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Relevant bibliographies by topics / Matched molecular pairs and series

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Academic literature on the topic 'Matched molecular pairs and series'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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Journal articles on the topic "Matched molecular pairs and series"

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Ding, Xiaoyu, Chen Cui, Dingyan Wang, et al. "Bioactivity Prediction Based on Matched Molecular Pair and Matched Molecular Series Methods." Current Pharmaceutical Design 26, no. 33 (2020): 4195–205. http://dx.doi.org/10.2174/1381612826666200427111309.

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Background: Enhancing a compound’s biological activity is the central task for lead optimization in small molecules drug discovery. However, it is laborious to perform many iterative rounds of compound synthesis and bioactivity tests. To address the issue, it is highly demanding to develop high quality in silico bioactivity prediction approaches, to prioritize such more active compound derivatives and reduce the trial-and-error process. Methods: Two kinds of bioactivity prediction models based on a large-scale structure-activity relationship (SAR) database were constructed. The first one is ba

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Hu, Ye, Antonio de la Vega de León, Bijun Zhang, and Jürgen Bajorath. "Matched molecular pair-based data sets for computer-aided medicinal chemistry." F1000Research 3 (February 4, 2014): 36. http://dx.doi.org/10.12688/f1000research.3-36.v1.

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Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the latest release of the ChEMBL

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Hu, Ye, Antonio de la Vega de León, Bijun Zhang, and Jürgen Bajorath. "Matched molecular pair-based data sets for computer-aided medicinal chemistry." F1000Research 3 (February 21, 2014): 36. http://dx.doi.org/10.12688/f1000research.3-36.v2.

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Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the ChEMBL database (release 17)

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Naveja, José J., and Martin Vogt. "Automatic Identification of Analogue Series from Large Compound Data Sets: Methods and Applications." Molecules 26, no. 17 (2021): 5291. http://dx.doi.org/10.3390/molecules26175291.

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Analogue series play a key role in drug discovery. They arise naturally in lead optimization efforts where analogues are explored based on one or a few core structures. However, it is much harder to accurately identify and extract pairs or series of analogue molecules in large compound databases with no predefined core structures. This methodological review outlines the most common and recent methodological developments to automatically identify analogue series in large libraries. Initial approaches focused on using predefined rules to extract scaffold structures, such as the popular Bemis–Mur

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Kumar, Rahul, Maximilian Deng, Kyle Smith, et al. "PATH-54. MULTI-DIMENSIONAL MOLECULAR CHARACTERIZATION OF PATIENT-MATCHED MEDULLOBLASTOMA AT DIAGNOSIS AND RELAPSE." Neuro-Oncology 21, Supplement_6 (2019): vi155. http://dx.doi.org/10.1093/neuonc/noz175.649.

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Abstract INTRODUCTION Recurrent medulloblastoma (MB) confers an abysmal prognosis with ~10% 5-year overall survival. Optimal treatment paradigms for relapsed disease are largely unknown. Conservation of molecular subgroup at relapse has been described and divergent clonal evolution implicated, yet multi-dimensional molecular characterization of larger cohorts are warranted to substantiate these findings and to disclose potential mechanisms underlying treatment failure and disease recurrence. METHODS A multi-institutional series of 85 patient-matched, primary MBs and their relapses was profiled

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Lorentino, Francesca, Fabio Ciceri, Myriam Labopin, et al. "HLA Disparities Impact on Outcomes after Unmanipulated Haploidentical Hematopoietic Stem Cells Transplantation (HaploSCT) in Acute Leukemia: A Study from the Acute Leukemia Working Party of the European Group for Blood and Marrow Transplantation (EBMT)." Blood 126, no. 23 (2015): 399. http://dx.doi.org/10.1182/blood.v126.23.399.399.

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Abstract Background: HaploSCT from unmanipulated graft is a practiced option for high risk acute leukemia (AL) patients (pts) who lack a matched related or unrelated donor (Piemontese, Leukemia 2015). Since several haploidentical donors are available for most pts, selection based on optimal HLA mismatching could be relevant, but evidence on this issue is scarce. We aimed to evaluate the impact of donor-recipient HLA mismatches (HLAmm) on unshared haplotype on HaploSCT outcomes, hypothesizing that the number of HLAmm and the different HLA loci involved could be associated with specific transpla

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Gupta-Ostermann, Disha, Yoichiro Hirose, Takenao Odagami, and Jürgen Bajorath. "Follow-up: Prospective compound design using the ‘SAR Matrix’ method and matrix-derived conditional probabilities of activity." F1000Research 4 (March 23, 2015): 75. https://doi.org/10.12688/f1000research.6271.1.

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Details of the conditional probability calculations on exemplary the matrix provided in Figure 3 of the publication (see Gupta-Ostermann, Hirose, Odagami & Bajorath, Follow-up: Prospective compound design using the ‘SAR Matrix’ method and matrix-derived conditional probabilities of activity, F1000Research 2015, 4:75 , DOI: 10.12688/f1000research.6271.1 ) is provided in an excel sheet.  Informative SARMs from the PRISM library are included. Due to proprietary issues the structural information of compounds is not included. Key and value fragments of SARMs are provided w

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Riera Aroche, Raúl, Esli C. Sánchez Moreno, Yveth M. Ortiz García, et al. "The Transcription Machinery and the Driving Force of the Transcriptional Molecular Condensate: The Role of Phosphates." Current Issues in Molecular Biology 47, no. 7 (2025): 571. https://doi.org/10.3390/cimb47070571.

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The dynamic phosphorylation of the human RNA Pol II CTD establishes a code applicable to all eukaryotic transcription processes. However, the ability of these specific post-translational modifications to convey molecular signals through structural changes remains unclear. We previously explained that each gene can be modeled as a combination of n circuits connected in parallel. RNA Pol II accesses these circuits and, through a series of pulses, matches the resonance frequency of the DNA qubits, enabling it to extract genetic information and quantum teleport it. Negatively charged phosphates re

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Gagné, David, Elmira Shajari, Marie-Pier Thibault, et al. "Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis." International Journal of Molecular Sciences 23, no. 19 (2022): 11601. http://dx.doi.org/10.3390/ijms231911601.

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Necrotizing enterocolitis (NEC) is a life-threatening condition for premature infants in neonatal intensive care units. Finding indicators that can predict NEC development before symptoms appear would provide more time to apply targeted interventions. In this study, stools from 132 very-low-birth-weight (VLBW) infants were collected daily in the context of a multi-center prospective study aimed at investigating the potential of fecal biomarkers for NEC prediction using proteomics technology. Eight of the VLBW infants received a stage-3 NEC diagnosis. Stools collected from the NEC infants up to

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Makarevic, Anastasia, Carmen Rapp, Steffen Dettling, et al. "Increased Radiation-Associated T-Cell Infiltration in Recurrent IDH-Mutant Glioma." International Journal of Molecular Sciences 21, no. 20 (2020): 7801. http://dx.doi.org/10.3390/ijms21207801.

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Most gliomas are associated with a fatal prognosis and remain incurable because of their infiltrative growth. Consequently, the addition of immunotherapy to conventional therapy may improve patient outcomes. Here, we analyzed T-cell infiltration and, therefore, a major prerequisite for successful immunotherapy in a series of primary (n = 78) and recurrent (n = 66) isocitrate dehydrogenase (IDH)-mutant glioma and their changes following treatment with radio- and/or chemotherapy. After multicolor immunofluorescence staining, T cells were counted in entire tumor sections using a software-based se

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Dissertations / Theses on the topic "Matched molecular pairs and series"

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Vega, de Leon Antonio de la [Verfasser]. "Methods for the analysis of matched molecular pairs and chemical space representations / Antonio de la Vega de Leon." Bonn : Universitäts- und Landesbibliothek Bonn, 2016. http://d-nb.info/1119888913/34.

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Books on the topic "Matched molecular pairs and series"

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(Editor), Claude Camy-Peyret, and Andrei A. Vigasin (Editor), eds. Weakly Interacting Molecular Pairs: Unconventional Absorbers of Radiation in the Atmosphere (Nato Science Series: IV: Earth and Environmental Sciences). Springer, 2003.

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Weakly Interacting Molecular Pairs: Unconventional Absorbers of Radiation in the Atmosphere (Nato Science Series: IV: Earth and Environmental Sciences). Springer, 2003.

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Book chapters on the topic "Matched molecular pairs and series"

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Ruggiero, A. J., N. F. Scherer, M. Du, and G. R. Fleming. "Impulsive Phase Coherent Femtosecond Spectroscopy of Atomic and Molecular Transients with Phase-Locked Pulse Pairs." In Springer Series in Chemical Physics. Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-84269-6_102.

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Gąsiorkiewicz Jan, Krzysiek Mateusz, Miszczyk Justyna, et al. "Studies on Response to the Challenging Dose of X-rays in Lymphocytes of Patients Undergoing Diagnosis and Treatment with Iodine –131." In NATO Science for Peace and Security Series - E: Human and Societal Dynamics. IOS Press, 2010. https://doi.org/10.3233/978-1-60750-645-4-221.

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Iodine-131 is used in nuclear medicine both diagnostically and therapeutically. Internal exposure to radioiodine can lead to cellular DNA damage not only in thyroid cells but also in peripheral blood lymphocytes. The aim of our study is to investigate the influence of the the therapeutic treatment exposure to131Iodine on cellular DNA repair efficiency and to estimate potential side effects that could enhance a health risk. For that purpose in lymphocytes from patients undergoing diagnosis or treatment with radioiodine is investigated the sensitivity to ionizing radiation and repair rate of ind

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Li Xiaoping, Harrison James F., Gustafsson Magnus, Frommhold Lothar, and Hunt Katharine L.C. "The anisotropic polarizability of pairs of hydrogen molecules and the depolarized collision-induced roto-translational Raman light scattering spectra." In Atomic and Molecular Nonlinear Optics: Theory, Experiment and Computation. IOS Press, 2011. https://doi.org/10.3233/978-1-60750-742-0-254.

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In earlier work, Li, Ahuja, Harrison, and Hunt have calculated the collision-induced polarizability &Delta;&alpha; of a pair of hydrogen molecules at CCSD(T) level with an aug-cc-pV5Z basis, for 178 relative orientations of the pair, with the bond length in each molecule fixed at r = 1.449 a.u. Here we present new results from an expansion of the second-rank tensor components of &Delta;&alpha; as series in the spherical harmonics of the molecular orientation angles and the orientation angles of the intermolecular vector. The coefficients in this expansion depend on the separati

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Pope, Martin, and Charlese E. Swenberg. "Carrier generation and recombination." In Electronic Processes in Organic Crystals and Polymers. Oxford University PressNew York, NY, 1999. http://dx.doi.org/10.1093/oso/9780195129632.003.0013.

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Abstract a. Autoionization. In molecular crystals, it is well established that autoionization is the dominant process for the intrinsic generation of free carrier pairs (see Chapter Ill). In this process, the ground state of the crystal is electronically excited to a bound electron-hole state in which the electron-hole distance can vary from that of closest approach (electron and hole on the same molecule, or Frenkel exciton), to that just short of complete separation (electron and hole on different molecules but still Coulombically bound to each other, or CT exciton). Additional refinements t

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Luckow, Bruno, and Günther Schütz. "Linker scanning mutagenesis." In Directed Mutagenesis. Oxford University PressOxford, 1991. http://dx.doi.org/10.1093/oso/9780199631414.003.0006.

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Abstract Techniques for in vitro mutagenesis of DNA play a major role in molecular biology. They are powerful tools in dissecting the relationship between structure and function of a given gene. A typical analysis of gene function proceeds in several steps with an increasing degree of resolution. Deletion mutations are usually analysed first; once a functionally important region has been delimited by deletion mapping, this site can be characterized in more detail by linker scanning mutagenesis and by single point mutations introduced by methods described elsewhere in this book. In linker scann

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Morris, Huw R., and Andrew Singleton. "Neurodegenerative Disorders: Tauopathies and Synucleinopathies." In Genomics and Clinical Medicine. Oxford University PressNew York, NY, 2008. http://dx.doi.org/10.1093/oso/9780195188134.003.0018.

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Abstract Neurodegenerative disorders are common and usually affect the elderly. This is set to become the most pressing health concern in the developed world, because of the projected rapid expansion in the aged population. The prevalence of Alzheimer disease (AD) is predicted to quadruple in the United States over the next 50 years (Kawas and Brookmeyer, 2001). Unlike cancer and vascular disease, there are no disease-modifying therapies for patients with neurodegenerative diseases. There is an immediate need to develop new treatments, based on an understanding of the underlying disease biolog

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Mark, James E., Dale W. Schaefer, and Gui Lin. "General Properties." In The Polysiloxanes. Oxford University Press, 2015. http://dx.doi.org/10.1093/oso/9780195181739.003.0007.

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Many of the properties of the polysiloxanes have been tabulated in handbooks of polymer science and engineering. Recent work has included the stretching of polydimethylsiloxane (PDMS) chains, in some cases to their rupture points. The nature of the bonding in siloxane molecules has been of long-standing interest. Force fields for calculations of PDMS properties have been revised over the years and are now at an advanced state of development. Some of the simplest approaches employ the methods of molecular mechanics. Most of the experimental results have been obtained on solutions of polysiloxan

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Conference papers on the topic "Matched molecular pairs and series"

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Adilova, Fatima, and Alisher Ikramov. "Case study: Matched molecular pairs approach in QSAR modelling." In 2017 International Conference on Information Science and Communications Technologies (ICISCT). IEEE, 2017. http://dx.doi.org/10.1109/icisct.2017.8188583.

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Valdez Córdova, César Miguel. "Towards Learning Activity Cliff-Aware Molecular Representations." In LatinX in AI at International Conference on Machine Learning 2024. Journal of LatinX in AI Research, 2024. http://dx.doi.org/10.52591/lxai202407274.

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Current deep learning based methods for molecular property prediction show pronounced shortcomings when predicting molecular properties in the presence of activity cliffs (AC): pairs of structurally similar molecules with significant differences in potency. We investigate how inductive biases of increasing complexity, from simple Multilayer Perceptrons (MLPs) to selfsupervised models, impact the learning of representations from Extended-connectivity Fingerprints (ECFPs). Leveraging the Matched Molecular Pair (MMP) abstraction, we explore various pre-training schemes designed to capture AC rela

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Bedard, Philippe L., Amit Oza, Blaise Clarke, et al. "Abstract PR03: Molecular profiling of advanced solid tumors at Princess Margaret Cancer Centre and patient outcomes with genotype-matched clinical trials." In Abstracts: AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; June 13-16, 2015; Salt Lake City, UT. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1557-3265.pmsclingen15-pr03.

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Zhao, Zhengcai, Yucan Fu, Jiuhua Xu, and Yong Chen. "Measurement-Based Adaptive Machining by Direct Spatial Deformation of Template CAM Data." In ASME 2017 12th International Manufacturing Science and Engineering Conference collocated with the JSME/ASME 2017 6th International Conference on Materials and Processing. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/msec2017-2773.

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In production and manufacturing engineering, some redesign, distorted or worn parts cannot be milled according to their original CAD geometries due to the existed shape deviations. Generating CAM data in traditional manner for each individual part is time-consuming and labor intensive. This paper proposes a quick and convenient adaptive approach for machining distorted hollow blade, in which a template CAM data is spatially deformed according to some measured points from actual shape. The actual shape of the part was firstly inspected by on-machine measurement method. The measured points data

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Francis, C. W., and V. J. Marder. "RAPID FORMATION OF LARGE MOLECULAR WEIGHT O-P0LYMERS IN CROSSLINKED FIBRIN INDUCED BY HIGH FACTOR XIII CONCENTRATIONS: ROLE OF PLATELET FACTOR XIII." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643311.

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Following fibrin polymerization, activated factor XIII stabilizes the clot by catalyzing the formation of specific intermolecular covalent crosslinks between pairs of y chains to form dimers and also among two or more a chains to form polymers. We have identified a series of previously uncharacterized a chain polymers with a wide range of sizes, including some with apparent Mr in excess of several million. Additionally, we establish the role of high concentrations of factor XIII in the extent and rate of α-polymer formation and provide evidence that the factor XIII required can be provided by

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Telicheva, V. O., S. A. Nagorniy, L. A. Ermakova, N. V. Golovchenko, I. V. Kornienko, and E. I. Kirtanasova. "APPLICATION OF THE PCR METHOD TO DETECT DNA OF THE CAUSATIVE AGENT OF CYSTIC ECHINOCOCCOSIS IN THE BLOOD." In THEORY AND PRACTICE OF PARASITIC DISEASE CONTROL. VNIIP – FSC VIEV, 2024. http://dx.doi.org/10.31016/978-5-6050437-8-2.2024.25.405-411.

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Echinococcosis remains a complex multidisciplinary problem. Due to frequent intra- and postoperative complications, and distant recurrence of echinococcosis, the successful treatment of the patient depends on interaction of doctors in surgery and therapeutics. To date, there has been no consensus in the Russian Federation on management tactics of echinococcosis patients. There are no protocols or clinical guidelines to choose a surgical intervention volume and method or the duration of anti-relapse treatment courses. Currently, the main laboratory method to evaluate the effectiveness of surgic

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Chen, Jun, and Joseph Katz. "A Correlation Mapping Method to Eliminate the Peak-Locking Effect in PIV Analysis." In ASME 2004 Heat Transfer/Fluids Engineering Summer Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/ht-fed2004-56400.

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“Peak-locking” causes deterministic mean measurement bias in most of the existing cross-correlation based algorithms for PIV data analysis. This phenomenon is inherent to the typical smooth curve-fitting through discrete correlation values which are used to obtain the sub-pixel accuracy in velocity. In this paper we introduce a new algorithm/method for obtaining the sub-pixel accuracy, which eliminates the peak-locking effect. We refer to this procedure as “correlation mapping method”. In an ideal case, the second exposure (image 2) in a PIV measurement can be regarded as a mapping of the firs

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Arekhov, V., T. Zhainakov, T. Clemens, and J. Wegner. "Influence of Water Saturation, Temperature and Pressure on the Effective Hydrogen-Methane Gas Diffusion in Reservoir Rocks." In SPE Europe Energy Conference and Exhibition. SPE, 2024. http://dx.doi.org/10.2118/220008-ms.

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Abstract When hydrogen is stored underground in porous media, mixing of remaining hydrocarbon gas with hydrogen occurs. One of the major processes enhancing gas mixing is molecular diffusion. The magnitude of diffusion mixing depends on subsurface conditions (pressure and temperature), phase saturation, gas composition as well as rock properties (porosity and tortuosity). Limited data is available describing the hydrogen and methane diffusion through reservoir rocks. Moreover, minor attention has been given to the influence of temperatures and water saturation on effective diffusion through po

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Reports on the topic "Matched molecular pairs and series"

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Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7593398.bard.

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The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist bioph

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