bluuebunny/crossref_metadata_2025 huggingface dataset:
Removal of lead ions (Pb2+) from aqueous solution using chitosan/starch composite material: Experimental and density functional theory findings
Authors: Çelik Muhammed Safa , Çaylak Osman , Kütük Nurşah , Yenidünya Ali Fazıl , Çetinkaya Serap , Maslov Mikhail M. , Kaya Savaş
Published: February 2024

Treatment of wastewater has become vital to prevent environmental pollution in recent years. Adsorption is an easily applicable, low-cost and efficient method and is the subject of this study. In this study, an adsorbent was synthesized to be used in heavy metal removal using chitosan and starch. The composite was characterized by Fourier transform infrared (FTIR) spectrophotometry, X-ray powder diffraction (XRD), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM), energy-dispersive X-ray (EDX) analysis. It was determined that the composite had an amorphous and compact structure. Adsorption experiments were carried out under the optimized parameters such as solution pH, concentration, adsorbent amount, equilibrium time, and temperature. It shows that during adsorption, with the increase in pH, the adsorption efficiency and adsorption capacity first increase and then a fluctuation occurs. The highest adsorption efficiency and Q value were reached at pH 3.46 as 78% and 0.038 mol/kg, respectively. Moreover, the adsorption capacity (Q) reached its highest value with a value of 0.067 mol/kg in the presence of 30 mg adsorbent. Equilibrium experiments were validated by the Langmuir, Freundlich, Temkin and Dubinin–Radushkevich isotherm models. To investigate the adsorption mechanism, pseudo-first-order (PFO) and pseudo-second-order (PSO) kinetic models were used. It was determined that the adsorption process followed the D-R isotherm (R2 = 0.99) and PSO (R2 = 0.99). Therefore, the existence of chemical adsorption can be mentioned. Thermodynamic parameters enthalpy (∆H), Gibbs free energy (∆G) and entropy change (∆S) were investigated. The adsorbate-adsorbent interactions were studied by density functional theory (DFT).
Protective role of SARS-CoV-2 anti-S IgG against breakthrough infections among European healthcare workers during pre and post-Omicron surge—ORCHESTRA project
Authors: Spiteri Gianluca , D’Agostini Marika , Abedini Mahsa , Ditano Giorgia , Collatuzzo Giulia , Boffetta Paolo , Vimercati Luigi , Sansone Emanuele , De Palma Giuseppe , Modenese Alberto , Gobba Fabriziomaria , Liviero Filippo , Moretto Angelo , dell’Omo Marco , Fiordi Tiziana , Larese Filon Francesca , Mauro Marcella , Violán Concepción , Mates Dana , Oravec Bérešová Jana , Monaco Maria Grazia Lourdes , Carta Angela , Verlato Giuseppe , Porru Stefano
Published: February 2024

Purpose

Anti SARS-CoV-2 vaccination initially showed high effectiveness in preventing COVID-19. However, after the surge of variants of concern, the effectiveness dropped. Several studies investigated if this was related to the decrease of the humoral response over time; however, this issue is still unclear. The aim of this study was to understand whether SARS-CoV-2 anti-S IgG levels can be used to predict breakthrough infection risk and define the timing for further booster doses administration.

Method

Within the framework of the ORCHESTRA Project, over 20,000 health workers from 11 European centers were enrolled since December 2020. We performed two Cox proportional hazards survival analyses regarding pre-Omicron (from January to July 2021) and Omicron (December 2021–May 2022) periods. The serological response was classified as high (above the 75th percentile), medium (25th-75th), or low (< 25th).

Results

Seventy-four (0.33%) and 2122 (20%) health workers were infected during the first and second periods, respectively. Both Cox analyses showed that having high anti-S titer was linked to a significantly lower risk of infection as compared to having medium serological response [HR of high vs medium anti-S titer = 0.27 (95% CI 0.11–0.66) during the first phase, HR = 0.76 (95% CI 0.62–0.93) during the second phase].

Conclusion

Vaccine effectiveness wanes significantly after new variants surge, making anti-S titer unsuitable to predict optimal timing for further booster dose administration. Studies on other immunological indicators, such as cellular immunity, are therefore needed to better understand the mechanisms and duration of protection against breakthrough infection risk.
Investigating indigenous knowledge awareness among South African science teachers for developing a guideline
Authors: Photo Patricia , McKnight Marcell
Published: February 2024

This research article explores the development of preliminary guidelines for the integration of Indigenous Knowledge Systems (IKS) into science classrooms. The study addresses the need for such guidelines to enhance learning outcomes in STEM. Grounded in Vygotsky’s sociocultural theory, the research investigates science teachers’ familiarity with IKS, their beliefs about its relevance, and their proposed strategies for its effective incorporation into science education. The study employed an interpretive qualitative research approach, conducting two independent case studies with a total of five teachers from primary and secondary schools in Hazyview, Mpumalanga. Through surveys and interviews, teachers’ perspectives were explored. A combination of inductive and deductive thematic analysis was used. The findings reveal varied levels of familiarity among teachers, differing perceptions of IKS relevance, and few proposed strategies for IKS integration. Additionally, preliminary guidelines were developed to bridge a gap between cultural knowledge and scientific understanding. These guidelines aim to empower teachers to transition from the familiar (IKS) to the unfamiliar (Western science), fostering a more culturally responsive science education environment. The study acknowledges the limitations of a small sample size, emphasizing the depth of qualitative awareness over generalizability. The proposed guidelines offer a foundation for further research and practical implementation, contributing to the advancement of inclusive and culturally relevant science education.
Effects of Seafood Mushroom Spent Substrate Solid-State Fermentation Combined with PGPR as a Microbial Fertilizer on the Soil Environment and Growth Promotion of Cenchrus fungigraminus
Authors: Li Jing , Lei Yufang , Qin Zheng , Liu Junyuan , Rensing Christopher , Lin Zhanxi , Lin Dongmei
Published: February 2024

Purpose

Careless burning, discarding, or overfertilization of spent mushroom substrate (SMS) is environmentally harmful. The reuse of SMS resources is a matter of concern.

Methods

Spent seafood mushroom substrate solid-state fermentation combined with Rhizobium pusense solution was added to soil to evaluate its environmental and Cenchrus fungigraminus seedling growth effects in pot trial experiments.

Results

The 40% fermented seafood mushroom SMS (fresh weight) with R. pusense treatment had significantly higher total nitrogen (TN), ammonium nitrogen (AMN), organic matter, etc., and decreased soil electrical conductivity (EC) and increased pH compared with other treatment. Soil catalase (CAT), dehydrogenase (DHA), and urease (UE) activities were significantly improved; there were no differences in CAT and UE activities between 40% (T4) and 50% (T5) SMS additions. C. fungigraminus seedling height and leaf length increased gradually and were significantly different from those of the positive control. The 30–50% seafood mushroom SMS treatment increased plant TN by 5.76–10.00% and total phosphorus by 15.44–16.55%. Plant root length and root activity peaked in T4; however, plant split root number and root activity in T5 decreased by 43.96% and 26.97% compared with those in T4. According to Pearson correlation and one-dimensional regression analyses, the seafood mushroom SMS content affected fertility > enzyme activity > plant growth. Principal component analysis and redundancy analysis showed that the effect of the seafood mushroom SMS concentration on the soil environment was mainly reflected in plant aboveground and root activity.

Conclusions

Under an SMS addition amount of 40%, plant growth-promoting rhizobacteria promoted the growth of C. fungigraminus seedlings to a greater extent.
Drunken Mountains: Analysis of the Bennett and Ponce Monoliths of Tiwanaku (AD 500–1100) from a Multispecies Perspective
Authors: Villanueva Criales Juan
Published: February 2024

Archaeological research on the architecture and sculpture of Tiwanaku society in the south-central Andes follows two separate paths: one emphasizes iconographic interpretation, whereas the other studies lithic materials’ origin and spatial relations. This separation, stemming from dualistic modern thought, is an obstacle to a comprehensive understanding of lithic sculptures and their role in Tiwanaku society. This article focuses on the Ponce and Bennett monoliths, the two largest and most complex sculptures of the Tiwanaku ceremonial center. It presents the results of an iconographic analysis identifying minimal design components ordered in a three-level nested hierarchy and their distribution over the spatial structures of both sculptures. This analysis incorporates existing information about lithic materials and quarries, the monoliths’ locations, and spatial relationships. All those data are interpreted in the light of Aymara and Quechua ontologies about the relationships between mountains, stones, and images. Characterizing aspects of the Tiwanaku site and its role in lithic production, this article extends the limits of Tiwanaku society to include nonhuman agents and suggests that we overcome anthropocentric biases.
Classroom-based extensive reading: a review of recent research
Authors: Robb Thomas N. , Ewert Doreen
Published: February 2024

This survey of recent research on extensive reading (ER) for language learners focuses on ER in the classroom. While early adopters of ER imagined the quick emergence of an intrinsically motivated independent reader, the reality of much classroom-based language learning is that without considerable teacher guidance and supportive transitional activities, students are not likely to reach self-motivated independent ER either in or out of the classroom. Many of the studies included here, mostly non-experimental and classroom-based, reflect this reality. These studies confirm previous research on the general efficacy of ER in promoting motivation, vocabulary, and fluency development, but they also provide evidence for a variety of ways to support reluctant and grade-focused students who are only willing to engage with the target language in the classroom. This review also considers the many impediments that restrict the implementation of ER with language learners in school contexts. Separate sections discuss ER motivation and attitudes, ER and vocabulary, the effects of ER on reading fluency, as well as speculation on the relationship between “time on task” and progress in the various reading subskills. Each major section concludes with a table summarizing the research that has been discussed and suggestions for future investigation.
Masers in accretion burst sources
Authors: Bayandina Olga ,   the M2O collaboration, Kobak Agnieszka , Caratti o Garatti Alessio , Tolmachev Alexander , Volvach Alexandr , Alakoz Alexei , Wootten Alwyn , Bisyarina Anastasia , Dzodzomenyo Andrews , Sobolev Andrey , Bartkiewicz Anna , Aberfelds Artis , Stecklum Bringfried , Kramer Busaba , Macdonald Callum , Cyganowski Claudia , Colomer Fransisco , Miro Cristina Garcia , Brogan Crystal , Li Dalei , Smits Derck , Engels Dieter , Ladeyschikov Dmitry , Johnstone Doug , Popova Elena , Proven-Adzri Emmanuel , van den Heever Fanie , Orosz Gabor , Surcis Gabriele , Wu Gang , MacLeod Gordon , Linz Hendrik , Imai Hiroshi , van Langevelde Huib , Val’tts Irina , Shmeld Ivar , Chibueze James O. , Brand Jan , Kumar Jayender , Green Jimi , Vorster Job , Eislöffel Jochen , Kim Jungha , Sugiyama Koichiro , Menten Karl , Immer Katharina , Rygl Kazi , Sunada Kazuyoshi , Kim Kee-Tae , Volvach Larisa , Moscadelli Luca , Jordan Lucas , Uscanga Lucero , Gray Malcolm , Szymczak Marian , Olech Mateusz , Hoare Melvin , Durjasz Michał , Uchiyama Mizuho , Shakhvorostova Nadya , Wolak Pawel , Gulyaev Sergei , Khaibrakhmanov Sergey , Breen Shari , Goedhart Sharmila , Casu Silvia , Ellingsen Simon , Kurtz Stan , Weston Stuart , Yoshihiro Tanabe , Natusc Tim , Hunter Todd , Hirota Tomoya , Baan Willem , Vlemmings Wouter , Chen Xi , Gong Yan , Yonekura Yoshinori , Szabó Zsófia Marianna , Abraham Zulema
Published: February 2024

Recently, remarkable progress has been made in understanding the formation of high mass stars. Observations provided direct evidence that massive young stellar objects (MYSOs), analogously to low-mass ones, form via disk-mediated accretion accompanied by episodic accretion bursts, possibly caused by disk fragmentation. In the case of MYSOs, the mechanism theoretically provides a means to overcome radiation pressure, but in practice it is poorly studied - only three accretion bursts in MYSOs have been caught in action to date. A significant contribution to the development of the theory has been made with the study of masers, which have proven to be a powerful tool for locating “bursting” MYSOs. This overview focuses on the exceptional role that masers play in the search and study of accretion bursts in massive protostars.
Case Management mit älteren Opioidabhängigen
Authors: Schmid Martin , Vogt Irmgard , Arendt Ines , Follmann-Muth Klaudia
Published: February 2024

Zusammenfassung: Zielsetzung: Von 2015 bis 2017 wurde in Deutschland in einer multizentrischen Studie ein auf die Zielgruppe der älteren Opioidabhängigen angepasstes manualisiertes Case Management-Verfahren erprobt. Ziel war, die Umsetzbarkeit des Verfahrens in den Strukturen der deutschen Sucht- und Drogenhilfe und in Abhängigkeit von verschiedenen Settings (niedrigschwellige Einrichtungen, psychosoziale Beratung, betreutes Wohnen) zu analysieren. Methodik: Dazu wurden im Prä-Post-Design vor Behandlungsbeginn und nach Abschluss der sechsmonatigen Intervention quantitative Daten zu 62 Klienten und Klientinnen erhoben. Mit den 21 Fachkräften wurden qualitative Interviews durchgeführt und zusätzliche quantitative Daten zur Durchführung des Case Managements erhoben. Ergebnisse: Die Ergebnisse zeigen, dass Case Management mit älteren Menschen mit Substanzkonsumproblemen umsetzbar ist, dass Veränderungen möglich sind und dass sowohl die Fachkräfte als auch die Klientinnen und Klienten mit dem Verfahren gut zurechtkommen. Dabei zeigen sich Unterschiede zwischen den jeweiligen Settings. Die Rollenvielfalt der Case Manager und doppelte Hilfeplanverfahren erschweren die Umsetzung. Schlussfolgerungen: Ein an die Zielgruppe angepasstes und mit kostenträgerseitigen Hilfeplanverfahren abgestimmtes Case Management könnte dazu beitragen, die Lebenssituation älterer Opioidabhängiger zu verbessern.
A Global Assessment of Heatwaves Since 1850 in Different Observational and Model Data Sets
Authors: Lipfert Laura , Hand Ralf , Brönnimann Stefan
Published: February 2024

We show that ModE‐Sim, a global ensemble of atmospheric model simulations that uses observed ocean boundary conditions and radiative forcings providing 36 members with daily climate information can be used to in‐depth analyze the known spatial and temporal variability of heatwaves in the Northern Hemisphere and Australia during the past 160 years. It can also be used to study actual past extreme events like heatwaves during the El Nino 1877/1878. To analyze past heatwaves we use a novel approach of a transient baseline climatology and compare to different observational data sets. Furthermore, we analyze sea surface temperature anomalies during the most extreme heatwave summers in North America, Europe and Australia and identify the most prominent anomaly patterns over the Subpolar North Atlantic and in the Central Pacific. Using a large ensemble of forced simulations, like ModE‐Sim can consequently contribute to a better understanding of preindustrial heatwaves, their decadal variability and their driving mechanisms.
Are Foreshocks Fore‐Shocks?
Authors: Zaccagnino Davide , Vallianatos Filippos , Michas Georgios , Telesca Luciano , Doglioni Carlo
Published: February 2024

Foreshocks are spatially clustered seismic events preceding large earthquakes. Since the dawn of seismology, their occurrence has been identified as a possible mechanism leading to further crustal destabilization, hence, to major failures. However, several cases occurred without any previous anomalous seismic activity, so that the hypothesis of foreshocks as reliable seismic precursors fails to pass statistical tests. Here, we perform an all‐round statistical comparative analysis of seismicity in Southern California to assess whether any differences can be identified between swarms and foreshocks. Our results suggest that extremely variable seismic patterns can forerun mainshocks, even though they tend to be preceded by clusters with more numerous events spread over larger areas than swarms and with a wider range of magnitudes. We provide a physical explanation of such dissimilarity and conclude, despite it, that foreshocks can hardly be reliable short‐term precursors of large earthquakes in California.
Comparison of Intense Summer Arctic Cyclones Between the Marginal Ice Zone and Central Arctic
Authors: Kong Yang , Lu Chuhan , Guan Zhaoyong , Chen Xiaoxiao
Published: February 2024

Arctic cyclone activity is an important component of the local climate, and the frequent occurrence of extreme summer storms has raised widespread scientific interest. In this paper, we investigated the distinctive structural characteristics of intense summer Arctic cyclones by utilizing ERA‐Interim reanalysis data and employing a deep learning algorithm for cyclone detection. We found that the northern edge of Eurasia (i.e., the marginal ice zone (MIZ)) and the Alpha Ridge of Arctic Ocean (AR, i.e. central Arctic) are the two most active regions for intense Arctic cyclone activities in summer (from June to September). However, the surface conditions and coupling frequency between surface cyclone and tropopause polar vortices (TPVs) are distinct over these two regions. By further analysis of 100 intense cyclone activities in these two areas, respectively, we found that cyclones in MIZ are often smaller in size but higher in intensity at their maximum intensity, and their life cycles are generally shorter. MIZ cyclones are typically accompanied by a large Eady growth rate and frontal structure in the lower troposphere and their intensification primarily attributed to the thermal‐baroclinic process. In contrast, cyclones in AR are more frequently associated with higher potential vorticity (PV) values and pronounced PV downward intrusion from the stratosphere, as well as notable “upper warm‐lower cold” structures. The downward intrusion of TPVs and stratosphere vortices contribute to a decrease in the upper and column air mass deficit, leading to the intensification of surface Arctic cyclones in these regions.
A Mixed‐Integer Linear Programming Framework for Optimization of Water Network Operations Problems
Authors: Thomas Meghna , Sela Lina
Published: February 2024

Water distribution systems (WDSs) are critical infrastructure used to convey water from sources to consumers. The mathematical framework governing the distribution of flows and heads in extended period simulations of WDSs lends itself to application in a wide range of optimization problems. Applying the classical mixed integer linear programming (MILP) approach to model WDSs hydraulics within an optimization framework can contribute to higher solution accuracy with lower computational effort. However, adapting WDSs models to conform to a MILP formulation has proven challenging because of the intrinsic non‐linearity of system hydraulics and the complexity associated with modeling hydraulic devices that influence the state of the WDS. This paper introduces MILPNet, an adjustable framework for WDSs that can be used to build and solve an extensive array of MILP optimization problems. MILPNet includes constraints that represent the mass balance and energy conservation equations, hydraulic devices, control rules, and status checks. To conform to MILP structure, MILPNet employs piece‐wise linear approximation and integer programming. MILPNet was implemented and tested using Gurobi Python API. Modeling accuracy was shown to be comparable to EPANET, a public domain software for hydraulic modeling, and sensitivity analyses were conducted to examine the impacts of the modeling assumptions on the performance of MILPNet. Additionally, application of the framework was demonstrated using pump scheduling optimization examples in single and rolling horizon scenarios. Our results show that MILPNet can facilitate the construction and solution of optimization problems for a range of applications in WDSs operations.
Large-scale groundwater flow and sedimentary diagenesis in continental shelves influence marine chemical budgets
Authors: Wilson Alicia M. , Osborne Andrew , White Scott M.
Published: February 2024

The major ion chemistry of the ocean has been assumed to be controlled by river input, hydrothermal circulation at mid-ocean ridges, carbonate production, and low-temperature alteration of seafloor basalt, but marine chemical budgets remain difficult to balance. Here we propose that large-scale groundwater flow and diagenetic reactions in continental shelf sediments have been overlooked as an important contributor to major ion budgets in the ocean. Based on data synthesized from 17 passive margin basins, continental shelves contribute fluid exchanges comparable to hydrothermal circulation at mid-ocean ridges. Chemical exchange is similarly significant, indicating removal of Mg2+ from the oceans at rates similar to mid-ocean ridge convection. Continental shelves likely contribute Ca2+ and K+ to the oceans at rates that, in combination with low-temperature basalt alteration, can close current budget deficits. Flow and reaction in continental shelf sediments should be included in a new generation of studies addressing marine isotope budgets.
Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast
Authors: Cautereels Charlotte , Smets Jolien , Bircham Peter , De Ruysscher Dries , Zimmermann Anna , De Rijk Peter , Steensels Jan , Gorkovskiy Anton , Masschelein Joleen , Verstrepen Kevin J.
Published: February 2024

Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells
Authors: Pennacchio Fabrizio A. , Poli Alessandro , Pramotton Francesca Michela , Lavore Stefania , Rancati Ilaria , Cinquanta Mario , Vorselen Daan , Prina Elisabetta , Romano Orso Maria , Ferrari Aldo , Piel Matthieu , Cosentino Lagomarsino Marco , Maiuri Paolo
Published: February 2024

In eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, current methods to measure cytoplasmic and nuclear volumes, including confocal 3D reconstruction, have limitations, such as relying on two-dimensional projections or poor vertical resolution. Here, to overcome these limitations, we describe a method, N2FXm, to jointly measure cytoplasmic and nuclear volumes in single cultured adhering human cells, in real time, and across cell cycles. We find that this method accurately provides joint size over dynamic measurements and at different time resolutions. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we show that N2FXm can give relevant insights on how mechanical forces exerted by the cytoskeleton on the nuclear envelope can affect the growth of nucleus volume by biasing nuclear import. Our method, by allowing for accurate joint nuclear and cytoplasmic volume dynamic measurements at different time resolutions, highlights the non-constancy of the nucleus/cytoplasm ratio along the cell cycle.
Statistics of modal condensation in nonlinear multimode fibers
Authors: Zitelli Mario , Mangini Fabio , Wabnitz Stefan
Published: February 2024

Optical pulses traveling through multimode optical fibers encounter the influence of both linear disturbances and nonlinearity, resulting in a complex and chaotic redistribution of power among different modes. In our research, we explore the phenomenon where multimode fibers reach stable states marked by the concentration of energy into both single and multiple sub-systems. We introduce a weighted Bose-Einstein law, demonstrating its suitability in describing thermalized modal power distributions in the nonlinear regime, as well as steady-state distributions in the linear regime. We apply the law to experimental results and numerical simulations. Our findings reveal that, at power levels situated between the linear and soliton regimes, energy concentration occurs locally within higher-order modal groups before transitioning to global concentration in the fundamental mode within the soliton regime. This research broadens the application of thermodynamic principles to multimode fibers, uncovering previously unexplored optical states that exhibit characteristics akin to optical glass.
Overlay databank unlocks data-driven analyses of biomolecules for all
Authors: Kiirikki Anne M. , Antila Hanne S. , Bort Lara S. , Buslaev Pavel , Favela-Rosales Fernando , Ferreira Tiago Mendes , Fuchs Patrick F. J. , Garcia-Fandino Rebeca , Gushchin Ivan , Kav Batuhan , Kučerka Norbert , Kula Patrik , Kurki Milla , Kuzmin Alexander , Lalitha Anusha , Lolicato Fabio , Madsen Jesper J. , Miettinen Markus S. , Mingham Cedric , Monticelli Luca , Nencini Ricky , Nesterenko Alexey M. , Piggot Thomas J. , Piñeiro Ángel , Reuter Nathalie , Samantray Suman , Suárez-Lestón Fabián , Talandashti Reza , Ollila O. H. Samuli
Published: February 2024

Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank—a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
Regulating protein corona on nanovesicles by glycosylated polyhydroxy polymer modification for efficient drug delivery
Authors: Miao Yunqiu , Li Lijun , Wang Ying , Wang Jiangyue , Zhou Yihan , Guo Linmiao , Zhao Yanqi , Nie Di , Zhang Yang , Zhang Xinxin , Gan Yong
Published: February 2024

The dynamic protein corona formed on nanocarriers has been revealed to strongly affect their in vivo behaviors. Precisely manipulating the formation of protein corona on nanocarriers may provide an alternative impetus for specific drug delivery. Herein, we explore the role of glycosylated polyhydroxy polymer-modified nanovesicles (CP-LVs) with different amino/hydroxyl ratios in protein corona formation and evolution. CP-LVs with an amino/hydroxyl ratio of approximately 0.4 (CP1-LVs) are found to efficiently suppress immunoglobulin adsorption in blood and livers, resulting in prolonged circulation. Moreover, CP1-LVs adsorb abundant tumor distinctive proteins, such as CD44 and osteopontin in tumor interstitial fluids, mediating selective tumor cell internalization. The proteins corona transformation specific to the environment appears to be affected by the electrostatic interaction between CP-LVs and proteins with diverse isoelectric points. Benefiting from surface modification-mediated protein corona regulation, paclitaxel-loaded CP1-LVs demonstrate superior antitumor efficacy to PEGylated liposomes. Our work offers a perspective on rational surface-design of nanocarriers to modulate the protein corona formation for efficient drug delivery.
One-pot redox cascade paired electrosynthesis of gamma-butyrolactone from furoic acid
Authors: Liu Shengqin , Jin Yangxin , Huang Shuquan , Zhu Qi , Shao Shan , Lam Jason Chun-Ho
Published: February 2024

The catalytic valorisation of biomass to afford synthetically useful small molecules is essential for sustainable biorefinery processes. Herein, we present a mild cascaded electrochemical protocol for converting furoic acid, a common biomass-derived feedstock, into a versatile platform chemical, gamma-butyrolactone. In the platinum(+)|nickel(−) electrode paired undivided cell, furoic acid is electrochemically oxidised with 84.2% selectivity to 2(5H)-furanone, the olefin of which is then hydrogenated to yield gamma-butyrolactone with 98.5% selectivity. The final gamma-butyrolactone yield is 69.1% with 38.3% Faradaic efficiency and 80.1% carbon balance when the reaction is performed with 100 mM furoic acid at 80 °C at +2.0 VAg/AgCl. Mechanistic investigation revealed the critical temperature and electrolyte pH conditions that maximise the production and protection of the key intermediate, furan radical, promoting its transition to 2(5H)-furanone rather than self-polymerising. The reaction is scalable, as 2.1 g of 98.1% pure gamma-butyrolactone is isolated through a simple solvent extraction.
Light-induced MOF synthesis enabling composite photothermal materials
Authors: Shelonchik Ofir , Lemcoff Nir , Shimoni Ran , Biswas Aritra , Yehezkel Elad , Yesodi Doron , Hod Idan , Weizmann Yossi
Published: February 2024

Metal-organic frameworks (MOFs) are a class of porous materials known for their large surface areas. Thus, over the past few decades the development of MOFs and their applications has been a major topic of interest throughout the scientific community. However, many current conventional syntheses of MOFs are lengthy solvothermal processes carried out at elevated temperatures. Herein, we developed a rapid light-induced synthesis of MOFs by harnessing the plasmonic photothermal abilities of bipyramidal gold nanoparticles (AuBPs). The generality of the photo-induced method was demonstrated by synthesizing four different MOFs utilizing three different wavelengths (520 nm, 660 nm and 850 nm). Furthermore, by regulating light exposure, AuBPs could be embedded in the MOF or maintained in the supernatant. Notably, the AuBPs-embedded MOF (AuBP@UIO-66) retained its plasmonic properties along with the extraordinary surface area typical to MOFs. The photothermal AuBP@UIO-66 demonstrated a significant light-induced heating response that was utilized for ultrafast desorption and MOF activation.
Dual heterogeneous interfaces enhance X-ray excited persistent luminescence for low-dose 3D imaging
Authors: Lei Lei , Yi Minghao , Wang Yubin , Hua Youjie , Zhang Junjie , Prasad Paras N. , Xu Shiqing
Published: February 2024

Lanthanide-doped fluoride nanoparticles (NPs) showcase adjustable X-ray-excited persistent luminescence (XEPL), holding significant promise for applications in three-dimensional (3D) imaging through the creation of flexible X-ray detectors. However, a dangerous high X-ray irradiation dose rate and complicated heating procedure are required to generate efficient XEPL for high-resolution 3D imaging, which is attributed to a lack of strategies to significantly enhance the XEPL intensity. Here we report that the XEPL intensity of a series of lanthanide activators (Dy, Pr, Er, Tm, Gd, Tb) is greatly improved by constructing dual heterogeneous interfaces in a double-shell nanostructure. Mechanistic studies indicate that the employed core@shell@shell structure could not only passivate the surface quenchers to lower the non-radiative relaxation possibility, but also reduce the interfacial Frenkel defect formation energy leading to increase the trap concentration. By employing a NPs containing flexible film as the scintillation screen, the inside 3D electrical structure of a watch was clearly achieved based on the delayed XEPL imaging and 3D reconstruction procedure. We foresee that these findings will promote the development of advanced X-ray activated persistent fluoride NPs and offer opportunities for safer and more efficient X-ray imaging techniques in a number of scientific and practical areas.
Photolipid excitation triggers depolarizing optocapacitive currents and action potentials
Authors: Bassetto Carlos A. Z. , Pfeffermann Juergen , Yadav Rohit , Strassgschwandtner Simon , Glasnov Toma , Bezanilla Francisco , Pohl Peter
Published: February 2024

Optically-induced changes in membrane capacitance may regulate neuronal activity without requiring genetic modifications. Previously, they mainly relied on sudden temperature jumps due to light absorption by membrane-associated nanomaterials or water. Yet, nanomaterial targeting or the required high infrared light intensities obstruct broad applicability. Now, we propose a very versatile approach: photolipids (azobenzene-containing diacylglycerols) mediate light-triggered cellular de- or hyperpolarization. As planar bilayer experiments show, the respective currents emerge from millisecond-timescale changes in bilayer capacitance. UV light changes photolipid conformation, which awards embedding plasma membranes with increased capacitance and evokes depolarizing currents. They open voltage-gated sodium channels in cells, generating action potentials. Blue light reduces the area per photolipid, decreasing membrane capacitance and eliciting hyperpolarization. If present, mechanosensitive channels respond to the increased mechanical membrane tension, generating large depolarizing currents that elicit action potentials. Membrane self-insertion of administered photolipids and focused illumination allows cell excitation with high spatiotemporal control.
Effects of open circuit immersion and vertex potential on potentiodynamic polarization scans of metallic biomaterials
Authors: Gattu V. K. , Obregon J. , Ebert W. L. , Indacochea J. E.
Published: February 2024

Electrodes made of commercially pure titanium (CP-Ti) and a CoCrMo alloy are immersed at an open circuit in a phosphate buffer saline electrolyte at room temperature for different durations prior to electrochemical analyses. Open circuit potential measurements, electrochemical impedance spectroscopy measurements, and cyclic potentiodynamic polarization (CPP) scans are used to assess the impact of the immersion time on derived property values. Stable passivation layers formed on both materials during immersion. The corrosion potentials determined from the anodic legs of CPP scans become more cathodic, and the corrosion currents decrease to lower values after longer immersion times. Measured currents indicate the layers formed on CP-Ti stabilize during forward anodic scans and persist to the vertex potential, whereas passivation breakdown occurs during anodic scans with CoCrMo with active corrosion at voltages up to the vertex potential. The characteristics of the return cathodic legs of CPP scans represent the surface conditions at the vertex potential: characteristic corrosion property values derived from the test responses represent passive surfaces on CP-Ti and leached surfaces on CoCrMo rather than intrinsic properties of those materials.
Potent induction of humoral and cellular immunity after bivalent BA.4/5 mRNA vaccination in dialysis patients
Authors: Bronder Saskia , Mihm Janine , Urschel Rebecca , Klemis Verena , Schmidt Tina , Marx Stefanie , Abu-Omar Amina , Hielscher Franziska , Guckelmus Candida , Widera Marek , Sester Urban , Sester Martina
Published: February 2024

Knowledge on immunogenicity of the bivalent Omicron BA.4/5 vaccine in dialysis patients and the effect of a previous infection is limited. Therefore, vaccine-induced humoral and cellular immunity was analyzed in dialysis patients and immunocompetent controls with and without prior infection. In an observational study, 33 dialysis patients and 58 controls matched for age, sex and prior infection status were recruited. Specific IgG, neutralizing antibody activity and cellular immunity towards the spike-antigen from parental SARS-CoV-2 and Omicron-subvariants BA.1, BA.2 and BA.4/5 were analyzed before and 13-18 days after vaccination. The bivalent vaccine led to a significant induction of IgG, neutralizing titers, and specific CD4+ and CD8+ T-cell levels. Neutralizing activity towards the parental strain was higher than towards the Omicron-subvariants, whereas specific T-cell levels towards parental spike and Omicron-subvariants did not differ indicating substantial cross-reactivity. Dialysis patients with prior infection had significantly higher spike-specific CD4+ T-cell levels with lower CTLA-4 expression compared to infection-naive patients. When compared to controls, no differences were observed between infection-naive individuals. Among convalescent individuals, CD4+ T-cell levels were higher in patients and neutralizing antibodies were higher in controls. Vaccination was overall well tolerated in both dialysis patients and controls with significantly less adverse events among patients. In conclusion, our study did not provide any evidence for impaired immunogenicity of the bivalent Omicron BA.4/5 vaccine in dialysis patients. Unlike in controls, previous infection of patients was even associated with higher levels of spike-specific CD4+ T cells, which may reflect prolonged encounter with antigen during infection.
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities
Authors: Peng Huadong , Darlington Alexander P. S. , South Eric J. , Chen Hao-Hong , Jiang Wei , Ledesma-Amaro Rodrigo
Published: February 2024

Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model and key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic and overexpression yeast strains that can be used to create co-cultures through exchange of essential metabolites. Using these strains as modules, we engineered two- and three-member consortia using different cross-feeding architectures. Through a combination of ensemble modelling and experimentation, we explored how cellular (for example, metabolite production strength) and environmental (for example, initial population ratio, population density and extracellular supplementation) factors govern population dynamics in these systems. We tested the use of the toolkit in a division of labour biomanufacturing case study and show that it enables enhanced and tuneable antioxidant resveratrol production. We expect this toolkit to become a useful resource for a variety of applications in synthetic ecology and biomanufacturing.
Mapping nanoscale carrier confinement in polycrystalline graphene by terahertz spectroscopy
Authors: Whelan Patrick R. , De Fazio Domenico , Pasternak Iwona , Thomsen Joachim D. , Zelzer Steffen , Mikkelsen Martin O. , Booth Timothy J. , Diekhöner Lars , Sassi Ugo , Johnstone Duncan , Midgley Paul A. , Strupinski Wlodek , Jepsen Peter U. , Ferrari Andrea C. , Bøggild Peter
Published: February 2024

Terahertz time-domain spectroscopy (THz-TDS) can be used to map spatial variations in electrical properties such as sheet conductivity, carrier density, and carrier mobility in graphene. Here, we consider wafer-scale graphene grown on germanium by chemical vapor deposition with non-uniformities and small domains due to reconstructions of the substrate during growth. The THz conductivity spectrum matches the predictions of the phenomenological Drude–Smith model for conductors with non-isotropic scattering caused by backscattering from boundaries and line defects. We compare the charge carrier mean free path determined by THz-TDS with the average defect distance assessed by Raman spectroscopy, and the grain boundary dimensions as determined by transmission electron microscopy. The results indicate that even small angle orientation variations below 5° within graphene grains influence the scattering behavior, consistent with significant backscattering contributions from grain boundaries.
Poverty prediction using E-commerce dataset and filter-based feature selection approach
Authors: Wijaya Dedy Rahman , Ibadurrohman Raden Ilham Fadhilah , Hernawati Elis , Wikusna Wawa
Published: February 2024

Poverty is a problem that occurs in many countries, notably in Indonesia. The common methods used to obtain poverty information are surveys and censuses. However, this process takes a long time and uses a lot of human resources. On the other hand, governments and policymakers need a faster approach to know social-economic conditions for area development plans. Hence, in this paper, we develop e-commerce data and machine learning algorithms as a proxy for poverty levels that can provide faster information than surveys or censuses. The e-commerce dataset is used and this high-dimensional data becomes a challenge. Hence, feature selection algorithms are employed to determine the best features before building a machine learning model. Furthermore, three machine learning algorithms such as support vector regression, linear regression, and k-nearest neighbor are compared to predict the poverty rate. Hence, the contribution of this paper is to propose the combination of statistical-based feature selection and machine learning algorithms to predict the poverty rate based on e-commerce data. According to the experimental results, the combination of f-score feature selection and support vector regression surpasses other methods. It shows that e-commerce data and machine learning algorithms can be potentially used as a proxy for predicting poverty.
Unsupervised analysis of whole transcriptome data from human pluripotent stem cells cardiac differentiation
Authors: P. Agostinho Sofia , A. Branco Mariana , E. S. Nogueira Diogo , Diogo Maria Margarida , S. Cabral Joaquim M. , N. Fred Ana L. , V. Rodrigues Carlos A.
Published: February 2024

The main objective of the present work was to highlight differences and similarities in gene expression patterns between different pluripotent stem cell cardiac differentiation protocols, using a workflow based on unsupervised machine learning algorithms to analyse the transcriptome of cells cultured as a 2D monolayer or as 3D aggregates. This unsupervised approach effectively allowed to portray the transcriptomic changes that occurred throughout the differentiation processes, with a visual representation of the entire transcriptome. The results allowed to corroborate previously reported data and also to unveil new gene expression patterns. In particular, it was possible to identify a correlation between low cardiomyocyte differentiation efficiencies and the early expression of a set of non-mesodermal genes, which can be further explored as predictive markers of differentiation efficiency. The workflow here developed can also be applied to analyse other stem cell differentiation transcriptomic datasets, envisaging future clinical implementation of cellular therapies.
Electric field modulation of ERK dynamics shows dependency on waveform and timing
Authors: Hu Minxi , Li Houpu , Zhu Kan , Guo Liang , Zhao Min , Zhan Huiwang , Devreotes Peter N. , Qing Quan
Published: February 2024

Different exogenous electric fields (EF) can guide cell migration, disrupt proliferation, and program cell development. Studies have shown that many of these processes were initiated at the cell membrane, but the mechanism has been unclear, especially for conventionally non-excitable cells. In this study, we focus on the electrostatic aspects of EF coupling with the cell membrane by eliminating Faradaic processes using dielectric-coated microelectrodes. Our data unveil a distinctive biphasic response of the ERK signaling pathway of epithelial cells (MCF10A) to alternate current (AC) EF. The ERK signal exhibits both inhibition and activation phases, with the former triggered by a lower threshold of AC EF, featuring a swifter peaking time and briefer refractory periods than the later-occurring activation phase, induced at a higher threshold. Interestingly, the biphasic ERK responses are sensitive to the waveform and timing of EF stimulation pulses, depicting the characteristics of electrostatic and dissipative interactions. Blocker tests and correlated changes of active Ras on the cell membrane with ERK signals indicated that both EGFR and Ras were involved in the rich ERK dynamics induced by EF. We propose that the frequency-dependent dielectric relaxation process could be an important mechanism to couple EF energy to the cell membrane region and modulate membrane protein-initiated signaling pathways, which can be further explored to precisely control cell behavior and fate with high temporal and spatial resolution.