cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Sequential virtual screening collaborated with machine-learning strategies for the discovery of precise medicine against non-small cell lung cancer
Creators: name: Thirunavukkarasu, Muthu Kumar
name: Veerappapillai, Shanthi
name: Karuppasamy, Ramanathan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer

description: Dysregulation of MAPK pathway receptors are crucial in causing uncontrolled cell proliferation in many cancer types including non-small cell lung cancer. Due to the complications in targeting the upstream components, MEK is an appealing target to diminish this pathway activity. Hence, we have aimed to discover potent MEK inhibitors by integrating virtual screening and machine learning-based strategies. Preliminary screening was conducted on 11,808 compounds using the cavity-based pharmacophore model AADDRRR. Further, seven ML models were accessed to predict the MEK active compounds using six molecular representations. The LGB model with morgan2 fingerprints surpasses other models ensuing 0.92 accuracy and 0.83 MCC value versus test set and 0.85 accuracy and 0.70 MCC value with external set. Further, the binding ability of screened hits were examined using glide XP docking and prime-MM/GBSA calculations. Note that we have utilized three ML-based scoring functions to predict the various biological properties of the compounds. The two hit compounds such as DB06920 and DB08010 resulted excellent binding mechanism with acceptable toxicity properties against MEK. Further, 200 ns of MD simulation combined with MM-GBSA/PBSA calculations confirms that DB06920 may have stable binding conformations with MEK thus step forwarded to the experimental studies in the near future. Communicated by Ramaswamy H. Sarma
Student’-Student Relationship and Academic Achievement in Cross River State Nigeria.pdf
Creators: name: Orji, Evelyn   Ijeoma
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 390304
subject: Primary education
classificationCode: 390303
subject: Higher education
classificationCode: 390306
subject: Secondary education

description: This study described the influence of students-student relationship and academic achievement of secondary school students in Cross River State. One research question and one null hypothesis guided the study. Literature was reviewed according to the variable under study. The ex-post facto design was adopted for the study. The population consisted of 15,080 SS2 students, in all the 272 public secondary schools in Cross River State. A sample of 1, 029 students was used for the study. An instrument named “Student-student relationship questionnaire was` used for data collection. The reliability of the instrument was determined using Cronbach Alpha reliability method .77. The study equally involved data from school administrative records which were students’ academic achievement records for 2018 promotion examinations in English language, Mathematics and Biology obtained from school authorities. Data collected from 1,029 of the subjects were analyzed using descriptive statistics. The findings from the results revealed that students-student relationship had positive significant influence on students’ academic achievement. It is therefore concluded that school routine activities influence academic achievement of senior secondary school students in Cross River State. Based on the above finding, it was recommended among others that peer group has both positive and negative
The OSIRIS-REx Visible and InfraRed Spectrometer (OVIRS): Spectral Maps of the Asteroid Bennu
Creators: name: Reuter, D. C.
name: Simon, A. A.
name: Hair, J.
name: Lunsford, A.
name: Manthripragada, S.
name: Bly, V.
name: Bos, B.
name: Brambora, C.
name: Caldwell, E.
name: Casto, G.
name: Dolch, Z.
name: Finneran, P.
name: Jennings, D.
name: Jhabvala, M.
name: Matson, E.
name: McLelland, M.
name: Roher, W.
name: Sullivan, T.
name: Weigle, E.
name: Wen, Y.
name: Wilson, D.
name: Lauretta, D. S.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The OSIRIS-REx Visible and Infrared Spectrometer (OVIRS) is a point spectrometer covering the spectral range of 0.4 to 4.3 microns (25,000-2300 cm-1). Its primary purpose is to map the surface composition of the asteroid Bennu, the target asteroid of the OSIRIS-REx asteroid sample return mission. The information it returns will help guide the selection of the sample site. It will also provide global context for the sample and high spatial resolution spectra that can be related to spatially unresolved terrestrial observations of asteroids. It is a compact, low-mass (17.8 kg), power efficient (8.8 W average), and robust instrument with the sensitivity needed to detect a 5% spectral absorption feature on a very dark surface (3% reflectance) in the inner solar system (0.89-1.35 AU). It, in combination with the other instruments on the OSIRIS-REx Mission, will provide an unprecedented view of an asteroid's surface.
description: 14 figures, 3 tables, Space Science Reviews, submitted
Aquaculture Technology Toolkit Catalogue.TAAT Clearinghouse. Clearinghouse Technical Report Series 012.
Creators: name: TAAT Clearinghouse
Publisher: name: Gates Open Research
Year: 2022

description: This catalogue describes a series of technologies related to the modernization of aquaculture in Africa. It is developed through a collaborative effort from the Technologies for African Agricultural Transformation (TAAT) program from the African Development Bank that seeks to increase stakeholder usage of proven agricultural technology, and its Aquaculture Compact project partners. The compilation is also supported by the Project Platform for Agricultural Solutions (ProPAS), an information portal where innovations are systematically characterized for open access. Both activities address the imperative to better connect proven technologies to those who need them, but each undertakes this goal differently. Aquaculture is one of nine commodity compacts with proven technologies that have the potential to ensure self-sufficiency in fish production and increase yields and benefits for upscaling. Fish is also targeted as an agro-industrial commodity for processing and trading on domestic and regional markets. The TAAT Aquaculture Compact, led by WorldFish, informs a wide variety of stakeholders through capacity development and technological outreach, and 2 this catalogue assists them in doing so. The countries targeted by the Aquaculture Compact are Benin, Burundi, Cameroon, Cote d'Ivoire, Democratic Republic of Congo, Ghana, Kenya, Malawi, Nigeria, Tanzania, Togo, and Zambia. The TAAT Program identified proven technologies that advance fish production and we have compiled them into a “Toolkit Catalogue” meant to promote understanding and stimulate adoption and investment. This is one of several such catalogues produced as a joint TAAT-ProPAS activity. For more information on the featured technologies or other solutions for the transformation of aquaculture in Sub-Saharan Africa, contact Prof. Bernadette Fregene at b.fregene@cgiar.org.
Additional file 1 of 2-D numerical experiments of thermal convection of highly viscous fluids under strong adiabatic compression: implications on mantle convection of super-Earths with various sizes
Creators: name: Kameyama, Masanori
Publisher: name: figshare
Year: 2025
Subjects: subject: Geology
subject: FOS: Earth and related environmental sciences

description: Supplementary material 1.
ESM 2. Sample-based rarefaction curve for bat ectoparasitic fly species observed and three species richness estimators (Bootstrap, Chao 2, and Jackknife 2). Data collected in a Caatinga dry forest area in the state of Bahia, north-eastern Brazil.
Creators: name: Barbier, Eder
name: Falcão, Fábio
name: Bernard, Enrico
Publisher: name: figshare
Year: 2022
Subjects: Ecology not elsewhere classified

description: Data from: Bat‑ectoparasitic fly relationships in a seasonally dry tropical forest in Brazil.
Developing a comprehensive solution aimed to disrupt LARS1/RagD protein-protein interaction
Creators: name: Raevsky, Alexey
name: Kovalenko, Oksana
name: Bulgakov, Elijah
name: Sharifi, Mohsen
name: Volochnyuk, Dmityi
name: Tukalo, Michael
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Hematology

description: Aminoacyl-tRNA synthetases are crucial enzymes involved in protein synthesis and various cellular physiological reactions. Aside from their standard role in linking amino acids to the corresponding tRNAs, they also impact protein homeostasis by controlling the level of soluble amino acids within the cell. For instance, leucyl-tRNA synthetase (LARS1) acts as a leucine sensor for the mammalian target of rapamycin complex 1 (mTORC1), and may also function as a probable GTPase-activating protein (GAP) for the RagD subunit of the heteromeric activator of mTORC1. In turn, mTORC1 regulates cellular processes, such as protein synthesis, autophagy, and cell growth, and is implicated in various human diseases including cancer, obesity, diabetes, and neurodegeneration. Hence, inhibitors of mTORC1 or a deregulated mTORC1 pathway may offer potential cancer therapies. In this study, we investigated the structural requirements for preventing the sensing and signal transmission from LARS to mTORC1. Building upon recent studies on mTORC1 regulation activation by leucine, we lay the foundation for the development of chemotherapeutic agents against mTORC1 that can overcome resistance to rapamycin. Using a combination of in-silico approaches to develop and validate an alternative interaction model, discussing its benefits and advancements. Finally, we identified a set of compounds ready for testing to prevent LARS1/RagD protein-protein interactions. We establish a basis for creating chemotherapeutic drugs targeting mTORC1, which can conquer resistance to rapamycin. We utilize in-silico methods to generate and confirm an alternative interaction model, outlining its advantages and improvements, and pinpoint a group of novel substances that can prevent LARS1/RagD interactions. Communicated by Ramaswamy H. Sarma
Screening of natural product libraries in MCF7 cell line reveals the pro-apoptotic properties of β tetralone
Creators: name: Shaikh, Nilofer
name: Sivaram, Aruna
name: Vyas, Renu
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Cell Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer
Hematology

description: Despite the exponential increase in research toward better treatment options for breast cancer patients, developing an effective drug with fewer side effects continues to remain a challenge. Natural compounds have emerged as a viable option and several drugs have been derived or inspired from them. In this study, we screened a library of natural compounds with diverse chemical structures against selected kinase proteins using in silico methods such as molecular docking and dynamics simulation. The best results were obtained between β tetralone and MDM2 E3 ubiquitin ligase protein. In vitro experiments such as cytotoxicity, scratch assays and flow cytometry analysis using an MCF7 cell line were performed to determine the anti-cancer potential of the compound. As the treatment resulted in cell death and apoptosis, β tetralone was screened in silico against anti-apoptotic targets where the best results were obtained between Bcl-w and β tetralone. This comprehensive study suggests that the anti-cancer activity of β tetralone is probably through the dual targeting of MDM2 E3 ubiquitin kinase and Bcl-w anti-apoptotic protein. Communicated by Ramaswamy H. Sarma
Towards Strong Field Tests of Beyond Horndeski Gravity Theories
Creators: name: Sakstein, Jeremy
name: Babichev, Eugeny
name: Koyama, Kazuya
name: Langlois, David
name: Saito, Ryo
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Theories of gravity in the beyond Horndeski class encompass a wide range of scalar-tensor theories that will be tested on cosmological scales over the coming decade. In this work, we investigate the possibility of testing them in the strong-field regime by looking at the properties of compact objects-neutron, hyperon, and quark stars-embedded in an asymptotically de Sitter space-time, for a specific subclass of theories. We extend previous works to include slow rotation and find a relation between the dimensionless moment of intertia, ($\bar{I}=Ic^2/G_{\rm N} M^3$), and the compactness, $\cal{C}=G_{\rm N} M/Rc^2$ (an $\bar{I}$-$\cal{C}$ relation), independent of the equation of state, that is reminiscent of but distinct from the general relativity prediction. Several of our equations of state contain hyperons and free quarks, allowing us to revisit the hyperon puzzle. We find that the maximum mass of hyperon stars can be larger than $2M_\odot$ for small values of the beyond Horndeski parameter, thus providing a resolution of the hyperon puzzle based on modified gravity. Moreover, stable quark stars exist when hyperonic stars are unstable, which means that the phase transition from hyperon to quark stars is predicted just as in general relativity, albeit with larger quark star masses. Two important and potentially observable consequences of some of the theories we consider are the existence of neutron stars in a range of masses significantly higher than in GR, and $\bar{I}$-$\mathcal{C}$ relations that differ from their GR counterparts. In the former case, we find objects that, if observed, could not be accounted for in GR because they violate the usual GR causality condition. We end by discussing several difficult technical issues that remain to be addressed in order to reach more realistic predictions that may be tested using gravitational wave searches or neutron star observations.
description: 15 pages, 7 figures, 1 table. Updated to reflect published version. Added section IVB and appendix A
Identifying potential neuroprotective polyphenols targeting endoplasmic reticulum stress through an in silico approach
Creators: name: Singh, Pooja
name: Kanhed, Ashish
name: Khatik, Gopal Lal
name: Datusalia, Ashok Kumar
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Mental Health

description: The endoplasmic reticulum (ER) is essential in many cellular processes, including protein processing, lipid metabolism, and calcium storage. Dysregulation of ER function has been linked with neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, etc. The primary pathological alteration explicated in the diseases is the accumulation of misfolded proteins in the neuronal cells. ER stress-associated activation of PERK-mediated pro-apoptotic cell death leads to neurodegeneration. In this study, we have primarily screened the potential polyphenols evidenced for neuroprotective activity. The 24 polyphenols were selected to explore their binding affinity towards various proteins of ER cascade such as pPERK (phospho-PERK), EIF2 (Eukaryotic Initiation Factor 2), and ATF4 (Activating Transcription Factor 4). On the basis of binding affinity, four phytopolyphenols were further selected for in-silico ADMET and molecular dynamic simulation. Among them curcumin found to be the most promising and serve as a potential hit against all three targets of ER cascade. The selected proteins’ active site has demonstrated high stability of curcumin binding according to molecular dynamics findings. Though curcumin exhibited a significant hit in interaction with targets but needs to be further improved in drug-ability criteria. Thus, seventy derivatives of curcumin scaffold (from the published literature) were also screened with improve in druggability criteria, which showed good interaction with unfolded protein response related targets. The new scaffolds serve considerable potential to be developed as novel polyphenolic lead for neurodegenerative disorders. Communicated by Ramaswamy H. Sarma
Machine learning and traditional QSAR modeling methods: a case study of known PXR activators
Creators: name: Neal, William M.
name: Pandey, Pankaj
name: Khan, Shabana I.
name: Khan, Ikhlas A.
name: Chittiboyina, Amar G.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Pharmacology
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Mathematical Sciences not elsewhere classified

description: Pregnane X receptor (PXR), extensively expressed in human tissues related to digestion and metabolism, is responsible for recognizing and detoxifying diverse xenobiotics encountered by humans. To comprehend the promiscuous nature of PXR and its ability to bind a variety of ligands, computational approaches, viz., quantitative structure–activity relationship (QSAR) models, aid in the rapid dereplication of potential toxicological agents and mitigate the number of animals used to establish a meaningful regulatory decision. Recent advancements in machine learning techniques accommodating larger datasets are expected to aid in developing effective predictive models for complex mixtures (viz., dietary supplements) before undertaking in-depth experiments. Five hundred structurally diverse PXR ligands were used to develop traditional two-dimensional (2D) QSAR, machine-learning-based 2D-QSAR, field-based three-dimensional (3D) QSAR, and machine-learning-based 3D-QSAR models to establish the utility of predictive machine learning methods. Additionally, the applicability domain of the agonists was established to ensure the generation of robust QSAR models. A prediction set of dietary PXR agonists was used to externally-validate generated QSAR models. QSAR data analysis revealed that machine-learning 3D-QSAR techniques were more accurate in predicting the activity of external terpenes with an external validation squared correlation coefficient (R2) of 0.70 versus an R2 of 0.52 in machine-learning 2D-QSAR. Additionally, a visual summary of the binding pocket of PXR was assembled from the field 3D-QSAR models. By developing multiple QSAR models in this study, a robust groundwork for assessing PXR agonism from various chemical backbones has been established in anticipation of the identification of potential causative agents in complex mixtures. Communicated by Ramaswamy H. Sarma
Anisotropic magnetic interactions and spin dynamics in the spin-chain compound Cu(py)$_2$Br$_2$: An experimental and theoretical study
Creators: name: Zeisner, J.
name: Brockmann, M.
name: Zimmermann, S.
name: Weiße, A.
name: Thede, M.
name: Ressouche, E.
name: Povarov, K. Yu.
name: Zheludev, A.
name: Klümper, A.
name: Büchner, B.
name: Kataev, V.
name: Göhmann, F.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We compare theoretical results for electron spin resonance (ESR) properties of the Heisenberg-Ising Hamiltonian with ESR experiments on the quasi-one-dimensional magnet Cu(py)$_2$Br$_2$ (CPB). Our measurements were performed over a wide frequency and temperature range giving insight into spin dynamics, spin structure, and magnetic anisotropy of this compound. By analyzing the angular dependence of ESR parameters (resonance shift and linewidth) at room temperature we show that the two weakly coupled inequivalent spin chain types inside the compound are well described by Heisenberg-Ising chains with their magnetic anisotropy axes perpendicular to the chain direction and almost perpendicular to each other. We further determine the full $g$-tensor from these data. In addition, the angular dependence of the linewidth at high temperatures gives us access to the exponent of the algebraic decay of a dynamical correlation function of the isotropic Heisenberg chain. From the temperature dependence of static susceptibilities we extract the strength of the exchange coupling ($J/k_B = 52.0\,\text{K}$) and the anisotropy parameter ($δ\approx -0.02$) of the model Hamiltonian. An independent compatible value of $δ$ is obtained by comparing the exact prediction for the resonance shift at low temperatures with high-frequency ESR data recorded at $4\,\text{K}$. The spin structure in the ordered state implied by the two (almost) perpendicular anisotropy axes is in accordance with the propagation vector determined from neutron scattering experiments. In addition to undoped samples we study the impact of partial substitution of Br by Cl ions on spin dynamics. From the dependence of the ESR linewidth on doping level we infer an effective decoupling of the anisotropic component $Jδ$ from the isotropic exchange $J$ in these systems.
description: 26 pages, 12 figures, section V.A.2 revised, appendices A and B shortened
Fragment-based investigation of thiourea derivatives as VEGFR-2 inhibitors: a cross-validated approach of ligand-based and structure-based molecular modeling studies
Creators: name: Banerjee, Suvankar
name: Kejriwal, Shristi
name: Ghosh, Balaram
name: Lanka, Goverdhan
name: Jha, Tarun
name: Adhikari, Nilanjan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Angiogenesis is mediated by the vascular endothelial growth factor (VEGF) that plays a key role in the modulation of progression, invasion and metastasis, related to solid tumors and hematological malignancies. Several small-molecule VEGFR-2 inhibitors are marketed, but their usage is restricted to specific cancers due to severe toxicities. Therefore, cost-effective novel small molecule VEGFR-2 inhibitors may be an alternative to overcome these adverse effects. Here, a set of thiourea-based VEGFR-2 inhibitors were considered for a combined fragment-based QSAR technique, structure-based molecular docking followed by molecular dynamics simulation studies to acquire insights into the key structural attributes and the binding pattern of enzyme-ligand interactions. Noticeably, amine-substituted quinazoline phenyl ring and a higher number of nitrogen atoms, and the hydrazide function in the molecular structure are crucial for VEGFR-2 inhibition whereas methoxy groups are detrimental to VEGFR-2 inhibition. The MD simulation study of sorafenib and thiourea derivatives explored the significance of urea and thiourea moiety binding at VEGFR-2 active site that can be utilized further in the future to design molecules for greater binding stability and better VEGFR-2 selectivity. Therefore, such findings can be beneficial for the development of newer VEGFR-2 inhibitors for further refinement to acquire better therapeutic efficacy. Communicated by Ramaswamy H. Sarma
The S-wave resonance contributions in the $B^0_s$ decays into $ ψ(2S,3S)$ plus pion pair
Creators: name: Rui, Zhou
name: Li, Ya
name: Wang, Wen-Fei
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The three-body decays $B^0_s \rightarrow ψ(2S,3S) π^+ π^-$ are studied based on the perturbative QCD approach. With the help of the nonperturbative two-pion distribution amplitudes, the analysis is simplified into the quasi-two-body processes. Besides the traditional factorizable and nonfactorizable diagrams at the leading order, the next-to-leading order vertex corrections are also included to cancel the scale dependence. The $f_0(980)$, $f_0(1500)$ resonance contributions as well as the nonresonant contributions are taken into account using the presently known $ππ$ time-like scalar form factor for the $s\bar{s}$ component. It is found that the predicted $B^0_s \rightarrow ψ(2S) π^+ π^-$ decay spectra in the pion pair invariant mass shows a similar behavior as the experiment. The calculated S-wave contributions to the branching ratio of $B^0_s \rightarrow ψ(2S) π^+ π^-$ is $6.0\times 10^{-5}$, which is in agreement with the LHCb data $\mathcal {B}(B^0_s \rightarrow ψ(2S) π^+ π^-)=(7.2\pm 1.2)\times 10^{-5} $ within errors. The estimate of $\mathcal {B}(B^0_s \rightarrow ψ(3S) π^+ π^-)$ can reach the order of $10^{-5}$, pending for the corresponding measurements.
description: 7 pages, 3 figures, 2 tables
A generalized public goods game with coupling of individual ability and project benefit
Creators: name: Zhong, Li-Xin
name: Xu, Wen-Juan
name: He, Yun-Xin
name: Zhong, Chen-Yang
name: Chen, Rong-Da
name: Qiu, Tian
name: Shi, Yong-Dong
name: Ren, Fei
Publisher: name: arXiv
Year: 2017
Subjects: subject: Physics and Society (physics.soc-ph)
subject: General Finance (q-fin.GN)
subject: FOS: Physical sciences
subject: FOS: Economics and business

description: Facing a heavy task, any single person can only make a limited contribution and team cooperation is needed. As one enjoys the benefit of the public goods, the potential benefits of the project are not always maximized and may be partly wasted. By incorporating individual ability and project benefit into the original public goods game, we study the coupling effect of the four parameters, the upper limit of individual contribution, the upper limit of individual benefit, the needed project cost and the upper limit of project benefit on the evolution of cooperation. Coevolving with the individual-level group size preferences, an increase in the upper limit of individual benefit promotes cooperation while an increase in the upper limit of individual contribution inhibits cooperation. The coupling of the upper limit of individual contribution and the needed project cost determines the critical point of the upper limit of project benefit, where the equilibrium frequency of cooperators reaches its highest level. Above the critical point, an increase in the upper limit of project benefit inhibits cooperation. The evolution of cooperation is closely related to the preferred group-size distribution. A functional relation between the frequency of cooperators and the dominant group size is found.
Additional file 1 of Models for predicting risk of endometrial cancer: a systematic review
Creators: name: Forder, Bea Harris
name: Ardasheva, Anastasia
name: Atha, Karyna
name: Nentwich, Hannah
name: Abhari, Roxanna
name: Kartsonaki, Christiana
Publisher: name: figshare
Year: 2025
Subjects: subject: Medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Mathematical Sciences not elsewhere classified

description: Additional file 1: eFigure 1 PRISMA flowchart of the systematic literature search conducted for gynaecological cancers risk prediction models.
Assessing the Impact of Age on Everyday Cognitive Function with Virtual Reality: the EcoKitchen task_Database
Creators: name: Julio, Filipa
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Clinical Psychology
subject: Cognitive Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: Aging; Executive Functions; Virtual Reality; Ecological Validity

description: This dataset includes demographic data of 53 healthy adults and their scores on several conventional neuropsychological tests and on three performance measures computed from a non-immersive virtual reality task called EcoKitchen described in Júlio, F., Ribeiro, M. J., Patrício, M., Malhão, A., Pedrosa, F., Gonçalves, H., Simões, M., van Asselen, M., Simões, M. R., Castelo-Branco, M., & Januário, C. (2019). A Novel Ecological Approach Reveals Early Executive Function Impairments in Huntington's Disease. Frontiers in Psychology, 10, 585. https://doi.org/10.3389/fpsyg.2019.00585
Repeated exposure and then BIAT
Creators: name: Heimer, Orit
name: Bar-Anan, Yoav
name: kron, assaf
name: Argaman, Yiftach
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Affective Valence
subject: BIAT
subject: Habituation
subject: Sematic Valence

description: The influence of repeated exposure to a stimulus on its semantic and affective modes of valence.
Dynamical Casimir effect for semitransparent mirrors
Creators: name: Fosco, C. D.
name: Giraldo, A.
name: Mazzitelli, F. D.
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the Dynamical Casimir Effect resulting from the oscillatory motion of either one or two flat semitransparent mirrors, coupled to a quantum real and massless scalar field. Our approach is based on a perturbative evaluation, in the coupling between mirrors and field, of the corresponding effective action, which is used to compute the particle creation rate. The amplitude of the oscillation is not necessarily small. We first obtain results for a single mirror, both for non-relativistic and relativistic motions, showing that only for the latter the effects may be significant. For two mirrors, on the other hand, we show that there are interesting interference effects, and that in some particular cases the results differ from those obtained assuming small amplitudes, already for non-relativistic motions.
description: 20 pages, 5 figures. Improved discussion of the ultrarelativistic case. New section on higher order corrections. Version to appear in Phys. Rev. D
Revealing anti-fungal potential of plant-derived bioactive therapeutics in targeting secreted aspartyl proteinase (SAP) of Candida albicans: a molecular dynamics approach
Creators: name: Dhanasekaran, Sivaraman
name: Selvadoss, Pradeep Pushparaj
name: Manoharan, Solomon Sundar
name: Jeyabalan, Srikanth
name: Rajeswari, Vijayarangan Devi
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Computational Biology

description: Candida species have established themselves as a major source of nosocomial infections. Increased expression of secreted aspartyl proteinases (SAP5) plays a crucial role in the pathogenesis of Candida species. Phytotherapeutics continue to serve as a viable resource for discovering novel antifungal agents. Hence the main aim of the present investigation is to explore the possible inhibitory role of the selected bioactive molecules against the SAP5 enzyme of C. albicans using in silico approach. Molecular docking and dynamic simulations were utilized to predict the binding affinity of the lead molecules using the AutoDock and Gromacs in-silico screening tools. Results of preliminary docking simulations show that the compounds hesperidin, vitexin, berberine, adhatodine, piperine, and chlorogenic acid exhibit significant interactions with the core catalytic residues of the target protein. The best binding ligands (hesperidin, vitexin, fluconazole) were subjected to molecular dynamics (MD) and essential dynamics of the trajectories. Results of the MD simulation confirm that the ligand-protein complexes became more stable from 20 ns until 100 ns. The calculated residue-level contributions to the interaction energy along a steady simulation trajectory of all three hits (hesperidin (−132.720 kJ/mol), vitexin (−83.963 kJ/mol) and fluconazole (−98.864 kJ/mol)) ensure greater stability of the leads near the catalytic region. Essential dynamics of PCA and DCCM analysis signifies that the binding of hesperidin and vitexin created a more structurally stable environment in the protein target. The overall outcomes of this study clearly emphasize that the bioactive therapeutics found in medicinal herbs may have remarkable scope in managing Candida infection. Communicated by Ramaswamy H. Sarma
A new strategy for making a sensitive sensor for aspirin drug: first-principles investigations by using pure and metal-doped BN nano-heterostructures
Creators: name: Rad, Ali Shokuhi
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Physical Sciences not elsewhere classified
Pharmacology
Biotechnology
Environmental Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Cancer
Science Policy
Computational Biology

description: The present study used the DFT method to investigate aspirin’s intermolecular interactions with boron nitride (BN) nanotubes modified with aluminum, gallium, and zinc. Our experiments obtained adsorption energy of −40.4 kJ/mol for aspirin on BN nanotubes. By doping each of the above metals on the surface of the BN nanotube, the aspirin adsorption energy increased dramatically. For BN nanotubes doped with Al, Ga, and Zn, this energy was −255, −251, and −250 kJ/mol. Thermodynamic analyses proved that all surface adsorptions are exothermic and spontaneous. Nanotubes’ electronic structures and dipole moments have been examined following aspirin adsorption. In addition, AIM analysis has been performed for all systems in order to understand how the links were formed. According to the obtained results, BN nanotubes doped with metals, as mentioned previously, have a very high electron sensitivity to aspirin. These nanotubes can therefore be used to manufacture aspirin-sensitive electrochemical sensors. Communicated by Ramaswamy H. Sarma
ENLIGHT RISE - Deliverable 1.3 - Three large strategic project proposals submitted (e.g. MSCA-COFUND)
Creators: name: ENLIGHT RISE WP1 - Establish a sustainable business model towards a collaborative R&I agenda
Publisher: name: Zenodo
Year: 2024
Subjects: European Universities
EUA
Research project proposals

description: Co-led by UBx and RUG, this deliverable provides an overview of the various research oriented proposals that have been submitted by the ENLIGHT alliance over the course of the ENLIGHT RISE project.
COVID-19 and change in religious devotion: A mixed-method analysis
Creators: name: Leonhardt, Nathan
name: FAHMI, Sarah
name: Impett, Emily
name: Stellar, Jennifer
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Religion
subject: Arts and Humanities
subject: Social Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: There were 1,021 participants from the United States recruited through Prolific. The sample is nationally representative in age, sex, and ethnicity. Data were collected between May 27th and May 31st, 2020 and have been collected for this study in full. What we are trying to understand is : what are the characteristics of people who have varying levels of change (i.e., increase, no change, decrease) in their religious devotion since COVID-19? These differences will be tested with chi-square and ANOVA analyses across the three self-reported groups of religious change. We have grouped the dependent variables we want to test into (1) Sociodemographics, (2) Religion, (3) Individual Differences, (4) COVID-19 attitudes and behaviors, (5) Well-being, and (6) Prosocial Emotions.
Stochastic gravitational waves associated with the formation of primordial black holes
Creators: name: Nakama, Tomohiro
name: Silk, Joseph
name: Kamionkowski, Marc
Publisher: name: arXiv
Year: 2016
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Primordial black hole (PBH) mergers have been proposed as an explanation for the gravitational wave events detected by the LIGO collaboration. Such PBHs may be formed in the early Universe as a result of the collapse of extremely rare high-sigma peaks of primordial fluctuations on small scales, as long as the amplitude of primordial perturbations on small scales is enhanced significantly relative to the amplitude of perturbations observed on large scales. One consequence of these small-scale perturbations is generation of stochastic gravitational waves that arise at second order in scalar perturbations, mostly before the formation of the PBHs. These induced gravitational waves have been shown, assuming gaussian initial conditions, to be comparable to the current limits from the European Pulsar Timing Array, severely restricting this scenario. We show, however, that models with enhanced fluctuation amplitudes typically involve non-gaussian initial conditions. With such initial conditions, the current limits from pulsar timing can be evaded. The amplitude of the induced gravitational-wave background can be larger or smaller than the stochastic gravitational-wave background from supermassive black hole binaries.
description: 15 pages, 3 figures, accepted in PRD
Detailed investigation of the duration of inflation in loop quantum cosmology for a Bianchi-I universe with different inflaton potentials and initial conditions
Creators: name: Martineau, Killian
name: Barrau, Aurélien
name: Schander, Susanne
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: There is a wide consensus on the correct dynamics of the background in loop quantum cosmology. In this article we make a systematic investigation of the duration of inflation by varying what we think to be the most important "unknowns" of the model: the way to set initial conditions, the amount of shear at the bounce and the shape of the inflaton potential.
Water network chemistry to exploit the nature of catalytic water molecules in Mtb DNA gyrase: a computational study to understand the binding mechanism of fluoroquinolones
Creators: name: Kumar, G. Siva
name: Sobhia, M. Elizabeth
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Computational Biology

description: The dynamics of DNA gyrase and mutants of DNA gyrA such as G88A, A90V, S91P, D94A, D94G, D94N, D94Y; and double-point mutant (S91P-D94G), are meticulously investigated using computational approaches. Molecular dynamics (MD) and hydration thermodynamics have shed light on the fundamental, mechanistic basis of mutations on the conformational stability of Quinolone Binding Pocket (QBP) of DNA gyrase. Analysis of MD results revealed the displacement of a single crystal water molecule (HOH201) from the catalytic site of wild-type (WT) and mutants of DNA gyrA. This prompted our research group to probe the five crystal water molecules present in the QBP of the enzyme using water thermodynamics. Hydration thermodynamics analysis revealed the displacement of HOH201 due to unstable thermodynamic signatures. Further, the analysis highlighted significant changes in thermodynamic signatures and locations of five crystal water hydration sites upon mutation. Integrated MD simulations and water thermodynamics provided promising insights into the conformational changes and inaccessibility of the catalytic water molecule that can influence the design of DNA gyrase inhibitors. Communicated by Ramaswamy H. Sarma
Gravitational radiation from compact binary systems in screened modified gravity
Creators: name: Zhang, Xing
name: Liu, Tan
name: Zhao, Wen
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Screened modified gravity (SMG) is a kind of scalar-tensor theory with screening mechanisms, which can suppress the fifth force in dense regions and allow theories to evade the solar system and laboratory tests. In this paper, we investigate how the screening mechanisms in SMG affect the gravitational radiation damping effects, calculate in detail the rate of the energy loss due to the emission of tensor and scalar gravitational radiations, and derive their contributions to the change in the orbital period of the binary system. We find that the scalar radiation depends on the screened parameters and the propagation speed of scalar waves, and the scalar dipole radiation dominates the orbital decay of the binary system. For strongly self-gravitating bodies, all effects of scalar sector are strongly suppressed by the screening mechanisms in SMG. By comparing our results to observations of binary system PSR J1738+0333, we place the stringent constraints on the screening mechanisms in SMG. As an application of these results, we focus on three specific models of SMG (chameleon, symmetron, and dilaton), and derive the constraints on the model parameters, respectively.
description: 21 pages, 3 figures, Phys. Rev. D accepted
Identifying potent inhibitory phytocompounds from Lagerstroemia speciosa against SARS-Coronavirus-2: structure-based virtual screening
Creators: name: Dagur, Hanuman Singh
name: Behmard, Esmaeil
name: Rajakumara, Eerappa
name: Barzegari, Ebrahim
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: The ongoing spillover of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) calls for expedited countermeasure through developing therapeutics from natural reservoirs and/or the use of less time-consuming drug discovery methodologies. This study aims to apply these approaches to identify potential blockers of the virus from the longstanding medicinal herb, Lagerstroemia speciosa, through comprehensive computational-based screening. Nineteen out of 22 L. speciosa phytochemicals were selected on the basis of their pharmacokinetic properties. SARS-CoV-2 Main protease (Mpro), RNA-directed RNA polymerase (RdRp), Envelope viroporin protein (Evp) and receptor-binding domain of Spike glycoprotein (S-RBD), as well as the human receptor Angiotensin-converting enzyme-2 (hACE2) were chosen as targets. The screening was performed by molecular docking, followed by 100-ns molecular dynamic simulations and free energy calculations. 24-Methylene cycloartanol acetate (24MCA) was found as the best inhibitor for both Evp and RdRp, and sitosterol acetate (SA) as the best hit for Mpro, S-RBD and hACE2. Dynamic simulations, binding mode analyses, free energy terms and share of key amino acids in protein–drug interactions confirmed the stable binding of these phytocompounds to the hotspot sites on the target proteins. With their possible multi-targeting capability, the introduced phytoligands might offer promising lead compounds for persistent fight with the rapidly evolving coronavirus. Therefore, experimental verification of their safety and efficacy is recommended. Communicated by Ramaswamy H. Sarma
A "nu" look at gravitational waves: The black hole birth rate from neutrinos combined with the merger rate from LIGO
Creators: name: Davis, Jonathan H.
name: Fairbairn, Malcolm
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We make projections for measuring the black hole birth rate from the diffuse supernova neutrino background (DSNB) by future neutrino experiments, and constrain the black hole merger fraction $ε$, when combined with information on the black hole merger rate from gravitational wave experiments such as LIGO. The DSNB originates from neutrinos emitted by all the supernovae in the Universe, and is expected to be made up of two components: neutrinos from neutron-star-forming supernovae, and a sub-dominant component at higher energies from black-hole-forming "unnovae". We perform a Markov Chain Monte Carlo analysis of simulated data of the DSNB in an experiment similar to Hyper-Kamiokande, focusing on this second component. Since all knowledge of the neutrino emission from unnovae comes from simulations of collapsing stars, we choose two sets of priors: one where the unnovae are well-understood and one where their neutrino emission is poorly known. By combining the black hole birth rate from the DSNB with projected measurements of the black hole merger rate from LIGO, we show that the fraction of black holes which lead to binary mergers observed today $ε$ could be constrained to be within the range $2 \cdot 10^{-4} \leq ε\leq 3 \cdot 10^{-2}$ at $3 σ$ confidence, after ten years of running an experiment like Hyper-Kamiokande.
description: 19 pages, 6 figures. v3: Matches version accepted to JCAP
Slowly rotating super-compact Schwarzschild stars
Creators: name: Posada, Camilo
Publisher: name: arXiv
Year: 2016
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The Schwarzschild interior solution, or `Schwarzschild star', which describes a spherically symmetric homogeneous mass with constant energy density, shows a divergence in pressure when the radius of the star reaches the Schwarzschild-Buchdahl bound. Recently Mazur and Mottola showed that this divergence is integrable through the Komar formula, inducing non-isotropic transverse stresses on a surface of some radius $R_{0}$. When this radius approaches the Schwarzschild radius $R_{s}=2M$, the interior solution becomes one of negative pressure evoking a de Sitter spacetime. This gravitational condensate star, or gravastar, is an alternative solution to the idea of a black hole as the ultimate state of gravitational collapse. Using Hartle's model to calculate equilibrium configurations of slowly rotating masses, we report results of surface and integral properties for a Schwarzschild star in the very little studied region $R_{s}
description: 11 pages, 15 figures
An integral representation for Herglotz-Nevanlinna functions in several variables
Creators: name: Luger, Annemarie
name: Nedic, Mitja
Publisher: name: arXiv
Year: 2017
Subjects: subject: Complex Variables (math.CV)
subject: FOS: Mathematics
subject: 32A26 (Primary), 32A40, 32A10 (Secondary)

description: In this article, a characterization of the class of Herglotz-Nevanlinna functions in $n$ variables is given in terms of an integral representation. Furthermore, alternative conditions on the measure appearing in this representation are discussed in detail. Symmetry properties induced by the integral representation are also investigated.
description: 26 pages