jimnoneill/paper-to-field-training huggingface dataset:
eLife Assessment: Ezrin defines TSC1 activation at endosomal compartments through EGFR-AKT signaling

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

Endosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events. Ezrin, a major membrane-actin linker that assembles and coordinates macromolecular signaling complexes at membranes, has emerged recently as an important regulator of lysosomal function. Here, we report that endosomal-localized EGFR/Ezrin complex interacts with and triggers the inhibition of the Tuberous Sclerosis Complex (TSC) in response to EGF stimuli. This is regulated through activation of the AKT signaling pathway. Loss of Ezrin was deficient in TSC repression by EGF and culminated in translocation of TSC to lysosomes triggering suppression of mTORC1 signaling. Overexpression of constitutively active EZRINT567D is sufficient to relocalize TSC to the endosomes and reactivate mTORC1. Our findings identify EZRIN as a critical regulator of autophagy via TSC in response to EGF stimuli and establish the central role of early endosomal signaling in the regulation of mTORC1. Consistently, Medaka fish deficient for Ezrin exhibit defective endo-lysosomal pathway, attributable to the compromised EGFR/AKT signaling, ultimately leading to retinal degeneration. Our data identify a pivotal mechanism of endo-lysosomal signaling involving Ezrin and its associated EGFR/TSC complex, which are essential for retinal function.
The Effect of Nitrogen and Carbon Supply on the Development of Soil Organism Populations and Pine Seedlings: A Microcosm Experiment

Field: Agricultural and Biological Sciences (Life Sciences)

Series of pots containing Scots pine seedlings and a humus-sand mixture were watered twice weekly for 398 d with different nutrient solutions (control treatment with complete plant nutrient solution less nitrogen; glucose addition; nitrogen addition; glucose and nitrogen addition). Analyses were made of organic and nitrogen contents in the substrate, plant weights and nitrogen contents, nitrogen fixation and respiration rates, abundance, biomass and in some cases species composition of different soil organism populations. The growth rate of pine seedlings was lowest in series supplied with glucose, which is most easily explained by a deficiency of nitrogen due to microbial immobilization. The fungi and yeast were stimulated by addition of an easily available carbon source whereas the bacteria needed both nitrogen and carbon to maintain high biomass. A positive correlation between fungal feeding soil organisms and amount of fungal mycelium was found while a more complex situation prevailed with regard to bacterial numbers and bacterial feeding nematodes. The systems are evaluated in relation to the different treatments and compared with the field situation. (Less)
EFFECTIVENESS OF A RECOMBINANT VACCINE BASED ON RNA2 CAPSID PROTEIN AGAINST NERVOUS NECROSIS VIRUS IN HYBRID GROUPER

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Nervous Necrosis Virus (NNV) is a devastating viral disease in marine aquaculture, causing significant economic losses worldwide, including in Indonesia. The virus mainly infects larvae and juveniles of marine fishes. This study aimed to determine the effectiveness of a recombinant vaccine from betanodavirus coat proteins expressed in Escherichia coli fish against NNV infection in hybrid grouper. An RNA2 capsid protein was selected and used as the recombinant vaccine. NNV-RNA2 gene was inserted into the protein expression system vector of pET SUMO and cloned in cells of bacteria Escherichia coli strain BL-21. The results of blast homology analysis exhibited that the amino acid sequence of the NNV-RNA2 showed high similarity with Lates calcarifer encephalitis viral coat protein gene. E. coli expressing NNV-RNA2 protein was inactivated using 0.03% formalin and mechanically inactivated by freeze-thaw and sonication methods. The inactivated recombinant E. coli vaccine was then injected intramuscularly into hybrid grouper juveniles (single vaccine). Subsequently, the juveniles were challenged with NNV at 7, 14, and 21 dpv (days post-vaccination). Injection of 0.1 mL sterile PBS served as the control. Single vaccine applications using formalin-inactivated vaccines resulted in higher antibody titers than those of mechanically-inactivated vaccines. Both vaccines were only able to increase antibody titer up to 7 dpv. Therefore, re-vaccination (booster vaccine) was done on day-10 after the first vaccination using a formalin-inactivated vaccine. The booster vaccine could protect hybrid grouper against NNV (P 0.05) after challenged with NNV for six weeks after. This recombinant vaccine has the potential to be developed into a polyvalent vaccine by combining viral and other bacterial vaccines in future research.
Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

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

Abstract The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.
Three-dimensional diffuse optical tomography of simulated hand joints with a 64 × 64-channel photodiodes-based optical system

Field: Medicine (Health Sciences)

A continuous-wave (CW) diffuse optical tomography (DOT) system that is specifically designed for three-dimensional (3D) imaging of hand joints is described in this paper. This DOT system consists of eight diode lasers coupled with 64 source optic fibre bundles for light excitations and 64 receiving optic fibre bundles in conjunction with 64 silicon photodiodes for light detection. It has a large dynamic range, high stability and low detective noise equivalent power. In this system, the excitation and detection fibre bundles are arranged in four layers each with 16 excitation and 16 detection fibre bundles, forming a cylindrical imaging volume where an inserted finger is supported by a solid coupling medium. A series of tissue-mimicking experiments have been conducted to evaluate the system using a simple joint model consisting of two 'bones' and one layer of 'cartilage'. These experiments also serve to identify optimal experimental and computational configurations for hand joint imaging. Coupled with our 3D finite-element based reconstruction algorithm, the phantom results suggest that the supporting/coupling medium with proper absorption and scattering coefficients is one of the key factors for high quality image reconstruction. In addition, these phantom investigations show that an off-centre positioned object can be significantly better imaged than a centre placed object. Studies have also been performed to determine an optimal mesh size for 3D hand joint imaging.
Computational assessment of cardiac pumping function and candidacy for coronary bypass surgery

Field: Medicine (Health Sciences)

The aim of this project is to explore the possibility of using high performance computing technology and modern computational science and engineering to develop a diagnostic system for giving cardiologists an alternative angle of rationality and a quantitative assessment in the diagnosis of cardiovascular diseases. Most cardiologists base their diagnosis of diseases almost exclusively by looking at images of organs such as X-ray or MRI scans etc. Decisions are based on the experience the cardiologists have acquired in their practice. High performance computing offers opportunities to apply computational mechanics to provide quantitative estimates based on the same very images the cardiologists use to make their decisions. In this report the development of one possible diagnostic system which will form one of the many possible tools for total Non-Invasive Cardiovascular Diagnostics Technology (NCDT) is described.
New test for thyrotoxicosis?

Field: Medicine (Health Sciences)

New Test for Thyrotoxicosis?In most patients with thyrotoxicosis the diagnosis can be made on clinical grounds alone.'In almost all the remaining patients in whom the diagnosis is more difficult the results of radioiodine (13'I) studies and determinations of proteinbound stable iodine (P.B.1271I) in the serum are adequate guides to the diagnosis.These considerations are rather less true, however, when thyrotoxicosis is suspected during pregnancy.In normal pregnancy complaints of tiredness, palpitation, dyspnoea, and intolerance to heat are not uncommon, and when these symptoms are associated with hot, moist hands, tachycardia,
%22Trojan Horse%22 strategy for deconstruction of biomass for biofuels production.

Field: Agricultural and Biological Sciences (Life Sciences)

Production of renewable biofuels to displace fossil fuels currently consumed in the transportation sector is a pressing multiagency national priority (DOE/USDA/EERE). Currently, nearly all fuel ethanol is produced from corn-derived starch. Dedicated 'energy crops' and agricultural waste are preferred long-term solutions for renewable, cheap, and globally available biofuels as they avoid some of the market pressures and secondary greenhouse gas emission challenges currently facing corn ethanol. These sources of lignocellulosic biomass are converted to fermentable sugars using a variety of chemical and thermochemical pretreatments, which disrupt cellulose and lignin cross-links, allowing exogenously added recombinant microbial enzymes to more efficiently hydrolyze the cellulose for 'deconstruction' into glucose. This process is plagued with inefficiencies, primarily due to the recalcitrance of cellulosic biomass, mass transfer issues during deconstruction, and low activity of recombinant deconstruction enzymes. Costs are also high due to the requirement for enzymes and reagents, and energy-intensive cumbersome pretreatment steps. One potential solution to these problems is found in synthetic biology-engineered plants that self-produce a suite of cellulase enzymes. Deconstruction can then be integrated into a one-step process, thereby increasing efficiency (cellulose-cellulase mass-transfer rates) and reducing costs. The unique aspects of our approach are the rationally engineered enzymes which become Trojan horses during pretreatment conditions. During this study we rationally engineered Cazy enzymes and then integrated them into plant cells by multiple transformation techniques. The regenerated plants were assayed for first expression of these messages and then for the resulting proteins. The plants were then subjected to consolidated bioprocessing and characterized in detail. Our results and possible implications of this work on developing dedicated energy crops and their advantage in a consolidated bioprocessing system.
The New Insulins—Lente, Ultralente, and Semilente

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

I8 20 22 24 DAYS OF TREATMENT FIG.2.-Fasting and noon blood sugars, glycosuria, ketosis, and dosage of lente insulin in a male patient aged 40.New case; control good.There have been remarkably few hypoglycaemic reac- tions either in the in-patients or in the out-patients.Such reactions as have occurred have been quite typical and relatively mild, except in one or two instances in which the dose given has been clearly too large and had to be greatly reduced.Reactions have been observed at 10 a.m., three hours after injection, and at noon in the same patient, but not on the same day.The commonest times at which patients on lente insulin before breakfast are liable to have hypoglycaemic reactions appear to be during the morning or afternoon.Nocturnal reactions are uncommon in our experience, and hypoglvcaemia rarely occurs in the early hours of the morning.
The Role of Artificial Intelligence in Exercise-Based Cardiovascular Health Interventions: A Scoping Review

Field: Medicine (Health Sciences)

Background: As cardiovascular medicine advances rapidly, the integration of artificial intelligence (AI) has garnered increasing attention. Despite its growing application across various domains, the role of AI in exercise-based interventions remains relatively underexplored, offering a novel and promising direction for future research. Objective: This scoping review aimed to identify and analyse original studies that have applied AI to exercise-based interventions designed to improve cardiovascular outcomes. Methods: Following the PRISMA-ScR guidelines, PubMed, Scopus, Web of Science, Embase, and IEEE Xplore were searched for articles published between January 2015 and August 2025. Eligible studies were peer-reviewed human research employing AI (machine learning or deep learning) to deliver, adapt, or monitor an exercise intervention with cardiovascular outcomes. Reviews, diagnostic-only studies, protocols without data, and animal studies were excluded. Data extraction focused on study design, AI method, exercise modality, outcomes, and findings. Results: From 2,183 records, 11 studies met the inclusion criteria. Designs included feasibility pilots, randomized controlled trials (RCTs), and validation studies. AI applications encompassed adaptive step goals, reinforcement learning for engagement, coaching apps, machine learning–based exercise prescription, and continuous monitoring (e.g., VO₂ estimation). These AI methods, such as machine learning and reinforcement learning, were used to personalize exercise interventions and improve cardiovascular outcomes. Reported outcomes included blood pressure reduction, improved adherence, increased daily steps, improvement in VO₂max, continuous physiological monitoring, and enhanced diagnostic accuracy. Conclusions: Although evidence remains limited, findings demonstrate AI’s potential to personal exercise interventions, enable continuous monitoring, and enhance adherence in cardiovascular care. These findings suggest that AI could be a valuable tool in the development of more effective and personalized exercise-based interventions. However, large-scale RCTs, methodological standardization, and explainable AI approaches are urgently needed to ensure reliability, equity, and clinical translation. These future research directions are crucial for the successful integration of AI in cardiovascular care.
IGFBP2 is a Potential Master-Regulator Driving Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme

Field: Medicine (Health Sciences)

Only two percent of Glioblastoma multiforme (GBM) patients respond to standard care and survive beyond 36 months (long-term survivors, LTS) while the majority survives less than 12 months (short-term survivors, STS). To understand the mechanism leading to poor survival, we analyzed publicly available datasets of 113 STS and 58 LTS. This analysis revealed 198 differentially expressed genes (DEGs) that co-occur with aggressive tumor growth and may be responsible for the poor prognosis. These genes belong largely to the GO-categories &ldquo;epithelial to mesenchymal transition&rdquo; and &ldquo;response to hypoxia&rdquo;. In this paper we applied upstream analysis approach which involves state-of-art promoter analysis and network analysis of the dysregulated genes potentially responsible for short survival in GBM. Transcription factors associated with GBM pathology like NANOG, NF-&kappa;B, REST, FRA-1, PPARG and seven others were found enriched in regulatory regions of the dysregulated genes. Based on network analysis, we propose novel gene regulatory network regulated by five master regulators &ndash; IGFBP2, VEGFA, VEGF165, PDGFA, AEBP1 and OSMR which can potentially act as therapeutic targets for enhancing GBM prognosis. Critical analysis of this gene regulatory network gives insights on mechanism of gene regulation by IGFBP2 via several transcription factors including the key molecule of GBM tumor invasiveness and progression FRA-1. All the observations are validated in independent cohorts and their impact on overall is studied on TCGA-GBM RNA seq data.
Histologic Evaluation and Treatment Outcome after Sequential Radiofrequency Ablation and Hepatic Resection for Primary and Metastatic Tumors

Field: Medicine (Health Sciences)

Operative manipulation during hepatic resection (HR) causes tumor cell shedding which is a factor in disease recurrence. Radiofrequency ablation (RFA) causes coagulative necrosis and was used to destroy the tumor before HR. We evaluated tumor necrosis and recurrence of hepatic malignancies treated by sequential RFA/HR. A retrospective review of patients treated with sequential RFA/HR from April 1999 to January 2002 was performed. A Radionics 500-kW RF generator was used to ablate lesions via H 2 O-cooled electrodes under ultrasound guidance. Segmental HR was performed after RFA. Resected specimens were reviewed with hematoxylin and eosin staining and for apoptosis. Patient follow-up ranged from 10 to 33 months with evaluation of salient clinical, radiologic, and laboratory parameters. Seven patients (four male and three female) ages 62.1 ± 10.3 years had sequential RFA/HR. Four patients had hepatocellular carcinoma (HCC) and three had colorectal metastases (CRm). The tumors were unifocal right-lobe lesions measuring 4.1 ± 0.9 cm with a resection margin of 0.4 to 2.5 cm. Extensive necrosis was noted but intact nests of tumor cells occurred in all specimens with minimal apoptosis. Three of seven patients (two HCC and one CRm) developed pulmonary metastases at 3 to 20 months with one HCC patient developing concurrent liver metastases. Two deaths occurred in the HCC group. Sequential RFA/HR may minimize local recurrence; however, the high incidence of pulmonary metastases raises concern of transvenous migration. The histologic findings demonstrate foci of intact tumor cells after RFA. Controlled study of additional patients with long-term follow-up is necessary to better understand these findings.
The time course of morphological processing in a second language

Field: Psychology (Social Sciences)

We report findings from psycholinguistic experiments investigating the detailed timing of processing morphologically complex words by proficient adult second (L2) language learners of English in comparison to adult native (L1) speakers of English. The first study employed the masked priming technique to investigate - ed forms with a group of advanced Arabic-speaking learners of English. The results replicate previously found L1/L2 differences in morphological priming, even though in the present experiment an extra temporal delay was offered after the presentation of the prime words. The second study examined the timing of constraints against inflected forms inside derived words in English using the eye-movement monitoring technique and an additional acceptability judgment task with highly advanced Dutch L2 learners of English in comparison to adult L1 English controls. Whilst offline the L2 learners performed native-like, the eye-movement data showed that their online processing was not affected by the morphological constraint against regular plurals inside derived words in the same way as in native speakers. Taken together, these findings indicate that L2 learners are not just slower than native speakers in processing morphologically complex words, but that the L2 comprehension system employs real-time grammatical analysis (in this case, morphological information) less than the L1 system.
HYPERDATA - BASIC HYPERSONIC DATA AND EQUATIONS

Field: Engineering (Physical Sciences)

In an effort to place payloads into orbit at the lowest possible costs, the use of air-breathing space-planes, which reduces the need to carry the propulsion system oxidizer, has been examined. As this approach would require the space-plane to fly at hypersonic speeds for periods of time much greater than that required by rockets, many factors must be considered when analyzing its benefits. The Basic Hypersonic Data and Equations spreadsheet provides data gained from three analyses of a space-plane's performance. The equations used to perform the analyses are derived from Newton's second law of physics (i.e. force equals mass times acceleration); the derivation is included. The first analysis is a parametric study of some basic factors affecting the ability of a space-plane to reach orbit. This step calculates the fraction of fuel mass to the total mass of the space-plane at takeoff. The user is able to vary the altitude, the heating value of the fuel, the orbital gravity, and orbital velocity. The second analysis calculates the thickness of a spherical fuel tank, while assuming all of the mass of the vehicle went into the tank's shell. This provides a first order analysis of how much material results from a design where the fuel represents a large portion of the total vehicle mass. In this step, the user is allowed to vary the values for gross weight, material density, and fuel density. The third analysis produces a ratio of gallons of fuel per total mass for various aircraft. It shows that the volume of fuel required by the space-plane relative to the total mass is much larger for a liquid hydrogen space-plane than any other vehicle made. This program is a spreadsheet for use on Macintosh series computers running Microsoft Excel 3.0. The standard distribution medium for this package is a 3.5 inch 800K Macintosh format diskette. Documentation is included in the price of the program. Macintosh is a registered trademark of Apple Computer, Inc. Microsoft is a registered trademark of Microsoft Corporation.
Platelets and the Environment

Field: Medicine (Health Sciences)

IN THE past two decades, a body of evidence has accumulated to suggest that the formed elements of the blood may play roles in a variety of disease states other than those usually considered to be hematologic diseases. Thus, a role for the platelet in atherogenesis has become accepted,1and the concept has prompted large clinical trials of antiplatelet agents for secondary prophylaxis in myocardial infarction and stroke2-9; evidence for a similar role for granulocytes and monocytes is beginning to unfold.10-14At the same time, another body of evidence has accumulated that links environmental effects to disease states, in many cases the same disease states for which a role of the formed elements of the blood has been shown. Thus, behavioral factors, lipid and sodium content of the diet, smoking, work load, pollutant exposure, and and personality type have all attracted attention for possible association with atherosclerosis.