Natural product bioactivities and synthesis
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Impact of improper sample handling on Cobas CT/NG testing platform with dual swab sample collection kit for detecting <i>Chlamydia trachomatis</i> and <i>Neisseria gonorrhoeae</i>

ABSTRACT In the realm of molecular diagnostics, accurate and reliable test results are imperative for effective clinical decision-making. This study delves into the effects of non-compliant sample collection practices on the Cobas CT/NG testing platform. Deviating from the manufacturer’s recommendation of single swab collection, our laboratory received dual swabs during sample collection. Subsequently, we embarked on an investigation to ascertain the cause behind a noticeable rise in invalid results, which were found to be exacerbated by improper sample handling practices, accounting for a significant 30% of cases. Through a comprehensive comparative analysis, we found that the use of dual swabs in testing contributed to a substantial increase in both invalid and false-negative results when compared to properly collected samples submitted with a single swab. This study underscores the importance of adhering to recommended protocols for sample collection to ensure accurate and reliable molecular diagnostic outcomes. IMPORTANCE The importance of this observation lies in its potential to directly impact testing outcomes and patient care. By identifying improper sample handling as a contributing factor to a substantial number of invalid results, we emphasize the need for meticulous adherence to recommended protocols during sample collection. Laboratories that overlook or are unaware of such deviations may inadvertently compromise the reliability and efficacy of their diagnostic processes, leading to misdiagnoses, delayed treatment, and patient dissatisfaction.

Topic: Reproductive tract infections research
Subfield: Microbiology
Field: Immunology and Microbiology
Domain: Life Sciences
Adoption of Breeding and Calf Rearing Practices in Modern Dairy Farms of Gujarat

A study was carried out to compare the breeding and calf rearing practices of modern specialized dairy farms of north and south Gujarat. The data was collected from ten specialized dairy farms, each from the north and south Gujarat. The study revealed that farms of the southern region mostly reared buffaloes, which relied on natural service, whereas northern farms mostly reared cows, and AI was more popular. Around 22.2 and 16.7% of dairy farms preferred pedigreed and sex-sorted semen from the private sector, respectively. Most of the dairy farms (60%) purchased frozen semen doses from the co-operative sector. About 20% of dairy farms used sex-sorted semen at the price of Rs. 2100-3000 per dose. One farm from the north and another one from south were using Delaval® heat detector system. The majority (75%) of the dairy farms adopted the practice of colostrum feeding by allowing for natural suckling. The majority (70%) of the dairy farms provided first colostrum feeding within 2 to 4 hours of calf birth. Some dairy farms (20%) possessed individual calf boxes. From the research finding, it can be concluded that artificial insemination was more famous in north Gujarat. Many specialized dairy farms of north Gujarat were adopting most advanced breeding practices by the use of sex-sorted and pedigreed semen of private companies to produce an offspring of the desired sex, high milk yielding potential and healthy one.

Topic: Livestock Management and Performance Improvement
Subfield: Agronomy and Crop Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The effect of glycerine on the penetration of coloring liquid and the hardness of zirconia

The purpose of this study was to evaluate the effect of glycerine on the penetration of coloring liquid on zirconia and hardness of zirconia. Three A2 coloring liquids (Prettau Aquarell Colour liquid, D.max coloring liquid, and Bruxzir coloring liquid) were used to perform this study. Glycerine were mixed with each coloring liquid at the ratio of 1 : 1 by volume. The immersion periods of zirconia specimen in the mixing solution were 1, 3, 6, 9, and 12 hrs, respectively. The penetration depth of coloring liquid were measured by vernier calliper. Color characterization of experimental specimen was performed by spectrophotometer, and hardness of the specimen was measured by Vickers hardness tester. From the results of penetration depth measurement, glycerine was supposed to affect the penetration depth of coloring liquid on zirconia regardless of immersion periods. By color analysis, L＊ value of glycerine treated specimen was significantly higher than that of control group(P 0.05). In terms of the results of Vickers hardness test, there were no significant statistical differences between control group and experimental groups. Therefore, glycerine was expected to affect the penetration of coloring liquid on zirconia and the shade of zirconia.

Topic: Dental materials and restorations
Subfield: Orthodontics
Field: Dentistry
Domain: Health Sciences
Female Transsexualism

Research Articles| February 04 2010 Female Transsexualism Subject Area: Psychiatry and Psychology D. Christodorescu D. Christodorescu Psychiatric Department of the 'G. Marinescu' Hospital, Bucharest Search for other works by this author on: This Site PubMed Google Scholar Psychiatria Clinica (1971) 4 (1): 40–45. https://doi.org/10.1159/000283162 Article history Published Online: February 04 2010 Content Tools Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Tools Icon Tools Get Permissions Cite Icon Cite Search Site Citation D. Christodorescu; Female Transsexualism. Psychiatria Clinica 1 January 1971; 4 (1): 40–45. https://doi.org/10.1159/000283162 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsPsychiatria Clinica Search Advanced Search Article PDF first page preview Close Modal 1971Copyright / Drug Dosage / DisclaimerCopyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. You do not currently have access to this content.

Topic: LGBTQ Health, Identity, and Policy
Subfield: Social Psychology
Field: Psychology
Domain: Social Sciences
Will China Eat Our Lunch or Take Us Out to Dinner? Simulating the Transition Paths of the U.S., EU, Japan, and China

"This paper develops a dynamic, life-cycle, general equilibrium model to study the interdependent demographic, fiscal, and economic transition paths of China, Japan, the U.S., and the EU. Each of these countries/regions is entering a period of rapid and significant aging requiring major fiscal adjustments. In previous studies that excluded China we predicted that tax hikes needed to pay benefits along the developed world's demographic transition would lead to capital shortage, reducing real wages per unit of human capital. Adding China to the model dramatically alters this prediction. Even though China is aging rapidly, its saving behavior, growth rate, and fiscal policies are very different from those of developed countries. If this continues to be the case, the model's long run looks much brighter. China eventually becomes the world's saver and, thereby, the developed world's savoir with respect to its long-run supply of capital and long-run general equilibrium prospects. And, rather than seeing the real wage per unit of human capital fall, the West and Japan see it rise by one fifth by 2030 and by three fifths by 2100. These wage increases are over and above those associated with technical progress"--National Bureau of Economic Research web site.

Topic: Economic Growth and Productivity
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
LHD dcece #185405.1

The electron cyclotron emission (ECE) imaging to determine the electron temperature profile by measuring the intensity of each frequency of ECE. This system uses a wide-band two-dimensional horn-antenna mixer array (HMA) whose frequency response is between 50 and 110 GHz and the ECE signal is selected using a 95 GHz local oscillator and a 93 GHz high-pass filter.

Topic: Sperm and Testicular Function
Subfield: Reproductive Medicine
Field: Medicine
Domain: Health Sciences
The production of functionality by the elderly: a household production function approach

This paper extends Becker's model of the household production function of human capital to the production of elderly functionality. In this model, elderly functionality is produced with the direct inputs of assistive devices, personal assistance, and nutritional intake. Education, endowment variables (like genetic endowment and sex) and health conditions (like stroke) determine the production function environment. Data from the Survey of Asset and Health Dynamics Among the Oldest-Old (AHEAD) are used to estimate a production function of bathing functionality, using a two-stage estimation procedure. In the first stage, input demands for the endogenous functionality inputs are estimated, recognizing health heterogeneity. The results suggest that reverses in functionality caused by age and health conditions can be partially compensated for by the use of assistive devices (like grab bars and bathing equipment), secure nutritional intake, and moderate alcohol consumption. However, non-inputs like chronic health conditions, age, sex and genetic endowment exert a strong influence on the level of functionality.

Topic: Retirement, Disability, and Employment
Subfield: Demography
Field: Social Sciences
Domain: Social Sciences
LARGE FARMS IN POLAND FOUNDED ON THE BASIS OF THE PROPERTY OF FORMER STATE - OWNED FARMS (PGRS)

This paper presents economic results of three groups of large farms, in the years 2000-2005, which were founded on the basis of the property of former state-owned farms in Poland. They were divided according their legal and organisational form into : farms purchased, farms on lease and shareholder companies of the State Treasury. On the basis of the results of the analysis it was concluded that all three groups are economically effective, however, farms purchased, as a legal and organisational form, are protected against the production and market risk in the highest degree. Hence, the final direction of privatisation in Poland at the present stage of restructuring should be the purchase of farms. It does not mean, however, that there is a need to liquidate shareholder companies of the State Treasury which due to their specificity play a significant role in implementing biological progress in agriculture.

Topic: Agricultural economics and policies
Subfield: Safety Research
Field: Social Sciences
Domain: Social Sciences
Disorder Chaos in Short-Range, Diluted, and Lévy Spin Glasses

In a recent breakthrough [arXiv:2301.04112], Chatterjee proved site disorder chaos in the Edwards-Anderson (EA) short-range spin glass model utilizing the Hermite spectral method. In this paper, we demonstrate the further usefulness of this Hermite spectral approach by extending the validity of site disorder chaos in three related spin glass models. The first, called the mixed even $p$-spin short-range model, is a generalization of the EA model where the underlying graph is a deterministic bounded degree hypergraph consisting of hyperedges with even number of vertices. The second model is the diluted mixed $p$-spin model, which is allowed to have hyperedges with both odd and even number of vertices. For both models, our results hold under general symmetric disorder distributions. The main novelty of our argument is played by an elementary algebraic equation for the Fourier-Hermite series coefficients for the two-spin correlation functions. It allows us to deduce necessary geometric conditions to determine the contributing coefficients in the overlap function, which in spirit is the same as the crucial Lemma 1 in [arXiv:2301.04112]. Finally, we also establish disorder chaos in the Lévy model with stable index $α\in (1, 2)$.

Topic: Theoretical and Computational Physics
Subfield: Condensed Matter Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Fact extraction from bash in support of script migration

Owl Computing Technologies provides software and hardware that facilitates secure unidirectional data transfer across the Internet. Bash scripts are used to facilitate customer installation of Owl's client/server software, and to provide high level management, control, and monitoring of client/server interfaces. With the evolution of more robust scripting languages, Owl now wishes to convert their bash scripts to other scripting languages. As part of this conversion exercise the configuration and customization of their bash scripts will no longer involve direct end user modifications of the script logic. It will instead be achieved through appropriate modification of a supporting XML configuration file, which is read by each script. This avoids the risk that end users erroneously change scripts, and makes legitimate end user customization of their scripts simpler, more obvious, and easier to discern. An open source fact extractor was implemented that determines the dynamic usage made of every variable within an arbitrary bash script. This tool reports errors in a script and generates an XML configuration file that describes variable usage. Those variables whose value may not be assigned by an end user are manually removed from this XML configuration file. A second program reads this configuration file, generates the appropriate bash variable assignment statements, and these are then applied within bash by using the bash eval command. Collectively this provides a simple mechanism for altering arbitrary bash scripts so that they use an external XML configuration file, as a first step in the larger exercise of migrating bash scripts to other scripting languages.

Topic: Software Engineering Research
Subfield: Information Systems
Field: Computer Science
Domain: Physical Sciences