jimnoneill/paper-to-field-training huggingface dataset:
Proteomic Insights of Cowpea Response to Combined Biotic and Abiotic Stresses

Field: Agricultural and Biological Sciences (Life Sciences)

The co-occurrence of biotic and abiotic stresses in agricultural areas severely affects crop performance and productivity. Drought is one of the most adverse environmental stresses, and its association with root-knot nematodes further limits the development of several economically important crops, such as cowpea. Plant responses to combined stresses are complex and require novel adaptive mechanisms through the induction of specific biotic and abiotic signaling pathways. Therefore, the present work aimed to identify proteins involved in the resistance of cowpea to nematode and drought stresses individually and combined. We used the genotype CE 31, which is resistant to the root-knot nematode Meloidogyne spp. And tolerant to drought. Three biological replicates of roots and shoots were submitted to protein extraction, and the peptides were evaluated by LC-MS/MS. Shotgun proteomics revealed 2345 proteins, of which 1040 were differentially abundant. Proteins involved in essential biological processes, such as transcriptional regulation, cell signaling, oxidative processes, and photosynthesis, were identified. However, the main defense strategies in cowpea against cross-stress are focused on the regulation of hormonal signaling, the intense production of pathogenesis-related proteins, and the downregulation of photosynthetic activity. These are key processes that can culminate in the adaptation of cowpea challenged by multiple stresses. Furthermore, the candidate proteins identified in this study will strongly contribute to cowpea genetic improvement programs.
Decoding cancer prognosis with deep learning: the ASD-cancer framework for tumor microenvironment analysis

Field: Computer Science (Physical Sciences)

ABSTRACT Deep learning is revolutionizing biomedical research by facilitating the integration of multi-omics data sets while bridging classical bioinformatics with existing knowledge. Building on this powerful potential, Zhang et al. proposed a semi-supervised learning framework called Autoencoder-Based Subtypes Detector for Cancer (ASD-cancer) to improve the multi-omics data analysis (H. Zhang, X. Xiong, M. Cheng, et al., 2024, mSystems 9:e01395-24, https://doi.org/10.1128/msystems.01395-24 ). By utilizing autoencoders pre-trained on The Cancer Genome Atlas data, the ASD-cancer framework outperforms the baseline model. This approach also makes the framework scalable, enabling it to process new data sets through transfer learning without retraining. This commentary explores the methodological innovations and scalability of ASD-cancer while suggesting future directions, such as the incorporation of additional data layers and the development of adaptive AI models through continuous learning. Notably, integrating large language models into ASD-cancer could enhance its interpretability, providing more profound insights into oncological research and increasing its influence in cancer subtyping and further analysis.
Gastric Fluid Volume and pH after Fentanyl, Enflurane, or Halothane-Nitrous Oxide Anesthesia with or without Atropine or Glycopyrrolate

Field: Medicine (Health Sciences)

Gastric fluid volume and pH were determined immediately following the induction of anesthesia and again after 2 hours of anesthesia consisting of 60% nitrous oxide plus either fentanyl, enflurane, or halothane. Adult patients undergoing elective, but not upper abdominal, operations were subjects for this study. Preanesthetic medication included intramuscular morphine with or without either atropine (0.4 mg) or glycopyrrolate (0.2 mg). Gastric fluid volume after 2 hours of anesthesia was significantly less (p < 0.05) than immediately after induction of anesthesia. Gastric volume was similar for all anesthetics and was not influenced by the inclusion of anticholinergic drugs in the preanesthetic medication. Compared with control gastric pH (only patients with an initial pH less than 3.5 were studied) there was no change in pH after 2 hours of fentanyl anesthesia with or without either atropine or glycopyrrolate. Likewise, pH did not change during halothane anesthesia without anticholinergic drugs. Enflurane anesthesia with or without anticholinergic drugs and halothane combined with atropine or glycopyrrolate were associated with significant increases (p < 0.05) in gastric pH. Glycopyrrolate was associated with greater increases in pH than was atropine (p < 0.05). These data suggest that gastric fluid production is minimal during anesthesia irrespective of anesthetic drugs or preanesthetic medication. Halothane or enflurane, but not fentanyl, when combined with glycopyrrolate preanesthetic medication was associated with the greatest increase in gastric pH. However, the increased pH was not seen in all patients and often the increase was not sufficiently great to protect against pneumonitis should aspiration have occurred.
Automating Quality Analysis: Toward a New Paradigm in Ink and Toner Assessment

Field: Engineering (Physical Sciences)

As a major distributor of parts and consumables for ink and toner based imaging systems, assessment of source materials is a priority in vendor selection, qualification and on-going quality control. The sheer volume of prints necessary for comprehensive analysis is prohibitive when it comes to manual measurement or visual inspection.In order to provide the best quality products and to improve our internal tracking and communication, we have updated our inspection process to include automation of image quality measurement.Working with a test equipment supplier, we have integrated a flatbed scanner-based system into our process that we use in conjunction with specialized color and density measurement equipment to provide a wide range of image quality measurements for both toner and ink based prints.This move toward automated, instrumented analysis has improved the efficiency and repeatability of our inspections, and has enabled us to comply with industry-standard measurement methodology. In addition, the new system has allowed us to increase our throughput while providing us with a wider range of analytical data specific to each printing technology.This paper will detail several of our assessment methods for both toner and ink-based prints, and will discuss the benefits we have achieved as a result of implementing these new processes into our workflow.
Erythromycin derivative made by mutagenesis

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

An erythromycin derivative with increased stability under acidic conditions has been produced by targeted mutagenesis of the genome of Saccharopolyspora erythraea , the organism that naturally produces erythromycin, according to researchers at Abbott Laboratories in North Chicago, Ill. It is well known that genes that encode the enzymes responsible for biosynthesis of a particular antibiotic often cluster together. A team of Abbott scientists led by microbiologist Mark Weber used mutagenesis techniques to disrupt a relatively uncharacterized region of the gene cluster responsible for erythromycin biosynthesis [ Science , 252 , 114 (1991)]. One mutant strain of S. erythraea produced 6–deoxyerythromycin instead of erythromycin. Researchers have been trying to produce this derivative for some time because it should possess significantly improved stability in an acid environment. The 6–hydroxyl group of erythromycin, Weber explains, is involved in the acid–catalyzed decomposition of the antibiotic, a series o...
Matrix Metalloproteinase-9 Deficiency Results in Enhanced Allergen-Induced Airway Inflammation

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

Abstract Matrix metalloproteinases (MMPs) are a large family of endopeptidases that proteolytically degrade extracellular matrix. Many different cells produce MMP-9, and levels have been shown to be up-regulated in patients with allergic asthma. The aim of this study was to investigate the in vivo role of MMP-9 during allergen-induced airway inflammation. Acute allergic pulmonary eosinophilia was established in MMP-9 knockout (KO) and wild-type (WT) control mice by sensitization and challenge with OVA. Cell recruitment was significantly increased in both bronchoalveolar lavage (BAL) and lung tissue compartments in MMP-9 KO mice compared with WT mice. This heightened cell recruitment was primarily due to increased eosinophils and Th2 cells in the BAL and lung tissue of MMP-9 KO mice in comparison with WT controls. Moreover, levels of the Th2 cytokines, IL-4 and IL-13, and the chemokines eotaxin/CCL11 and macrophage-derived chemokine/CCL22 were substantially increased in MMP-9 KO mice compared with WT after OVA challenge. Resolution of eosinophilia was similar between MMP-9 KO and WT mice, but Th2 cells persisted in BAL and lungs of MMP-9 KO mice for longer than in WT mice. Our results indicate that MMP-9 is critically involved in the recruitment of eosinophils and Th2 cells to the lung following allergen challenge, and suggest that MMP-9 plays a role in the development of Th2 responses to allergen.
p-Chlorophenyl Methyl Sulfide, p-Chlorophenyl Methyl Sulfoxide, and p-Chlorophenyl Methyl Sulfone. III. Toxicokinetics and Metabolism in Rats and Rhesus Monkeys

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Pharmacokinetic properties of p-chlorophenyl methyl sulfide, p-chlorophenyl methyl sulfoxide, and p-chlorophenyl methyl sulfone were evaluated in rats and rhesus monkeys following oral administration of 14 C radiolabeled test materials. In addition, urinary metabolite formation in treated rats was partially assessed, as was microsomal enzyme induction as determined by hexobarbital sleep time assays. All test materials were found to be rapidly absorbed following gavage dosing with a biphasic diminution of blood radiolabel in the rat. As an apparent result of higher dosage levels, rhesus monkeys exhibited both a delayed attainment of peak blood levels and a lower rate of elimination of blood 14 C. A minor portion (5–7%) of urinary radioactivity from treated rats was not extractable with chloroform until incubation with deconjugation enzymes was conducted, releasing up to 50%. The values for rhesus monkeys were 15–62% and 50%, respectively; the former values are apparently elevated (relative to rat) due to saturation of conjugate-formation pathways. Decreases were observed for hexobarbital sleep times following 3-day treatment with 50 mg/kg of each of the test compounds and, consistent with hepatomegaly observed in subchronic studies, suggest induction of hepatic microsomal enzymes. The study supports evidence that these chemicals are cleared primarily via the urine in a dose-dependent manner, and are conjugated to water-soluble metabolites in both rats and rhesus monkeys.
[Comparison of three different methods of anesthesia during transrectal ultrasound guided prostate biopsy: a prospective, double-blind, randomized trial.].

Field: Medicine (Health Sciences)

Combination of intraprostatic anesthesia and PNB is effective and safe technique during transrectal ultrasound guided prostate biopsy without increasing the incidence of complications. PNB or PNB plus intrarectal lidocaine gel couldn't significantly reduce pain during biopsy.
Evaluation of Upper Airway Characteristics Using Computational Fluid Dynamics

Field: Medicine (Health Sciences)

Introduction: Obstructive sleep apnea (OSA) involves a disruption of nocturnal respiration due to cessation of airflow. The research objectives were to: 1) determine if upper airway characteristics (minimal cross-sectional area and total volume) change significantly between low risk, healthy non-OSA subjects and OSA subjects during inhalation and exhalation using cone-beam computed tomography (CBCT) imaging, and 2) if pressure (minimum, maximum, and pressure range) changes significantly in steady-state k-ω model computational fluid dynamics (CFD) fluid flow simulations. Materials and Methods: CBCT imaging was collected at both end-inhalation and end-exhalation for 16 low-risk healthy adult non-OSA subjects recruited at the UIC College of Dentistry, Department of Orthodontics and compared to existing CBCT data from 7 OSA subjects. The CBCT images were imported into Dolphin Imaging System (Chatsworth, CA), segmented into stereolithography (STL) files of the naso- and oro- pharyngeal spaces for area and volumetric measurements. Subsequently, 5 non-OSA subject and 5 OSA subject STL models met pre-processing criteria for CFD simulations using ANSYS Fluent Meshing (Canonsburg, PA). An unstructured mesh consisting of hexahedral, tetrahedral, and octagonal cells was generated and the Commercial CFD package Fluent (version R2021) was used to solve the standard dual equation turbulence model (k-ω). Both objective and supplemental descriptive measures were obtained from a combination of imaging, simulations, and questionnaires and subsequent statistical analyses were performed using IBM SPSS with both parametric and nonparametric tests to evaluate statistical significance at 0.05 level. Results/Conclusion: Regarding Dolphin area and volumetric assessments, there were statistically significant mean differences in Total Volume, Minimum CSA between non-OSA and OSA groups at inhalation and exhalation, p-values equal (p=0.002, 0.003, 0.004, and 0.007), respectively. There were statistically significant mean differences in volume and min CSA between the inhalation and exhalation for the non-OSA group, (p<0.001 and 0.002), respectively. Lastly, there was a statistically significant mean difference in total volume pre- and post-OA therapy in OSA subjects on inhalation only (p=0.006). With respect to the CFD simulations, limitations of the CFD simulation method used and the outstanding data available that could not be implemented rendered testing and subsequent results to be inconclusive, requiring further investigation. An observed trend, however, was that the OSA subject group for the CFD simulation featured airway models whose point of lowest pressure coincided with the area of maximum constriction. Further studies of increasing power and increasing accuracy of simulation method in regard to the airway are needed to further characterize the upper airway in order to learn more about its function in ideal conditions and in obstructive sleep apnea.
MENINGKATKAN HASIL BELAJAR IPS MELALUI PENGGUNAAN PEMBELAJARAN SNOWBALL THROWING KELAS VIII SMP NEGERI 2 KECAMATAN KELAYANG KABUPATEN INDRAGIRI HULU

Field: Social Sciences (Social Sciences)

The objectives of this research are: 1) To find out the implementation of teaching activities of teachers by using Snowball Throwing models for eighth grade students of SMPN 1 Kelayang, Indragiri Hulu Regency, 2) To find out the implementation of student activity learning using Snowball Throwing models for VIII grade students of SMPN 1 Kelayang Regency of Indragiri Hulu, 3) To find out the extent of the success of teaching and learning by using Snowball Throwing models in class VIII students of SMPN 1 Kelayang Regency of Indragiri Hulu. This research was conducted in 2 cycles. The subjects in this study were all students of class VIII1 of SMPN 1 Kelayang, Indragiri Hulu Regency, amounting to 33 people. The data analysis technique in this research uses descriptive quantitative. The results showed that student learning outcomes have increased with the average daily cycle repetition is 68.63% and increased on the daily cycle II replications by obtaining an average value of 72.87%. Then it can be concluded that by using the Snowball Throwing model can be the results of learning history subjects of eighth grade students of SMPN 1 Kelayang, Indragiri Hulu Regency.
Photoconductance from the Bent-to-Planar Photocycle between Ground and Excited States in Single-Molecule Junctions

Field: Chemistry (Physical Sciences)

Single-molecule conductance measurements for 9,14-diphenyl-9,14-dihydrodibenzo[a,c]phenazine (DPAC) may offer unique insight into the bent-to-planar photocycle between the ground and excited states. Herein, we employ DPAC derivative DPAC-SMe as the molecular prototype to fabricate single-molecule junctions using the scanning tunneling microscope break junction technique and explore photoconductance dependence on the excited-state structural/electronic changes. We find up to ∼200% conductance enhancement of DPAC-SMe under continuous 340 nm light irradiation than that without irradiation, while photoconductance disappears in the case where structural evolution of the DPAC-SMe is halted through macrocyclization. The in situ conductance modulation as pulsed 340 nm light irradiation is monitored in the DPAC-SMe-based junctions alone, suggesting that the photoconductance of DPAC-SMe stems from photoinduced intramolecular planarization. Theoretical calculations reveal that the photoinduced structural evolution brings about a significant redistribution of the electron cloud density, which leads to the appearance of Fano resonance, resulting in enhanced conductance through the DPAC-SMe-fabricated junctions. This work provides evidence of bent-to-planar photocycle-induced conductance differences at the single-molecule level, offering a tailored approach for tuning the charge transport characteristics of organic photoelectronic devices.
Measurement of a subsystem of a coupled quantum system

Field: Physics and Astronomy (Physical Sciences)

The Stern-Gerlach (SG) apparatus for measuring the spin of an uncharged spin-1/2 particle is the archetypal quantum sensing device. We study this device for the new problem of measuring the spin of a particle that is coupled externally to another particle. Specifically, we treat two coupled particles in which a single particle is measured by the SG device while the other is not. We show simulations of how the binding energy associated with the external coupling is completely converted to potential energy and kinetic energy as the single particle separates spatially within the magnetic field of the SG device. Additionally we show simulations of how the initial particle acceleration within the SG devices relates to the coupling, the quantum state of the two-particle system, and the initial spatial dispersion of the particle within the SG device. The results of our analysis, though obtained specifically for the SG apparatus, may be generic to other quantum measurement devices with similar external coupling.
The industrial organization of an Indian Province

Field: Economics, Econometrics and Finance (Social Sciences)

The paramount question-the one which is of prime importance to the vast majority of the people of civilized lands -is, What makes the rate of wages ?' -' The Distribution of Products,' by Ed.Atkinson.* Those who amuse themselves by the manipulation of conjectural statistics may be interested in the result obtained by comparing Mr. F. J. Atkinson's estimate of the annual income of British India with Mr. Chiozza Money's estimate of the annual income of the United Kingdom.Such a comparison yields this result : Wages of 35s. a week in England represent the same proportion of the national dividend as Rs.7 a month in India.I am inclined to think from personal observation that this is not very far from the truth : the man who earns Rs. 7 a month in India probably does occupy about the same position in the social scale as the artisan who earns 35s. a week in England.The figures for wages in ' Prices and Wages ' are so untrustworthy that no statistical comparison can be made.The figures upon which the above calculation is based are : Population in Millions.
Loss of virus specific epitopes on JE virus 'E' glycoprotein by acetone treatment.

Field: Immunology and Microbiology (Life Sciences)

It seems that the acetone treatment might result in HA property of the antigen which is no longer inhibited by an antibody in the HI test. The characterization of such labile and conformation-dependent epitopes is currently been undertaken to elucidate their role either in protection or immunopathogenesis of JE.
Abstract 174: Na + -H + Exchanger 1 Determines Atherosclerotic Lesion Acidification and Promotes Atherogenesis

Field: Medicine (Health Sciences)

Background: The pH in atherosclerotic lesions varies between individuals. Immunoglobulin E (IgE) activates macrophage Na + -H + exchanger (Nhe1) and induces extracellular acidification and cell apoptosis. Here we examined the function of Nhe1 in human atherosclerotic lesions and in mouse model of diet-induced atherosclerosis. Methods: We crossbred Nhe1-deficient ( Nhe1 +/– ) mice with apolipoprotein E-deficient ( Apoe –/– ) mice and generated Apoe –/– Nhe1 +/– and Apoe –/– Nhe1 +/+ littermates, followed by feeding them an atherogenic diet for 3 months. We used a pH-sensitive fluorescent dye pHrodo-succinimidyl ester (SE) to monitor pH changes in atherosclerotic lesions. We also performed fluorescent molecular tomography-computed tomography (FMT-CT) imaging on Apoe –/– Nhe1 +/– mice and Apoe –/– Nhe1 +/+ mice with pH sensitive probe LS662 to monitor atherosclerotic lesions in live mice. Results: The pH-sensitive pHrodo probe identifies acidic regions in human and murine atherosclerotic lesions that colocalize with macrophages, IgE, and cell apoptosis. In Apoe -/- mice, Nhe1-insufficiency reduces atherosclerosis and blocks lesion acidification in regions rich in macrophages, IgE, and apoptosis. Reduced atherosclerosis in Apoe -/- mice receiving bone-marrows from Nhe1- and IgE receptor FcεR1-deficeint mice, co-immunoprecipitation of Nhe1 and FcεR1 from IgE-treated macrophages, and their colocalization in atherosclerotic lesion macrophages support a role of IgE-mediated macrophage Nhe1 activation in atherosclerosis. Intravenous administration of a near-infrared (NIR) fluorescent pH-sensitive probe LS662, followed by FMT-CT imaging localizes acidic regions in atherosclerotic lesions in live mice. LS662 detects diminished lesion acidity in Nhe1-insufficient mice. Ex vivo pHrodo detection and immunohistochemical analysis following FMT-CT imaging localize acidic regions to areas rich in macrophages, IgE, and cell apoptosis in atherosclerotic lesions. Conclusion: This study tests the role of Nhe1 in reducing atherosclerotic lesion pH and in promoting atherogenesis, and proposes a non-invasive and radiation-free imaging approach to localize and monitor the atherosclerotic lesions in live subjects.
Challenges and Applications of Supramolecular Metalate Chemistry

Field: Chemistry (Physical Sciences)

Abstract While the supramolecular chemistry of simple anions is ubiquitous, the targeting and exploitation of their metal‐containing relatives, the metalates, is less well understood. This mini review highlights the latest advances in this emergent area by discussing the supramolecular chemistry of metalates thematically, with a focus on the exploitation of metalates in a diversity of applications, including medical imaging and therapy, environmental remediation, molecular magnetism, catalysis, perovskite materials, and metal separations. The unifying features of these systems are identified with a view to allow the supramolecular chemist to target the unique material properties of the metalates, even in areas that are currently relatively immature.