cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Novel hydrazone schiff’s base derivatives of polyhydroquinoline: synthesis, in vitro prolyl oligopeptidase inhibitory activity and their Molecular docking study
Creators: name: Talab, Faiz
name: Alam, Aftab
name: Zainab
name: Ullah, Saeed
name: Elhenawy, Ahmed A.
name: Shah, Syed Adnan Ali
name: Ali, Mumtaz
name: Halim, Sobia Ahsan
name: Khan, Ajmal
name: Latif, Abdul
name: Al-Harrasi, Ahmed
name: Ahmad, Manzoor
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Hematology
subject: Infectious Diseases
subject: FOS: Health sciences

description: This research work reports the synthesis of new derivatives of the hydrazone Schiff bases (1–17) based on polyhydroquinoline nucleus through multistep reactions. HR-ESIMS,1H- and 13C-NMR spectroscopy were used to structurally infer all of the synthesized compounds and lastly evaluated for prolyl oligopeptidase inhibitory activity. All the prepared products displayed good to excellent inhibitory activity when compared with standard z-prolyl-prolinal. Three derivatives 3, 15 and 14 showed excellent inhibition with IC50 values 3.21 ± 0.15 to 5.67 ± 0.18 µM, while the remaining 12 compounds showed significant activity. Docking studies indicated a good correlation with the biochemical potency of compounds estimated in the in-vitro test and showed the potency of compounds 3, 15 and 14. The MD simulation results confirmed the stability of the most potent inhibitors 3, 15 and 14 at 250 ns using the parameters RMSD, RMSF, Rg and number of hydrogen bonds. The RMSD values indicate the stability of the protein backbone in complex with the inhibitors over the simulation time. The RMSF values of the binding site residues indicate that the potent inhibitors contributed to stabilizing these regions of the protein, through formed stable interactions with the protein. The Rg. analysis assesses the overall size and compactness of the complexes. The maintenance of stable hydrogen bonds suggests the existence of favorable binding interactions. SASA analysis suggests that they maintained stable conformations without large-scale exposure to the solvent. These results indicate that the ligand–protein interactions are stable and could be exploited to design new drugs for disease treatment.
Additional file 2 of Coverage and factors associated with completion of continuum of care for maternal health in sub-Saharan Africa: a multicountry analysis
Creators: name: Alem, Adugnaw Zeleke
name: Shitu, Kegnie
name: Alamneh, Tesfa Sewunet
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Cancer
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2.
Coalgebraic Satisfiability Checking for Arithmetic $μ$-Calculi
Creators: name: Hausmann, Daniel
name: Schröder, Lutz
Publisher: name: arXiv
Year: 2022
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences
subject: F.4.1
subject: 03B70, 03B44

description: The coalgebraic $μ$-calculus provides a generic semantic framework for fixpoint logics over systems whose branching type goes beyond the standard relational setup, e.g. probabilistic, weighted, or game-based. Previous work on the coalgebraic $μ$-calculus includes an exponential-time upper bound on satisfiability checking, which however relies on the availability of tableau rules for the next-step modalities that are sufficiently well-behaved in a formally defined sense; in particular, rule matches need to be representable by polynomial-sized codes, and the sequent duals of the rules need to absorb cut. While such rule sets have been identified for some important cases, they are not known to exist in all cases of interest, in particular ones involving either integer weights as in the graded $μ$-calculus, or real-valued weights in combination with non-linear arithmetic. In the present work, we prove the same upper complexity bound under more general assumptions, specifically regarding the complexity of the (much simpler) satisfiability problem for the underlying one-step logic, roughly described as the nesting-free next-step fragment of the logic. The bound is realized by a generic global caching algorithm that supports on-the-fly satisfiability checking. Notably, our approach directly accommodates unguarded formulae, and thus avoids use of the guardedness transformation. Example applications include new exponential-time upper bounds for satisfiability checking in an extension of the graded $μ$-calculus with polynomial inequalities (including positive Presburger arithmetic), as well as an extension of the (two-valued) probabilistic $μ$-calculus with polynomial inequalities.
Developing skills for sustainability change agents with a participatory backcasting teaching toolbox
Creators: name: Kordas, Olga
name: Pereverza, Kateryna
name: Pasichnyi, Oleksii
name: Nikiforovich, Eugene
Publisher: name: The University of British Columbia
Year: 2015

description: The paper describes and analyses a participatory backcasting teaching toolbox (PBTT) designed to develop a set of skills required for sustainability change agents, including critical and systems thinking, future orientation, ability to work in transdisciplinary frameworks, personal involvement, conflict resolution and consensus building, dealing with complexity and uncertainty, creativity, practical problem-solving and action skills. The PBTT has evolved through experience and insights gained from the implementation of participatory backcasting (PB) methodology within two research projects and from three years of PB teaching practices. The PBTT includes twelve modules based on different steps and procedures of the PB process. The paper describes effects of the PBTT on the development of students’ skills that have been observed throughout ten teaching cases. Furthermore, the potentials and limitations of the PBTT for building up the sustainable development related skills are discussed.
On harmonious coloring of hypergraphs
Creators: name: Czerwiński, Sebastian
Publisher: name: arXiv
Year: 2023
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C15

description: A harmonious coloring of a $k$-uniform hypergraph $H$ is a vertex coloring such that no two vertices in the same edge have the same color, and each $k$-element subset of colors appears on at most one edge. The harmonious number $h(H)$ is the least number of colors needed for such a coloring.
 The paper contains a new proof of the upper bound $h(H)=O(\sqrt[k]{k!m})$ on the harmonious number of hypergraphs of maximum degree $Δ$ with $m$ edges. We use the local cut lemma of A. Bernshteyn.
A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks
Creators: name: Aduddell, Rebekah
name: Fairbanks, James
name: Kumar, Amit
name: Ocal, Pablo S.
name: Patterson, Evan
name: Shapiro, Brandon T.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Category Theory (math.CT)
subject: FOS: Biological sciences
subject: FOS: Mathematics

description: Regulatory networks depict promoting or inhibiting interactions between molecules in a biochemical system. We introduce a category-theoretic formalism for regulatory networks, using signed graphs to model the networks and signed functors to describe occurrences of one network in another, especially occurrences of network motifs. With this foundation, we establish functorial mappings between regulatory networks and other mathematical models in biochemistry. We construct a functor from reaction networks, modeled as Petri nets with signed links, to regulatory networks, enabling us to precisely define when a reaction network could be a physical mechanism underlying a regulatory network. Turning to quantitative models, we associate a regulatory network with a Lotka-Volterra system of differential equations, defining a functor from the category of signed graphs to a category of parameterized dynamical systems. We extend this result from closed to open systems, demonstrating that Lotka-Volterra dynamics respects not only inclusions and collapsings of regulatory networks, but also the process of building up complex regulatory networks by gluing together simpler pieces. Formally, we use the theory of structured cospans to produce a lax double functor from the double category of open signed graphs to that of open parameterized dynamical systems. Throughout the paper, we ground the categorical formalism in examples inspired by systems biology.
description: Final version published in Compositionality
Understanding the basis of thermostability for enzyme “Nanoluc” towards designing industry-competent engineered variants
Creators: name: Nair, Adwaita S. R.
name: Samanta, Arup
name: Hazra, Saugata
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: As a leading contender in the study of luminescence, nanoluciferase has recently attracted attention and proven effective in a wide variety of research areas. Although numerous attempts have been made to improve activity, there has yet to be a thorough exploration of further possibilities to improve thermostability. In this study, protein engineering in tandem with molecular dynamics simulation at various temperatures (300 K, 400 K, 450 K and 500 K) was used to improve our understanding of nanoluciferase dynamics and identification of factors that could significantly enhance the thermostability. Based on these, three novel mutations have been narrowed down, which were hypothesised to improve thermostability. Root mean square deviation and root mean square fluctuation studies confirmed higher stability of mutant at high temperature. Solvent-accessible surface area and protein unfolding studies revealed a decreased tendency of mutant to unfold at higher temperatures. Further free energy landscape and principal component analysis was adapted to get deeper insights into the thermodynamic and structural behavior of these proteins at elevated temperature. Thus, this study provides a deeper insight into the dynamic factors for thermostability and introduces a novel, enhanced nanoluciferase candidate with potential use in industry.
Biochemical and computational inhibition of α-glucosidase by novel metronidazole-linked 1H-1,2,3-triazole and carboxylate moieties: kinetics and dynamic investigations
Creators: name: Ullah, Saeed
name: Halim, Sobia Ahsan
name: Waqas, Muhammad
name: Mansoor, Farheen
name: Avula, Satya Kumar
name: Khan, Farhan A.
name: Perviaz, Muhammad
name: Ogaly, Hanan A.
name: Khan, Ajmal
name: Al-Harrasi, Ahmed
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: In the current study, metronidazole derivatives containing 1H-1,2,3-triazole and carboxylate moieties were evaluated in vitro and by computational methods for their anti-diabetic potential to insight into their medicinal use for the management of type II diabetes mellitus. Interestingly all 14 compounds displayed high to significant inhibitory capability against the key carbohydrate’s digestive enzyme α-glucosidase with IC50 values in range of 9.73–56.39 μM, as compared to marketed drug acarbose (IC50 = 873.34 ± 1.67 μM). Compounds 5i and 7c exhibited the highest inhibition, therefore, these two compounds were further evaluated for their mechanistic studies to explore its type of inhibition. Compounds 5i and 7c both displayed a concentration-dependent (competitive type of inhibition) with Ki values 7.14 ± 0.01, 6.15 ± 0.02 μM, respectively, which conclude their favourable interactions with the active site residues of the α-glucosidase. Interestingly all compounds are non-cytotoxic against BJ cell line. To further validate our findings, in-silico approaches like molecular docking, and molecular dynamic simulations were applied to investigate the mode of bindings of compounds with the enzyme and identifies their inhibition mechanism, which strongly complements our experimental findings.
Additional file 1 of Chin tuck against resistance exercise with feedback to improve swallowing, eating and drinking in frail older people admitted to hospital with pneumonia: protocol for a feasibility randomised controlled study
Creators: name: Smithard, David G.
name: Swaine, Ian
name: Ayis, Salma
name: Gambaruto, Alberto
name: Stone-Ghariani, Aoife
name: Hansjee, Dharinee
name: Kulnik, Stefan T.
name: Kyberd, Peter
name: Lloyd-Dehler, Elizabeth
name: Oliff, William
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. SPIRIT Checklist.
Proofs as stateful programs: A first-order logic with abstract Hoare triples, and an interpretation into an imperative language
Creators: name: Powell, Thomas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Logic (math.LO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: We introduce an extension of first-order logic that comes equipped with additional predicates for reasoning about an abstract state. Sequents in the logic comprise a main formula together with pre- and postconditions in the style of Hoare logic, and the axioms and rules of the logic ensure that the assertions about the state compose in the correct way. The main result of the paper is a realizability interpretation of our logic that extracts programs into a mixed functional/imperative language. All programs expressible in this language act on the state in a sequential manner, and we make this intuition precise by interpreting them in a semantic metatheory using the state monad. Our basic framework is very general, and our intention is that it can be instantiated and extended in a variety of different ways. We outline in detail one such extension: A monadic version of Heyting arithmetic with a wellfounded while rule, and conclude by outlining several other directions for future work.
OMEGA: an open source environment to facilitate the execution of motion analysis workflows, to estimate error and to share results
Creators: name: Rigano, Alessandro
name: Galli, Vanni
name: Giulietti, Raffaello
name: Leidi, Tiziano
name: Valle, Mario
name: Sbalzarini, Ivo
name: Castillia, Caterina Strambio De
Publisher: name: F1000Research
Year: 2016

description: Introduction:

The quantitative analysis of intracellular dynamic processes is vital for understanding molecular mechanisms fundamental to the understanding of disease. This is particularly true in the case of intracellular trafficking of vesicles and viruses, including HIV-1. While several image-analysis algorithms and open-source applications for tracking the movement of such sub-resolution particles have been implemented, a tool capable of executing a complete single particle tracking and motion analysis pipeline, while at the same time monitoring error propagation and maintaining key links between experimental conditions, image data, metadata, analysis definition parameters and numerical output, has not been available to date.

Results:

Open Microscopy Environment inteGrated Analysis (OMEGA) implements a complete, single-particle tracking (SPT) and motion analysis workflow (Fig. 1), within a user-friendly (Fig. 6), modular software infrastructure (Fig. 2) designed to: 1) Import image data and metadata from OMERO; 2) Run spot detection and linking, facilitate results inspection and parameter optimization, assist manual trajectory editing and segmentation, perform mobility, velocity, and diffusivity analysis as well as motion classification (Fig. 3); 3) Estimate the uncertainty associated with each analysis step, evaluate its propagation through the analysis pipeline, and report it as appropriate (Fig. 5). 4) Store analysis results and metadata on the basis of the “Minimum Information about a Biomedical or Biological Investigation” (MIBBI) standard (Fig. 4); 5) Interface with other open-source tools and incorporate novel algorithms as they are developed. The software has been benchmarked with standardized SPT datasets.

Conclusions:

OMEGA greatly facilitates the execution of tasks connected to viral and vesicle tracking and to the biological interpretation of the resulting trajectories. These include motion analysis and pattern classification. It does so by preforming trajectory identification and quantitative motion analysis in the context of a modular, interoperable, and user-friendly software platform that rigorously monitors error propagation and utilizes minimum information principles to facilitate the exchange of both results and analytical methods between communities of users and developers. This is expected to impact both scientists already engaged with the OME initiative as well those that have not yet been reached by such efforts.
Supplementary document for Al2O3-YAG:Ce/YAG composite phosphor ceramics in transmissive configuration for high-brightness laser-driven lighting - 6096772.pdf
Creators: name: Sang, Pengfei
name: Zhang, Le
name: Kang, Jian
name: li, yanbin
name: chen, shiwei
name: yang, peng
name: Sun, Bingheng
name: Li, Yang
name: Chen, Hao
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Supplemental Document (revised)
Additional file 1 of Web-based application for predicting the potential target phenotype for recombinant human thrombomodulin therapy in patients with sepsis: analysis of three multicentre registries
Creators: name: Goto, Tadahiro
name: Kudo, Daisuke
name: Uchimido, Ryo
name: Hayakawa, Mineji
name: Yamakawa, Kazuma
name: Abe, Toshikazu
name: Shiraishi, Atsushi
name: Kushimoto, Shigeki
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Methods.
Arzneimittelinteraktionen – ein unabhängiger Risikofaktor für einen verlängerten Krankenhausaufenthalt bei der Behandlung einer ambulant erworbenen Pneumonie?
Creators: name: Schmitt, Johannes Peter
Publisher: name: Universitäts- und Landesbibliothek Bonn
Year: 2024
Subjects: subject: ddc:610

description: Im Zuge des demographischen Wandels werden Multimorbidität und Polypharmazie und in deren Folge auch das Risiko für unerwünschte Arzneimittelinteraktionen ansteigen.
 Ziel der Arbeit war es herauszufinden, ob Arzneimittelinteraktionen ein unabhängiger Risikofaktor für eine Verlängerung der Krankenhausverweildauer sind.
 Hierzu wurden im Rahmen einer retrospektiven, monozentrischen Studie alle verordneten Medikamente, die ein Patient während der Behandlung seiner ambulant erworbenen Pneumonie im Krankenhaus erhielt, auf unerwünschte Arzneimittelinteraktionen geprüft und anschließend deren Assoziationen auf die Krankenhausverweildauer mithilfe einer negativen binominalen Regressionsanalyse untersucht.
 Es konnte schließlich gezeigt werden, dass unerwünschte Arzneimittelinteraktionen einen unabhängigen Risikofaktor für eine signifikante Verlängerung der Krankenhausverweildauer darstellen.
 Im Hinblick auf gesundheitsökonomische Aspekte in einer alternden Gesellschaft mit steigender Multimorbidität und Polypharmazie sollten Hilfsmittel wie Computerprogramme konsequent Anwendung finden, um abwendbare, unerwünschte Arzneimittelinteraktionen zukünftig besser erkennen und vermeiden zu können.
Navigating sustainable transitions considering uncertainties and evolving goals/means
Creators: name: Jørgensen, Ulrik
Publisher: name: The University of British Columbia
Year: 2015

description: Sustainable transitions are at the core of engineering design and in societal discourse of how to deal with climate and socio-economic challenges. As natural and societal conditions are different from place to place and are continuously changing transitions processes are to take place considering uncertain futures and changing pairs of goals and means. To cater for this the focus in training of professionals within engineering and design as well as in economic/policy topics must take into account the lack of finite metrics and operate with navigational approaches that need adjustments as part of the process. The character of uncertainties and consequentially the challenges to stage actor-configurations and navigate changes are core to this presentation. Based on results from studies of historic and contemporary transitions and their aspirations to achieve sustainable solutions as well as experiences from training design-engineers specialized in sustainable design the paper will present models of the mapping of arenas of development and how to navigate within and across these arenas. The paper concludes in outlining learning programs based on the navigational approach to sustainable transitions.
The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations
Creators: name: Poddar, Sayan
name: Roy, Rajarshi
name: Kar, Parimal
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The Hepatitis C Virus (HCV), responsible for causing hepatitis and a significant contributor to liver disorders, presents a challenge for treatment due to its high genetic variability. Despite efforts, there is still no effective medication available for this virus. One of the promising targets for drug development involves targeting glycoprotein E2. However, our understanding of the dynamic behavior of E2 and its associated glycans remains limited. In this study, we investigated the dynamic characteristics of E2 with varying degrees of glycosylation using all-atom molecular dynamics simulations. We also explored glycan’s interactions with the protein and among themselves. An overall increase in correlation between the vital protein regions was observed with an increase in glycan number. The protein dynamics is followed by the analysis of glycan dynamics, where the flexibility of the individual glycans was analyzed in their free and bound state, which revealed a decrease in their fluctuation in some cases. Furthermore, we generated the free energy landscape of individual N-glycan linkages in both free and bound states and observed both increases and decreases in flexibility, which can be attributed to the formation and breakage of hydrogen bonds with amino acids. Finally, we found that for a high glycosylation system, glycans interact with glycoprotein and form hydrogen bonds among themselves. Moreover, the hydrogen bond profiles of a given glycan can vary when influenced by other glycans. In summary, our study provides valuable insights into the dynamics of the core region of HCV E2 glycoprotein and its associated glycans.
Perturbation results for distance-edge-monitoring numbers
Creators: name: Yang, Chenxu
name: Klasing, Ralf
name: He, Changxiang
name: Mao, Yaping
Publisher: name: arXiv
Year: 2023
Subjects: subject: Discrete Mathematics (cs.DM)
subject: Data Structures and Algorithms (cs.DS)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Foucaud et al. recently introduced and initiated the study of a new graph-theoretic concept in the area of network monitoring. Given a graph $G=(V(G), E(G))$, a set $M \subseteq V(G)$ is a distance-edge-monitoring set if for every edge $e \in E(G)$, there is a vertex $x \in M$ and a vertex $y \in V(G)$ such that the edge $e$ belongs to all shortest paths between $x$ and $y$. The smallest size of such a set in $G$ is denoted by $\operatorname{dem}(G)$. Denoted by $G-e$ (resp. $G \backslash u$) the subgraph of $G$ obtained by removing the edge $e$ from $G$ (resp. a vertex $u$ together with all its incident edges from $G$). In this paper, we first show that $\operatorname{dem}(G-e)- \operatorname{dem}(G)\leq 2$ for any graph $G$ and edge $e \in E(G)$. Moreover, the bound is sharp. Next, we construct two graphs $G$ and $H$ to show that $\operatorname{dem}(G)-\operatorname{dem}(G\setminus u)$ and $\operatorname{dem}(H\setminus v)-\operatorname{dem}(H)$ can be arbitrarily large, where $u \in V(G)$ and $v \in V(H)$. We also study the relation between $\operatorname{dem}(H)$ and $\operatorname{dem}(G)$, where $H$ is a subgraph of $G$. In the end, we give an algorithm to judge whether the distance-edge monitoring set still remain in the resulting graph when any edge of the graph $G$ is deleted.
Additional file 2 of Web-based application for predicting the potential target phenotype for recombinant human thrombomodulin therapy in patients with sepsis: analysis of three multicentre registries
Creators: name: Goto, Tadahiro
name: Kudo, Daisuke
name: Uchimido, Ryo
name: Hayakawa, Mineji
name: Yamakawa, Kazuma
name: Abe, Toshikazu
name: Shiraishi, Atsushi
name: Kushimoto, Shigeki
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Science Policy
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2: Table S1. Missingness in predictors and outcome variables.
A new teaching pedagogy to enhance societal needs, sustainability, innovation and entrepreneurial skills
Creators: name: Hamouda, A. M. S.
name: Tarlochan, Faris
Publisher: name: The University of British Columbia
Year: 2015

description: Design is a common element in most Mechanical and Industrial Engineering programs globally. In the design course, various aspects of product embodiment, manufacturing processes and material selection are discussed. To bring further flavour to the design course in Qatar University element such as life cycle, innovation and entrepreneurship with active learning was introduced. The students were divided in few groups. Each group had to address a societal need within or external to Qatar. The solutions address the issues of sustainability. The students were given sessions about tools for idea generation and creativity techniques. Once the problem had been identified, these groups were advised and coached to prepare a comprehensive business plan that include selection of materials and manufacturing processes, life cycle, organizational structure, how they will market their product, market segmentation and penetration, break even analysis and economic analysis as well as environmental impact. From the course assessment and student course outcomes surveys, it was found that the interest and learning curve for students increased drastically for this course. Besides improving the interest and learning curve, the approach had indirectly exposed the student to project management skills, economic analysis – balance sheet and cash flow and breakeven point analysis, lifelong learning, communication and teamwork. In whole, the approach was an interesting and led to further enhance the student learning process by using different learning styles through varied and innovative teaching techniques.
Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies
Creators: name: Thai, Quynh Mai
name: Phung, Huong T. T.
name: Pham, Ngoc Quynh Anh
name: Horng, Jim-Tong
name: Tran, Phuong-Thao
name: Tung, Nguyen Thanh
name: Ngo, Son Tung
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: VP39, an essential 2′-O-RNA methyltransferase enzyme discovered in Monkeypox virus (MPXV), plays a vital role in viral RNA replication and transcription. Inhibition of the enzyme may prevent viral replication. In this context, using a combination of molecular docking and molecular dynamics (MDs) simulations, the inhibitory ability of NCI Diversity Set VII natural compounds to VP39 protein was investigated. It should be noted that the computed binding free energy of ligand via molecular docking and linear interaction energy (LIE) approaches are in good agreement with the corresponding experiments with coefficients of R=0.72 and 0.75, respectively. NSC 319990, NSC 196515 and NSC 376254 compounds were demonstrated that can inhibit MPVX methyltransferase VP39 protein with the similar affinity compared to available inhibitor sinefungin. Moreover, nine residues involving Gln39, Gly68, Gly72, Asp95, Arg97, Val116, Asp138, Arg140 and Asn156 may be argued that they play an important role in binding process of inhibitors to VP39.
Additional file 1 of Cardiometabolic diseases, total mortality, and benefits of adherence to a healthy lifestyle: a 13-year prospective UK Biobank study
Creators: name: Xu, Chenjie
name: Cao, Zhi
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer

description: Additional file 1: Text S1 Diet score extended information. Text S2 Variable assessment. Table S1. Risk of all-cause mortality according to number of lifestyle factors. Table S2. The association of separate lifestyle factors with total mortality. Table S3. Mortality rate and hazard ratio of CMDs status and lifestyle factors in relation to mortality. Table S4. The association of CMDs status and lifestyle factors with total mortality in subgroup of sex. Table S5. The association of CMDs status and lifestyle factors with total mortality in subgroup of age. Table S6. Joint effect of CMDs and lifestyle factors on total mortality in subgroup of sex. Table S7. Joint effect of CMDs status and lifestyle factors on total mortality in subgroup of age. Table S8. Hazard ratios for cancers after exclusion of first two years of follow-up across CMDs status and lifestyle factors. Table S9. Joint associations of CMDs status and lifestyle factors with total mortality when missing covariates are imputed by multiple imputation. Table S10. Risk of all-cause mortality according to lifestyle factors category within CMDs status by constructing a weighted lifestyle score. Table S11. Risk of all-cause mortality according to lifestyle factors category within CMDs status after adjusting PM 10, PM 2.5, and NO2. Table S12. Risk of all-cause mortality according to lifestyle factors category within CMDs status after adjusting family history of CMDs. Figure S1. Participant flow diagram.
Additional file 1 of Parents’ awareness and perceptions of the Change4Life 100 cal snack campaign, and perceived impact on snack consumption by children under 11 years
Creators: name: Day, Rhiannon E.
name: Bridge, Gemma
name: Austin, Kate
name: Ensaff, Hannah
name: Christian, Meaghan S.
Publisher: name: figshare
Year: 2022
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1.
Cracking a cancer code DNA methylation in epigenetic modification: an in-silico approach on efficacy assessment of Sri Lanka-oriented nutraceuticals
Creators: name: R., Dushanan
name: S., Weerasinghe
name: P., Dissanayake D.
name: R., Senthilnithy
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
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: Cancer

description: DNA methyltransferase (DNMTs) are essential epigenetic modifiers that play a critical role in gene regulation. These enzymes add a methyl group to cytosine’s 5'-carbon, specifically within CpG dinucleotides, using S-adenosyl-L-methionine. Abnormal overexpression of DNMTs can alter the gene expression patterns and contribute to cancer development in the human body. Therefore, the inhibition of DNMT is a promising therapeutic approach to cancer treatment. This study was aimed to identify potential nutraceutical inhibitors from the Sri Lanka Flora database using computational methods, which provided an atomic-level description of the drug binding site and examined the interactions between nutraceuticals and amino acids of the DNMT enzyme. A series of nutraceuticals from Sri Lanka-oriented plants were selected and evaluated to assess their inhibitory effects on DNMT using absorption, distribution, metabolism, excretion and toxicity analysis, virtual screening, molecular docking, molecular dynamics simulation and trajectory analysis. Azacitidine, a DNMT inhibitor approved by the US Food and Drug Administration, was selected as a reference inhibitor. The complexes with more negative binding energies were selected and further assessed for their potency. Seven molecules were identified from 200 nutraceuticals, demonstrating significantly negative binding energies against the DNMT enzyme. Various trajectory analyses were conducted to investigate the stability of the DNMT enzyme. The results indicated that petchicine (NP#0003), ouregidione (NP#0011) and azacitidine increased the stability of the DNMT enzyme. Consequently, these two nutraceuticals showed inhibitory efficacies similar to azacitidine, making them potential candidates for therapeutic interventions targeting DNMT enzyme-related cancers. Additional bioassay testing is recommended to confirm the efficacies of these nutraceuticals and explore their applicability in clinical treatments.
Contact graphs of boxes with unidirectional contacts
Creators: name: Gonçalves, Daniel
name: Limouzy, Vincent
name: Ochem, Pascal
Publisher: name: arXiv
Year: 2023
Subjects: subject: Discrete Mathematics (cs.DM)
subject: Combinatorics (math.CO)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: This paper is devoted to the study of particular geometrically defined intersection classes of graphs. Those were previously studied by Magnant and Martin, who proved that these graphs have arbitrary large chromatic number, while being triangle-free. We give several structural properties of these graphs, and we raise several questions.
description: Minor change
Multidimensional sustainability assessment of solar products : educating engineers and designers
Creators: name: Flipsen, Bas
name: Bakker, Conny
name: Verwaal, Martin
Publisher: name: The University of British Columbia
Year: 2015

description: Since 2008 the faculty of Industrial Design Engineering at the TU Delft hosts the minor Sustainable Design Engineering. The minor has been highly useful as a platform to pilot new ways of teaching engineering for sustainable development. Instead of having students make life cycle assessments and introduce them to straightforward checklists to improve their product designs, we challenge our students to develop a critical understanding of sustainability and use multidimensional assessments. Sustainability is not just about environmental benefits but also about useful products and added value. This paper describes our educational approach in the photovoltaics practicum (part of the minor). Our objective is to illustrate how such a multidimensional assessment works in practice and how it has helped students to develop a more critical, systemic perspective on sustainability. Students are asked to evaluate a PV-powered product on its sustainability by assessing the technology, usability and the environmental impact. To date, over 150 students have followed the minor, which gives us a large database of multidimensional assessments on a wide range of PV powered products. This paper describes the conclusions we have drawn on the validity of our approach. Our findings show that many of the currently available products with integrated PV systems are initially perceived as “green” but after assessing the product on multidimensional aspects students invariably reach a more nuanced perspective, with some products failing to pass the test. Students indicated how the multidimensional assessment has made them better equipped to see through the “greenwash” and give a balanced evaluation of the real value of solar cells integrated in products. The paper will elaborate the methods used in the multidimensional assessment in more detail, illustrated with student work.
ПОЛИКОМПЛЕКСЫ НАТРИЙКАРБОКСИМЕТИЛЦЕЛЛЮЛОЗЫ С ПОЛИАКРИЛАМИДОМ – ОСНОВА ДЛЯ МЯГКИХ ЛЕКАРСТВЕННЫХ ПРЕПАРАТОВ
Creators: name: Саидисломова, Н.С.
name: Инагамов, С.Я.
Publisher: name: Zenodo
Year: 2024

description: Полимерные комплексы (ПК) являются перспективными продуктами в фармации и находят все более широкое применение в качестве загустителей и стабилизаторов, пролонгаторов действия лекарственных веществ, пленкообразователей для капсул и таблеток, как основы для мазей и мягких лекарственных форм, поскольку обнаруживают ряд уникальных и наиболее ценных свойств.
Zingiberaceae-derived phytomolecules inhibit Japanese encephalitis virus RNA dependent RNA polymerase: a molecular dynamics study
Creators: name: Alam, Aftab
name: Anjum, Asma
name: Moglad, Ehssan H.
name: Jawaid, Talha
name: Foudah, Ahmed I.
name: Alotaibi, Faisal
name: Alkhayl, Faris F. Aba
name: Kamal, Mohammad Azhar
name: Warsi, Mohiuddin Khan
name: Balaha, Mohamed F.
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology
subject: Computational Biology

description: The Japanese encephalitis virus, (JEV), is a flavivirus mostly transmitted by Culex mosquitoes mostly present in Southeast Asia and the Western Pacific region. Ardeid-wading birds are the natural reservoir of JEV; nonetheless, pigs are frequently a key amplifying host during epidemics in human populations. Although more domestic animals and wildlife are JEV hosts, it is unclear how these animals fit into the ecology and epidemiology of the virus. Even though there is no specific therapy, vaccines are available to prevent this infection. However, current vaccinations do not work against every clinical isolate and can cause neurological problems in certain people. In this study, we have screened 501 phytochemical compounds from various plants from the Zingeberaceae family against the RdRp protein of JEV. Based on this, the top five compounds (IMPHY014466, IMPHY004928, IMPHY007097, IMPHY014179 and IMPHY005010) were selected based on the obtained docking scores, which was above −8.0 Kcal/mol. Further, the binding affinity of these selected ligands was also analysed using molecular interaction, and the presence of interactions like hydrogen bonds, hydrophobic bonds and polar bonds with respective active residues were identified and studied elaborately. Furthermore, the dynamic stability of the docked RdRp protein with these selected phytochemicals was studied using Molecular dynamic simulation and essential dynamics. The free energy landscape analysis also provided information about the energy transition responsible stability of the complex. The results obtained advocated phytochemical compounds from the zingeberaceae family for future experimental validation, as these compounds exhibited significant potential as JEV antagonists.
2018 IEEE SoutheastCon Hardware Competition
Creators: name: Choate, Andrew
name: Mitchell, Bryan
name: Derrington, Jesse
name: Wargel, Collin
Publisher: name: Unknown
Year: 2018

description: The aim of this project is to design and construct an autonomous robot for the 2018
lEEE SoutheastCon Hardware Competition located in Saint Petersburg,
Florida. This competition consists of an arena where there will be six objectives to complete.
The six objectives included receiving an IR signal, pressing a button, pressing a pressure plate,
turning a 3D printed wheel on a rotary encoder knob and displaying the code, acquiring a
weighted box, and navigating the arena to each objective. The scope of the project detailed
herein includes three of the six objectives: navigation, receiving an IR signal and display the
code, and acquiring the weighted box. The design phase of this project involved both the testing
of pre-built sensors and components, and the designing of custom hardware. Once the final
designs were chosen, fabrication and testing began. Modifications to the designs were made
when testing and integrating the various subsystems, resulting in an effective and efficient robot.
Embedding sustainability in the curriculum at the engineering school of the University of Chile
Creators: name: Vargas, Luis S.
name: MacLean, Claudia A.
Publisher: name: The University of British Columbia
Year: 2015

description: The present paper presents two manners in which, by utilising the existing structures, sustainability is being integrated in the engineering degree programmes at the University of Chile. The first approach consists of including sustainability topics, principles and methodologies within the first two and a half years of compulsory courses; while the second one, entail the creation of two Minor programmes which can be undertaken by the students within a voluntary scheme. Additionally, this work describes the change process towards sustainability in teaching, and the main challenges found along the road. Moreover, in order to quantify the gap between the current and desired curriculum status in terms of sustainability incorporation, some context-specific assessment metrics are proposed.
Rigidity on Quantum Symmetry for a Certain Class of Graph C*-algebras
Creators: name: Karmakar, Ujjal
name: Mandal, Arnab
Publisher: name: arXiv
Year: 2023
Subjects: subject: Operator Algebras (math.OA)
subject: FOS: Mathematics

description: Quantum symmetry of graph $C^{*}$-algebras has been studied, under the consideration of different formulations, in the past few years. It is already known that the compact quantum group $(\underbrace{C(S^{1})*C(S^{1})*\cdots *C(S^{1})}_{|E(Γ)|-times}, Δ) $ always acts on a graph $C^*$-algebra for a finite, connected, directed graph $Γ$ in the category introduced by Joardar and Mandal, where $|E(Γ)|:=$ number of edges in $Γ$. In this article, we show that for a certain class of graphs including Toeplitz algebra, quantum odd sphere, matrix algebra etc. the quantum symmetry of their associated graph $C^*$-algebras remains $(\underbrace{C(S^{1})*C(S^{1})*\cdots *C(S^{1})}_{|E(Γ)|-times}, Δ) $ in the category as mentioned before. More precisely, if a finite, connected, directed graph $Γ$ satisfies the following graph theoretic properties : (i) there does not exist any cycle of length $\geq$ 2 (ii) there exists a path of length $(|V(Γ)|-1)$ which consists all the vertices, where $|V(Γ)|:=$ number of vertices in $Γ$ (iii) given any two vertices (may not be distinct) there exists at most one edge joining them, then the universal object coincides with $(\underbrace{C(S^{1})*C(S^{1})*\cdots *C(S^{1})}_{|E(Γ)|-times}, Δ) $. Furthermore, we have pointed out a few counter examples whenever the above assumptions are violated.
description: Final version of the article appeared in Journal of Mathematical Physics. According to the guidelines of the journal: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Math. Phys. 65, 083501 (2024) and may be found at https://doi.org/10.1063/5.0177215
Elucidating the EXOSC3-IRE1α interaction: a convergent study incorporating computational, in vitro and in vivo studies
Creators: name: Ashraf, Ariha
name: Majeed, Younis
name: Gul, Irfan
name: Banday, Mariam
name: Ramzan, Khalida
name: Fazili, Khalid Majid
Publisher: name: Taylor & Francis
Year: 2024
Subjects: Biophysics
Biochemistry
Cell Biology
Molecular Biology
Biological Sciences not elsewhere classified
Mental Health

description: The Unfolded protein response (UPR) is an adaptive signalling pathway which is triggered by accumulation of unfolded/misfolded protein in ER lumen. The UPR consist of three transmembrane proteins-IRE1α, PERK and ATF6 that sense ER stress which leads to activation and downstream signaling from ER lumen to cytosol to restore homeostasis. IRE1α is an evolutionary conserved arm of UPR and acts as an interaction platform for many potential proteins that become activated under ER stress conditions. We investigated potential partners of IRE1 α through MS studies and found EXOSC3 as one of the binding partner of IRE1α. Exosomal complex proteins have 3′5′ exonuclease properties (EXOSC3) that play an important role in mRNA surveillance. This property of exosomal proteins coincides with IRE1α ribonuclease activities and its mechanism of action is similar to that of IRE1α-RIDD pathway which degrades any unstable mRNA that disrupts cellular homeostasis. At the same time, studies have shown that knockdown of EXOSC3 causes ER stress in human cells, so we speculated that there might be a functional crosstalk between IRE1α and EXOSC3 under ER stress conditions. Therefore, we employed computational tools to predict and explore the stability and dynamics of the IRE1α-EXOSC3 complex. The analysis indicates that IRE1α and EXOSC3 exhibit potential interaction with the involvement of ScanNet, predicting binding pockets between the two proteins. Further, the interaction was validated via co-immunoprecipitation and yeast two-hybrid assays, thus suggesting EXOSC3 as a component of the UPRosome complex. Hence, this functional crosstalk might influence the dynamic functional output of IRE1α.