jimnoneill/paper-to-field-training huggingface dataset:
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions

Glycosaminoglycans (GAGs) are negatively charged polysaccharides found on cell surfaces, where they regulate transport pathways of foreign molecules toward the cell. The structural and functional diversity of GAGs is largely attributed to varied sulfation patterns along the polymer chains, which makes understanding their molecular recognition mechanisms crucial. Molecular dynamics (MD) simulations, thanks to their unmatched microscopic resolution, have the potential to be a reference tool for exploring the patterns responsible for biologically relevant interactions. However, the capability of molecular dynamics force fields used in biosimulations to accurately capture sulfation-specific interactions is not well established, partly due to the intrinsic properties of GAGs that pose challenges for most experimental techniques. In this work, we evaluate the performance of molecular dynamics force fields for sulfated GAGs by studying ion pairing of Ca<sup>2+</sup> to sulfated moieties─<i>N</i>-methylsulfamate and methylsulfate─that resemble N- and O-sulfation found in GAGs, respectively. We tested available nonpolarizable (CHARMM36 and GLYCAM06) and explicitly polarizable (Drude and AMOEBA) force fields, and derived new implicitly polarizable models through charge scaling (prosECCo75 and GLYCAM-ECC75) that are consistent with our developed "charge-scaling" framework. The calcium-sulfamate/sulfate interaction free energy profiles obtained with the tested force fields were compared against reference ab initio molecular dynamics (AIMD) simulations, which serve as a robust alternative to experiments. AIMD simulations indicate that the preferential Ca<sup>2+</sup> binding mode to sulfated GAG groups is solvent-shared pairing. Only our scaled-charge models agree satisfactorily with the AIMD data, while all other force fields exhibit poorer agreement, sometimes even qualitatively. Surprisingly, even explicitly polarizable force fields display a notable disagreement with the AIMD data, likely attributed to difficulties in their optimization and possible inherent limitations in depicting high-charge-density ion interactions accurately. Finally, the underperforming force fields lead to unrealistic aggregation of sulfated saccharides, which qualitatively disagrees with our understanding of the soft glycocalyx environment. Our results highlight the importance of accurately treating electronic polarization in MD simulations of sulfated GAGs and caution against over-reliance on currently available models without thorough validation and optimization.

Topic: Proteoglycans and glycosaminoglycans research
Subfield: Cell Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Wavelength dependence of polarisation mode dispersion in elliptical-core single-mode fibres

Polarisation mode dispersion in elliptical-core single-mode fibres has been measured by a spatial technique based on a visibility maximum position measurement in an interferometer. Using the technique, wavelength dependence of the modal dispersion has been measured by varying optical source wavelengths between 821 and 904 nm. As a result, contribution of geometrical and strain birefringences on the modal dispersion has been evaluated, and normalised frequency dependence of the modal dispersion has been clarified.

Topic: Advanced Fiber Optic Sensors
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Isolation of Mycosporine-like Amino Acids from Red Macroalgae and a Marine Lichen by High-Performance Countercurrent Chromatography: A Strategy to Obtain Biological UV-Filters

Marine organisms have gained considerable biotechnological interest in recent years due to their wide variety of bioactive compounds with potential applications. Mycosporine-like amino acids (MAAs) are UV-absorbing secondary metabolites with antioxidant and photoprotective capacity, mainly found in organisms living under stress conditions (e.g., cyanobacteria, red algae, or lichens). In this work, five MAAs were isolated from two red macroalgae (Pyropia columbina and Gelidium corneum) and one marine lichen (Lichina pygmaea) by high-performance countercurrent chromatography (HPCCC). The selected biphasic solvent system consisted of ethanol, acetonitrile, saturated ammonium sulphate solution, and water (1:1:0.5:1; v:v:v:v). The HPCCC process for P. columbina and G. corneum consisted of eight separation cycles (1 g and 200 mg of extract per cycle, respectively), whereas three cycles were performed for of L. pygmaea (1.2 g extract per cycle). The separation process resulted in fractions enriched with palythine (2.3 mg), asterina-330 (3.3 mg), shinorine (14.8 mg), porphyra-334 (203.5 mg) and mycosporine-serinol (46.6 mg), which were subsequently desalted by using precipitation with methanol and permeation on a Sephadex G-10 column. Target molecules were identified by HPLC, MS, and NMR.

Topic: Biocrusts and Microbial Ecology
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
A LIPID REQUIREMENT FOR INDUCTION OF LACTOSE TRANSPORT IN <i>Escherichia coli</i>

The rate of derepressed synthesis of a membrane protein required for lactose transport (M protein) by Escherichia coli is increased in response to increased gene dosage to the same extent as the rates of synthesis of β-galactosidase and galactoside acetylase. However, elevated gene dosage does not increase β-galactoside transport to the same extent that it increases synthesis of M protein and of the soluble proteins of the lac operon. Though the factor or factors other than M protein which limit induction of the transport system at high levels of lac operon expression have not been identified, studies with Escherichia coli mutants blocked in the synthesis of unsaturated fatty acids indicate that unsaturated fatty acids must be supplied during the course of induction of the lac operon to permit synthesis of a functional lactose transport system, but not of β-galactosidase or galactoside acetylase.

Topic: Amino Acid Enzymes and Metabolism
Subfield: Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Detection and evaluation of activation instances as change points in functional MR images

Change point analysis is an efficient method for understanding the unexpected behavior of the data used in many different disciplines including medical imaging. It is important to find the instances the activations occur as much as finding the activation areas in the analysis of functional magnetic resonance imaging (fMRI). Change point detection algorithms can be used to find the activation instances. In this study, a regression based point detection method is proposed to find the activation instances in fMRI experiments. The proposed method is applied to a fMRI experiment which includes a motor task. A linear based evaluation method is also proposed. The analyses show that the activations are in accordance with the established methods in the literature.

Topic: Functional Brain Connectivity Studies
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Study the Bacterial Activity Isolated from Colon and Rectal Cancer Biopsy in Cell Lines Culture

Colorectal cancer (CRC) is the most common disease and cause of death globally. The aim of the study is investigation and detection of some bacterial interfering with CRC occurrence and progression. The study conducted between September 2022 till February 2023, a total of 50 specimens were collected from confirmed CRC patients. In addition, 50 stool specimens were collected from Healthy volunteers, considers as control group. Isolation and identification of bacteria in all collected specimens were done by using cultural and differential media (blood agar, macconkey agar and Pfizer agar), as well as the VITEK- 2 compact system. The bacterial species, in the specimens of control were ( Escherichia coli 50 (86.20%), Klebsiella Pneumonia 3(5.17%), Salmonella typhi 2(3.44%), Staphylococcus aureus 1(1.72%), Proteus mirabilis 1(1.72%) and Pseudomonas aeruginosa 1(1.72%), while in the specimens of CRC and polyp were (Escherichia coli 30(38.69%), Streptococcus uberis 6(7.79%), Enterobacter cloacae 4(5.19%), Proteus mirabilis 11(14.28), Streptococcus constellatus pharyneis 1(1.29%), Micrococcus luteus 1(1.29%), Staphlococcus pseudintermedius 1(1.29%), Streptococcus thoraltensis 1(1.29%), Citrobacter freundii 1(1.29%), Streptoccus mutans 1(1.29%), Enterococcus faecium 5(6.49%), Enterococcus faecalis 4(5.19%), Granulicatella elegans 1(1.29%), Enterococcus gallinarum 2(2.59%), Serratia marcescens 1(1.29%), Streptococcus sangunis 1(1.29%), Staphylococcus lentus 1(1.29%), Comamons testosteroni 1(1.29%), Morganella morganii 1(1.29%), Pseudomonas aeruginosa 1(1.29%), Klebsiella pneumonia 2(2.59%). The bacteria which has been shown to be associated and more abundance in the specimens of CRC tissues are Escherichia.coli 30(38.96%), Streptococcus uberis 6(7.79%), Enterobacter cloacae 4(5.19%), Enterococcus faecium 5(6.49%), Enterococcus faecalis 4(5.19%). Cell-line culture techniques for the five species showed a cellular viability, sequentially Streptocccus uberis (16.12%), Enterococcus faecium (16.39%), Entreococcus faecalis (9.48%), Enterobacter cloacae (15.11%) and Escherichia coli (17.61%). The results statistically studied by using SPSS, which showed excellent or (highly) significant (p-value is in the range of 0.001).

Topic: Gut microbiota and health
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
The Anatomy of the Earthworm

ABSTRACT In the last number of this Journal the tegumentary, muscular, and digestive organs of the earthworm were briefly described, the form and structure of certain œsophageal appendages being more particularly noticed. The following pages will be devoted to the consideration of the Reproductive system, and of such secreting organs as are not of necessity connected either with it or the digestive system.

Topic: Invertebrate Taxonomy and Ecology
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
EBV-Positive Diffuse Large B-Cell Lymphoma of the Elderly - A New Provisional Entity of Lymphoma in the WHO Classification

Epstein-Barr virus (EBV) positive diffuse large B-cell lymphoma (DLBCL) of the elderly, initially described in 2003, is a provisional entity in the 2008 World Health Organization classification system, and is defined as an EBV-positive monoclonal large B-cell proliferation that occurs in patients&amp;gt; 50 years of age and in whom there is no known immunodeficiency or history of lymphoma. These tumors are more common in Asia, but also occur in North America and Europe at a low frequency. These neoplasms exhibit a morphologic continuum, from polymorphous to monomorphous, but morphologic features do not correlate with prognosis as all patients have a clinically aggressive course. Most EBV-positive DLBCL of the elderly patients have an activated B-cell immunophenotype and are characterized by prominent NF-κB activation. Cytogenetic complexity is usually low. In this review, we comprehensively delineate the data emerging from analyses of EBV latency program, microRNA-mediated EBV viral oncogenesis, functional genomics of EBV and its biology, as well as differential diagnosis challenge for EBV-positive DLBCL of the elderly. It is hoped that the improved understanding of these tumors will lead to development of novel therapeutic approaches, enhance the effective clinical trials and improve the prognosis.

Topic: Lymphoma Diagnosis and Treatment
Subfield: Pathology and Forensic Medicine
Field: Medicine
Domain: Health Sciences
HIP PROSTHESIS RESURFACING: MECHANICAL CONSEQUENCES OF FEMORAL IMPLANT POSITIONING

Purpose of the study: Hip resurfacing with a metal-on-metal bearing gives good mid-term clinical results. The design of the femoral piece has an effect on implant longevity, as does the vitality of the underlying cephalic bone. Computer-assisted surgery has been helpful in position the implant but the choice of the best position is still empirical. Prosthesis designers recommend valgus, but with too much there is a risk of a superolaterl notch which would weaken the neck. This leads the surgeon to use a larger femoral implant, and consequently to resect more acetabular bone. Anteversion is not evaluated. The purpose of this study was test mechanically different valgus/varus, anteversion/retroversion positions of the femoral implant. Material and methods: We implanted 15 femurs made of resin which were geometrically and mechanically identical. The following angles were tested: varus/valgus (−10°, neutral, +10°, +20°) and ante/retroversion (−10°, neutram, +10). A valgus notch (+20° and +10°) and a varus notch (−10°) were simulated. The femurs thus prepared were tested with Instron 8874. Load at failure was noted as well as the type of fracture: distance from the fracture line to the greater trochanter (FGT). Student’s t test was applied. Results: All of the femurs fractured at the neck. The fracture was closer to the implant (FGT: 11.0 mm) for the 20° valgus implantation (p Discussion: This study, unlike clinical studies, did not demonstrate any static mechanical superiority of the valgus position for the femoral piece. Another study on cadaver bones is planned for confirmation. Clinical studies reflect the vitality of the trabecular bone supporting the implant, a vitality which could be stimulated by the valgus position.

Topic: Orthopaedic implants and arthroplasty
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Metopes and architecture: the Hephaisteion and the Parthenon

The relationship of the metopes to the architecture of the peristasis of the Hephaisteion and the Parthenon is examined in order to ascertain the extent of planning which took place before the erection of a Classical Greek temple. All relevant published measurements are taken into consideration and critically compared. On the basis of the discrepancies of the corresponding architectural and sculptural members, it is argued that the working-out of the details of the plan was not the result of large-scale drawings, but was affected after the commencement of construction. While the Hephaisteion is built largely in accordance with the conventions of a Classical Doric temple, the Parthenon, due to its unique plan, provides indications of experimentation inferred from the extensive inconsistencies at its eastern end.

Topic: Classical Antiquity Studies
Subfield: Anthropology
Field: Social Sciences
Domain: Social Sciences
Cornerstones of ‘fair’ drug coverage: appropriate cost sharing and utilization management policies for pharmaceuticals

At the heart of all health insurance programs lies ethical tension between maximizing the freedom of patients and clinicians to tailor care for the individual and the need to make healthcare affordable. Nowhere is this tension more fiercely debated than in benefit design and coverage policy for pharmaceuticals. This paper focuses on three areas over which there is the most controversy about how to judge whether drug coverage is appropriate: cost-sharing provisions, clinical eligibility criteria, and economic-step therapy and required switching. In each of these domains we present ‘ethical goals for access’ followed by a series of ‘fair design criteria’ that can be used by stakeholders to drive more transparent and accountable drug coverage.

Topic: Health Systems, Economic Evaluations, Quality of Life
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Antioxidant and Anti-Inflammatory Activity of a New Formulation of Slow-Release Amino Acids in Human Intestinal Caco-2 Cells

Phenylalanine (Phe)-free protein substitutes (PSs) are used to provide an adequate intake of amino acids (AAs), except Phe, allowing control of blood Phe levels in patients with Phenylketonuria (PKU). Although indicated as a standard dietary treatment for these patients, free AAs mixtures are not absorbed as natural proteins, thus creating an oxidized and inflamed state in the intestine. Nowadays, PSs on the market also include slow-release amino acids (SR-AAs) formulas. The present work aims to investigate the effects of an SR-AAs formula on both oxidative and inflammatory status in human intestinal Caco-2 cells, comparing its mechanism of action with that of a mixture of free AAs. In more detail, oxidative stress and inflammation were induced at the cellular level using H2O2 and lipopolysaccharides (LPSs), respectively, and both free AAs and SR-AAs PSs were tested to evaluate if they were able to restore a more balanced condition. According to our findings, free AAs aggravate the intestinal oxidative and inflammatory status caused by H2O2 and LPS in human intestinal Caco-2 cells, which SR-AAs significantly improve. In conclusion, our results offer preclinical novelty on these products’ mechanisms of action, thus improving the dietary management of patients with PKU.

Topic: Metabolism and Genetic Disorders
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
OsGGC2, Gγ Subunit of Heterotrimeric G Protein, Regulates Plant Height by Functionally Overlapping with DEP1 in Rice

Plant heterotrimeric G proteins have been shown to regulate the size of various organs. There are three types of Gγ subunits in plants: type A, consisting of a canonical Gγ domain; type B, possessing a plant-specific domain at the N-terminus of the Gγ domain; and type C, possessing a plant-specific domain at the C-terminal of the Gγ domain. There is one type A, one type B, and three type C of the five γ-subunits in the rice genome. In type C Gγ subunits, GS3, which controls grain size; DEP1, which controls plant height and panicle branching; and their homolog OsGGC2, which affects grain size, have been reported; however, the function of each gene, their interactions, and molecular mechanisms for the control of plant height have not yet been clarified. In this study, we generated loss-of-function mutants of DEP1 and OsGGC2, which have high homology and similar expression, and investigated their phenotypes. Since both dep1 and osggc2 mutants were dwarfed and the double mutants showed a synergistic phenotype, we concluded that both DEP1 and OsGGC2 are positive regulators of plant height and that their functions are redundant.

Topic: Genetic Mapping and Diversity in Plants and Animals
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Actin Depolymerization Affects Stress-Induced Translational Activity of Potato Tuber Tissue1

Abstract Changes in polymerized actin during stress conditions were correlated with potato (Solanum tuberosum L.) tuber protein synthesis. Fluorescence microscopy and immunoblot analyses indicated that filamentous actin was nearly undetectable in mature, quiescent aerobic tubers. Mechanical wounding of postharvest tubers resulted in a localized increase of polymerized actin, and microfilament bundles were visible in cells of the wounded periderm within 12 h after wounding. During this same period translational activity increased 8-fold. By contrast, low-oxygen stress caused rapid reduction of polymerized actin coincident with acute inhibition of protein synthesis. Treatment of aerobic tubers with cytochalasin D, an agent that disrupts actin filaments, reduced wound-induced protein synthesis in vivo. This effect was not observed when colchicine, an agent that depolymerizes microtubules, was used. Neither of these drugs had a significant effect in vitro on run-off translation of isolated polysomes. However, cytochalasin D did reduce translational competence in vitro of a crude cellular fraction containing both polysomes and cytoskeletal elements. These results demonstrate the dependence of wound-induced protein synthesis on the integrity of microfilaments and suggest that the dynamics of the actin cytoskeleton may affect translational activity during stress conditions.

Topic: Plant Surface Properties and Treatments
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
CCDC 127085: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Lactobacillus plantarum PFM 105 Promotes Intestinal Development Through Modulation of Gut Microbiota in Weaning Piglets

Lactobacillus plantarum is a widespread bacterial species and is commonly used as a probiotic. L. plantarum PFM105 was isolated from the rectum of a healthy sow. Here we found that L. plantarum PFM105 showed probiotic effect on weaning piglets in which intestinal inflammation and unbalanced gut microbiota happened frequently. L. plantarum PFM105 was identified to improve the growth of weaning piglet and promote the development of small intestinal villi. Antibiotics are often used in weaning piglet to prevent intestinal infection and promote the growth of animal. We found that weaning piglets feeding with L. plantarum PFM105 showed similar growth promotion but decreased diarrhea incidence compared with those feeding with antibiotics. High-throughput sequencing was used to analyze the gut microbiota in weaning piglets treated with L. plantarum PFM105 or antibiotics. The relative abundance of beneficial microbes Prevotellaceae and Bifidobacteriaceae were increased in colon of weaning piglet feeding L. plantarum PFM105, while antibiotics increased the relative abundance of bacteria associated with pathogenicity, such as Spirochaeta and Campylobacteraceae. L. plantarum PFM 105 increased indicators of intestinal health including serum levels of IgM, IL-10, and TGF-β, and colonic levels of SCFAs. We found strong correlations between the alterations in gut microbiota composition caused by feeding antibiotics and probiotics and the measured growth and health parameters in weaning piglets. The addition of L. plantarum PFM105 could significantly increase the relative abundance of metabolic genes which may important to intestinal microbiota maturation. Altogether, we demonstrated here that L. plantarum PFM 105 could promote intestinal development through modulation of gut microbiota in weaning piglets.

Topic: Gut microbiota and health
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences