jimnoneill/paper-to-field-training huggingface dataset:
Thomas Hobbes' Fundamental View of Liberty and the Law and Conclusions Drawn

Field: Arts and Humanities (Social Sciences)

Thomas Hobbes (1588 - 1679) was one of the outstanding representatives of 17th century English materialism. Thomas Hobbes is also known for his outstanding work on political philosophy. His 1651 book, Leviathan, marked the foundation for many Western political philosophies that took into account the perspective of social relational theory. Thomas Hobbes' point of view reflects the spirit of the times, that is, the spirit of rule of law, considering the law as the basis to ensure human freedom. This study was conducted to analyze and clarify Thomas Hobbes' basic views on freedom, law and the conclusions drawn. Accordingly, there is a difference between freedom in the state of nature and freedom in the state (or civil society). Thomas Hobbes discovered the close relationship between law and human natural rights when he argued that natural laws are principles arising from human natural rights. These rights are personal freedoms through which people use their own power to protect their lives based on reason. The article also made three observations when learning about Thomas Hobbes' basic views on freedom and law; The limitation of this study is that it has not been able to compare Thomas Hobbes' views on freedom and law with those of modern philosophers John Locke, Montesquieu, J.J. Rousseau, Friedrich Hayek.
Targeted imaging of translocated calreticulin with 18F-labeled peptidic probe for early prediction of therapeutic response in small animal models

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

164 Objectives Calreticulin (CRT) is a multi-functional endoplasmic reticulum protein, involved in a spectrum of cellular processes. It has been known that anthracyclines induce immunogenic cell death characterized by translocation of CRT to the cell membrane (ecto-CRT) within 24 h before signs of apoptosis. Here, we imaged ecto-CRT after treatment of doxorubicin to assess as an early predictor of chemotherapy response. Methods CRT specific binding peptide (KLGFFKR, CRT-pep) was used for experiments. Cultured CT26 cells were treated with doxorubicin (dox) and confirmed the surface exposure of CRT after 4 h of treatment using Western blot analysis. IF staining and FACs analysis was performed to evaluate specific binding of CRT-pep to ecto-CRT. And we assessed ecto-CRT exposure in grafted CT26 mouse models (n = 10) after treatment with dox (10 mg/kg, three times) using Cy-5.5 or 18F- labeled CRT-pep ([18F]SFB-CRT-pep, 7.4 MBq). Results CRT translocation after treatment was confirmed by Western blot analysis. Specific binding of CRT-pep to the dox-treated cultured CT26 was observed by IF staining and FACs analysis: no binding was observed with scrambled peptide. Ecto-CRT was verified by in fluorescence and microPET images from 3 days after dox treatment. CRT-pep accumulation increased significantly from day 3 after treatment, that was similarly observed by optical and microPET images. MicroPET imaging showed 29.7 and 42.4 fold (p Conclusions The current study clearly demonstrated a potential usefulness of CRT imaging for prediction of therapeutic effect at the early time-point of post-chemotherapy.
Sequence-Based Nanobody-Antigen Binding Prediction

Field: Computer Science (Physical Sciences)

Nanobodies (Nb) are monomeric heavy-chain fragments derived from heavy-chain only antibodies naturally found in Camelids and Sharks. Their considerably small size (~3-4 nm; 13 kDa) and favorable biophysical properties make them attractive targets for recombinant production. Furthermore, their unique ability to bind selectively to specific antigens, such as toxins, chemicals, bacteria, and viruses, makes them powerful tools in cell biology, structural biology, medical diagnostics, and future therapeutic agents in treating cancer and other serious illnesses. However, a critical challenge in nanobodies production is the unavailability of nanobodies for a majority of antigens. Although some computational methods have been proposed to screen potential nanobodies for given target antigens, their practical application is highly restricted due to their reliance on 3D structures. Moreover, predicting nanobodyantigen interactions (binding) is a time-consuming and labor-intensive task. This study aims to develop a machine-learning method to predict Nanobody-Antigen binding solely based on the sequence data. We curated a comprehensive dataset of Nanobody-Antigen binding and nonbinding data and devised an embedding method based on gapped k-mers to predict binding based only on sequences of nanobody and antigen. Our approach achieves up to 90% accuracy in binding prediction and is significantly more efficient compared to the widely-used computational docking technique.
α-amylase production obtained from Aspergillus niger ATCC 1004 by solid state fermentation using Croton linearifolius residues as substrate

Field: Agricultural and Biological Sciences (Life Sciences)

The objective of this work was to optimize the production and characterize α-amylase produced by Aspergillus niger through solid state fermentation, using leaf residues of C. linearifolius as substrate. For optimization, the incubation temperature, initial humidity and fermentation time were combined based on Doehlert experimental design. The highest productivity of the enzyme was 122.88 Ug-1, at 33oC, 70% humidity and 14 days of time. In the enzymatic characterization, the enzyme extract presented pH 5.0 and temperature 50oC, and α-amylase was thermostable up to 60oC, maintaining more than 90% of the activity. In evaluation of the effect of salt addition, sodium carbonate, calcium chloride, iron chloride, and cobalt chloride increased the enzymatic activity of α-amylase, while potassium and sodium from their chlorides served as enzyme inhibitors. The Km and Vmax values ​​found were 0.04 mg/mL and 46.95 µmol/min/mL, respectively, indicating that the substrate has affinity for α-amylase. Therefore, the results demonstrate that the residues of C. linearifolius can be used as a substrate for A. niger in the production of enzymatic extracts, such as α-amylase.
Gamma interferon (IFN-gamma) and IFN-gamma-inducing cytokines interleukin-12 (IL-12) and IL-18 do not augment infection-stimulated bone resorption in vivo

Field: Medicine (Health Sciences)

Periapical granulomas are induced by bacterial infection of the dental pulp and result in destruction of the surrounding alveolar bone. In previous studies we have reported that the bone resorption in this model is primarily mediated by macrophage-expressed interleukin-1 (IL-1). The expression and activity of IL-1 is in turn modulated by a network of Th1 and Th2 regulatory cytokines. In the present study, the functional roles of the Th1 cytokine gamma interferon (IFN-gamma) and IFN-gamma-inducing cytokines IL-12 and IL-18 were determined in a murine model of periapical bone destruction. IL-12-/-, IL-18-/-, and IFN-gamma-/- mice were subjected to surgical pulp exposure and infection with a mixture of four endodontic pathogens, and bone destruction was determined by microcomputed tomography on day 21. The results indicated that all IL-12-/-, IL-18-/-, and IFN-gamma-/- mice had similar infection-stimulated bone resorption in vivo as wild-type control mice. Mice infused with recombinant IL-12 also had resorption similar to controls. IFN-gamma-/- mice exhibited significant elevations in IL-6, IL-10, IL-12, and tumor necrosis factor alpha in lesions compared to wild-type mice, but these
The Variability and Malleability of Frog Call-Timing Mechanisms are Neglected in Traditional Call-Timing Models

Field: Agricultural and Biological Sciences (Life Sciences)

Synopsis Males of many insect and anuran species send courtship calls to females from within crowded chorusing aggregations. Despite large phylogenetic distances between insects and frogs, many convergences in communication behavior are evident due to similar selection pressures arising when competing acoustically within choruses. Consequently, mechanistic call-timing models and theoretical frameworks originally derived from work on synchronizing insects have been applied fruitfully to alternating frogs. However, despite such similarities, there exist extensive differences in the details of the communication ecologies and nervous systems of these taxa, suggesting interesting differences may have been overshadowed by these broad similarities. Here, we synthesize recent findings regarding the call-timing mechanisms of túngara frogs, a species showing flexible calling interaction patterns across varied chorusing environments. Based on these findings, and hints present in other frogs, we suggest that the unique demands arising within the dense choruses frogs form have selected for call-timing mechanisms whose parameters are highly flexible, and malleable moment-to-moment in response to complex stimulation patterns arising in varied acoustic environments. Such fine-scale malleability and responsiveness to external stimulation are neglected in traditional theoretical models of call-timing mechanisms, possibly because the resulting variability would be detrimental to the highly structured interaction patterns of the synchronizing insects from which much of this work derives. Though further experiments are needed to fully vet our broader claims, we hope to inspire researchers to consider previously neglected factors influencing call-timing responses and chorusing dynamics, and to complement the impressive work on similarities across chorusing taxa with additional details on finer differences.
Tiotropium + olodaterol provides significant lung-function benefits compared to fluticasone + salmeterol regardless of prior bronchodilator use

Field: Medicine (Health Sciences)

Introduction: The ENERGITO® study demonstrated superior lung function with long-acting muscarinic antagonist (LAMA) tiotropium + long-acting β2-agonist (LABA) olodaterol (T+O) compared to inhaled corticosteroid (ICS) fluticasone + LABA salmeterol (F+S) in patients with COPD. Aim: To investigate if lung-function benefits of T+O compared to F+S were affected by prior ICS, LAMA or LABA treatment in ENERGITO®. Methods: In ENERGITO® (1237.11, NCT01969721; Phase IIIb, randomised, double-blind, double-dummy, four-period crossover), patients with moderate to severe COPD received once-daily T+O 2.5/5 or 5/5 µg and twice-daily F+S 250/50 or 500/50 µg for 6 weeks. A post hoc analysis evaluated FEV1 AUC0–12 and AUC0–24 responses in patients with or without LAMA, LABA or ICS therapy at screening. We describe results comparing T+O 5/5 µg to both doses of F+S. Results: 229 patients were enrolled and treated: 123 received prior LAMA, 141 LABA, 109 ICS. T+O significantly improved FEV1 AUC0–12 and AUC0–24 responses in patients with or without prior LAMA, LABA or ICS therapy compared to F+S (Table). Conclusions: In ENERGITO®, patients with moderate or severe COPD showed improved lung function with T+O compared to F+S regardless of prior treatment. T+O is a better choice than LABA/ICS to optimise lung function when initiating maintenance treatment. Funding: Boehringer Ingelheim.
Data from Epigenome-Wide Study Identifies Epigenetic Outliers in Normal Mucosa of Patients with Colorectal Cancer

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

<div>Abstract<p>Nongenetic predisposition to colorectal cancer continues to be difficult to measure precisely, hampering efforts in targeted prevention and screening. Epigenetic changes in the normal mucosa of patients with colorectal cancer can serve as a tool in predicting colorectal cancer outcomes. We identified epigenetic changes affecting the normal mucosa of patients with colorectal cancer. DNA methylation profiling on normal colon mucosa from 77 patients with colorectal cancer and 68 controls identified a distinct subgroup of normally-appearing mucosa with markedly disrupted DNA methylation at a large number of CpGs, termed as “Outlier Methylation Phenotype” (OMP) and are present in 15 of 77 patients with cancer versus 0 of 68 controls (<i>P</i> < 0.001). Similar findings were also seen in publicly available datasets. Comparison of normal colon mucosa transcription profiles of patients with OMP cancer with those of patients with non-OMP cancer indicates genes whose promoters are hypermethylated in the OMP patients are also transcriptionally downregulated, and that many of the genes most affected are involved in interactions between epithelial cells, the mucus layer, and the microbiome. Analysis of 16S rRNA profiles suggests that normal colon mucosa of OMPs are enriched in bacterial genera associated with colorectal cancer risk, advanced tumor stage, chronic intestinal inflammation, malignant transformation, nosocomial infections, and KRAS mutations. In conclusion, our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Prospective studies are needed to determine whether OMP could serve as a biomarker for an elevated epigenetic risk for colorectal cancer development.</p>Prevention Relevance:<p>Our study identifies an epigenetically distinct OMP group in the normal mucosa of patients with colorectal cancer that is characterized by a disrupted methylome, altered gene expression, and microbial dysbiosis. Identification of OMPs in healthy controls and patients with colorectal cancer will lead to prevention and better prognosis, respectively.</p></div>
VALORISATION DE LA POUDRE DE MARBRE COMME ADDITIF DANS LA FORMULATION DE BETONS AUTOPLAÇANTS

Field: Engineering (Physical Sciences)

The cement industry is a greenhouse gas-generatingactivity since approximately one ton of carbondioxide (CO2) is emitted into the atmosphere per tonof cement produced. Many mineral products can beadded to concrete to modify their technicalcharacteristics for particular applications and/or toimprove the environmental balance of their lifecycle. This article reports the study of the influenceof the addition of waste marble on the properties ofself-consolidating concrete (SCC). Several additionrates were tested Concrete were prepared with aWater/Binder (W/L) ratio of 0.33 and an equalPortland cement dosage of 400kg/m3. Used alone asa reference composition (white), or with additions ofmarble powder at dosages of 15, 20 and 30% relativeto the mass of the cement. The properties of theself-compacting concrete in the fresh and hardenedstate were tested using specific tests, by varying thefineness of the marble powder at 3000, 7000 and9000 cm2/g and the Superplasticizer content at 1 .5%and 1.75%. The results obtained show that the use ofmarble powder improves the properties of selfconsolidatingconcrete and is consistent with therecommendations of the French Association of CivilEngineering. L’industrie cimentaire est une activité génératrice degaz à effet de serre puisque de l’ordre d’une tonnede dioxyde de carbone (CO2) est émise dansl’atmosphère par tonne de ciment produit. Denombreux produits minéraux peuvent être ajoutésaux bétons pour modifier leurs caractéristiquestechniques en vue d’applications particulières et/oupour améliorer le bilan environnemental de leurcycle de vie. Cet article rapporte l’étude del’influence de l’addition des déchets de marbre surles propriétés du béton autoplaçant (BAP). Plusieurstaux d’addition ont été testés. Des bétons ont étépréparés avec un rapport Eau/Liant (E/L) de 0,33et un dosage en ciment Portland égal de400kg/m3. Utilisé seul comme composition deréférence (blanc), ou avec des ajouts de poudre demarbre à des dosages de 15, 20 et 30% par rapport àla masse du ciment. Les propriétés des bétonsautoplaçants à l’état frais et durcis ont été testées àl’aide d’essais spécifiques, en faisant varier la finessede la poudre de marbre à 3000, 7000 et 9000 cm2/get la teneur en superplastifiant à 1,5% et 1,75%. Lesrésultats obtenus montrent que l’utilisation de lapoudre de marbre améliore les propriétés desbétons autoplaçants et concordent avec lesrecommandations de l’Association Française deGénie Civil .
Factors Affecting Implant Salvage in Patients with Complications After Post-Mastectomy Implant-Based Reconstruction

Field: Medicine (Health Sciences)

Background: Implant-based reconstruction (IBR) is the most common method of breast reconstruction, but complications lead to patient distress and delays in cancer treatment. Management of implant complications is varied with no defined guidelines. The inability to salvage IBR is associated with infection, but the impact of antibiotics remains controversial. We aimed to analyze factors affecting salvage rates of threatened IBR requiring operative intervention. The primary outcomes were the rates of unplanned re-operation for threatened IBR for wound closure, exchange, or explant. We hypothesized antibiotic administration would improve salvage rates. Methods: A retrospective review of patients undergoing mastectomy with IBR from 2012 to 2023 was performed. Threatened IBR was defined as implant exposure, infection, skin necrosis, hematoma, seroma, or wound dehiscence without implant exposure. Management options for patients with implant infection included implant removal and antibiotic treatment, antibiotic treatment alone, implant replacement, washout and implant replacement, or implant removal without a salvage attempt. Results: In total, 6901 patients underwent post-mastectomy IBR, and 184 (2.7%) patients had an unplanned re-operation. A total of 166/184 patients (90.2%) underwent explantation, and 18/184 (9.8%) patients had implant salvage. Between the explant and salvage groups, there were no differences in patient demographics, oncologic treatments, or operative characteristics. The explant group had a higher rate of infection (77.7% vs. 22.2%, p < 0.0001). There was no difference in culture positivity or antibiotic administration history. Conclusions: Implant salvage is feasible but limited by infection. Antibiotic administration does not improve salvage rates. Patient factors, oncologic treatment factors, or operative factors do not impact the ability to salvage.
Automatically archiving reproducible studies with Docker

Field: Computer Science (Physical Sciences)

Reproducibility of computations is crucial in an era where data is born digital and analysed algorithmically. Most studies however only publish the results, often with figures as important interpreted outputs. But where do these figures come from? Scholarly articles must provide not only a description of the work but be accompanied by data and software. R offers excellent tools to create reproducible works, i.e. Sweave and RMarkdown. Several approaches to capture the workspace environment in R have been made, working around CRAN’s deliberate choice not to provide explicit versioning of packages and their dependencies. They preserve a collection of packages locally (packrat, pkgsnap, switchr/GRANBase) or remotely (MRAN timemachine/checkpoint), or install specific versions from CRAN or source (requireGitHub, devtools). Installers for old versions of R are archived on CRAN. A user can manually re-create a specific environment, but this is a cumbersome task.
We introduce a new possibility to preserve a runtime environment including both, packages and R, by adding an abstraction layer in the form of a container, which can execute a script or run an interactive session. The package containeRit automatically creates such containers based on Docker. Docker is a solution for packaging an application and its dependencies, but shows to be useful in the context of reproducible research (Boettiger 2015). The package creates a container manifest, the Dockerfile, which is usually written by hand, from sessionInfo(), R scripts, or RMarkdown documents. The Dockerfiles use the Rocker community images as base images. Docker can build an executable image from a Dockerfile. The image is executable anywhere a Docker runtime is present. containeRit uses harbor for building images and running containers, and sysreqs for installing system dependencies of R packages. Before the planned CRAN release we want to share our work, discuss open challenges such as handling linked libraries (see discussion on geospatial libraries in Rocker), and welcome community feedback. https://user2017.sched.com/event/785b77e931775df6849f108615605c01 https://github.com/o2r-project/containerit/
chief integration officer: a study of success factors in the implementation of clinical information technology

Field: Health Professions (Health Sciences)

This research examines the question what do participants in successful information technology (IT) implementations perceive were the factors that enabled success with these IT initiatives? Using grounded theory methodology the researcher conducted interviews with chief executives, information technology leaders, and medical informatics leaders from healthcare organizations that received industry recognition for their success with information technology. The researcher developed a theoretical framework of factors that contribute to successful clinical information systems implementation. The interview results led to formulation of a proposed two-part theoretical framework to answer the research question. This theoretical framework emphasizes the critical role of leadership in success, and the importance of integrating operational strategies and information technology strategies.
Survey on Seroprevalence of Anti-Toxoplasma Gondii Antibodies in Cattle in Tabriz (Iran) by IFAT

Field: Veterinary (Health Sciences)

Toxoplasmosis is a zoonotic disease in various species of animals caused by a sporozoan parasite, Toxoplasma gondii. The disease occurs throughout the world including Iran. This disease is a common infection of sheep, goats and it is recognized as one of major infection cause of reproductive failure. This survey was carried out to show the prevalence of this disease in cattle in Tabriz (Iran). 490 sera samples were collected from both native and industrial cattle. The Indirect Fluorescent Antibody Test (IFAT) was used to determine the rate of infection. The results of this survey are showed that the overall seroprevalence of antibody of Toxoplasma incattle in Tabriz is 15.91%. There was significant differences in infection to Toxoplasma gondii in the age group of cattle (P 1 years old cattle. Also a significant differences was observed between rate of infection and sex in cattle (P<0.0 l). In total the results of this study together with the previously recorded low seroprevalence of antibody to Toxoplasma in cattle in Iran and other countries support the impression that Toxoplasmosis is not widespread cause for abortion and a latent infection in cattle.
Optical stimulation of excised murine sciatic nerve using 1.8-μm wavelength laser

Field: Neuroscience (Life Sciences)

While recording of compound actions potentials is a mature technique, it becomes problematic to use traditional electrical nerve stimulation on very short nerves due to the large electrical stimulus artifact and short propagation times. Novel methods of stimulation using focused infrared laser radiation may permit stimulation and measurement in closer proximity with much finer spatial resolution than conventional techniques. This project involved the development of a murine sciatic nerve model for action potential stimulus and measurement in vitro, including refinement of a dissection protocol and development of a small-scale stimulation and measurement dish specific to murine sciatic nerve. It demonstrated successful recording of compound nerve action potentials (CNAPs) using traditional current-mode electrical stimulus. Lastly, optical nerve stimulation was attempted on the same nerve prep using an infrared laser source of 1.86μm. In this preliminary study, the conventional stimulus was been successfully demonstrated, however the optical stimulus failed to produce measurable CNAPs, We later learned that other investigators have only succeeded with in vivo experiments in the mouse sciatic nerve, and in vitro experiments have not been demonstrated. More work is needed to achieve success in the in vitro model.