Many Labs 5:Testing pre-data collection peer review as an intervention to increase replicability

Replication studies in psychological science sometimes fail to reproduce prior findings. If these studies use methods that are unfaithful to the original study or ineffective in eliciting the phenomenon of interest, then a failure to replicate may be a failure of the protocol rather than a challenge to the original finding. Formal pre-data-collection peer review by experts may address shortcomings and increase replicability rates. We selected 10 replication studies from the Reproducibility Project: Psychology (RP:P; Open Science Collaboration, 2015) for which the original authors had expressed concerns about the replication designs before data collection; only one of these studies had yielded a statistically significant effect (p < .05). Commenters suggested that lack of adherence to expert review and low-powered tests were the reasons that most of these RP:P studies failed to replicate the original effects. We revised the replication protocols and received formal peer review prior to conducting new replication studies. We administered the RP:P and revised protocols in multiple laboratories (median number of laboratories per original study = 6.5, range = 3?9; median total sample = 1,279.5, range = 276?3,512) for high-powered tests of each original finding with both protocols. Overall, following the preregistered analysis plan, we found that the revised protocols produced effect sizes similar to those of the RP:P protocols (?r = .002 or .014, depending on analytic approach). The median effect size for the revised protocols (r = .05) was similar to that of the RP:P protocols (r = .04) and the original RP:P replications (r = .11), and smaller than that of the original studies (r = .37). Analysis of the cumulative evidence across the original studies and the corresponding three replication attempts provided very precise estimates of the 10 tested effects and indicated that their effect sizes (median r = .07, range = .00?.15) were 78% smaller, on average, than the original effect sizes (median r = .37, range = .19?.50)

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Investigation of the site-specific binding interactions and sensitivity of ochratoxin with aluminum nitride (Al12N12) nanoclusters. An intuition from Quantum Chemical Calculations

Density functional theory (DFT) computing was used in this study to examine the feasibility for detecting the interaction of nitrogen ([email protected]), oxygen ([email protected]), and chlorine ([email protected]) with the surface of an aluminum nitride (Al12N12) nanocluster. The DFT/PBE0-D3/aug-cc-pVDZ approach was heavily utilised in the computations of the quantum electronic structural characteristics, interaction energies, and sensing parameters. Fascinatingly, the results showed that [email protected], with a value of 2.04 eV, possessed a higher energy gap, making it the most stable among the spatial orientations. Meanwhile, [email protected] had the lowest energy gap of 1.55 eV, making it the least stable and more reactive compound. More so, the natural bond analysis (NBO) analysis indicated that [email protected] has the highest energy of perturbation among adsorption atoms. However, a decrement was observed in the energy value for [email protected], [email protected], and [email protected] with energy values of 1.55, 1.82, and 2.04 eV, respectively, compared to the energy gap value of 2.37 eV of the Al12N12 nanocluster. Also, the adsorption study showed that [email protected] interaction had the greatest negative adsorption energy of -2.466 eV and thus, possesses the fastest recovery time of 3.3E-158 s. The recovery time for [email protected] was 1.6E-156 s, and the least responsive was [email protected] with a recovery time of 1.94E-86. [email protected] indicated the fastest response with a time of 1.616 s, followed by 1.757 s for [email protected], and the least responsive was [email protected] with 1.881 s. Thus, it can be inferred that [email protected] is the most preferred spatial orientation and interaction site of ochratoxin upon interaction with the AlN surface due to its high adsorption energy, stability, perturbation energy, and recovery time. Using the aforementioned method, this study provides valuable insights into the interactions of Ochra with the AlN surface and its potential as a sensing material

High throughput computations of the effective removal of liquified gases by novel perchlorate hybrid material

Abstract The utilization of hybrid materials in separation technology, sorbents, direct air capture (DAC) technology, sensors, adsorbents, and chiral material recognition has increased in the past decade due to the recognized impact of atmospheric pollutants and hazardous industrial gases on climate change. A novel hybrid material, perchlorate hybrid (PClH), has been proposed in this study for the effective sensory detection and trapping of atmospheric pollutants and industrial hazardous gases. The study evaluated the structural properties, adsorption mechanism, electronic sensitivity, and topological analysis of PClH using highly accurate computational methods (M062X-D3BJ/def2-ccpVTZ and DSDPBEP86/def2-ccpVTZ). The computational analysis demonstrated that PClH has considerable adsorption energies and favorable interaction with CO2, NO2, SO2, COCl2, and H2S. PClH is more suitable for detecting liquefiable gases such as COCl2, CO2, and SO2, and can be easily recovered under ambient conditions. Developing such materials can contribute to reducing hazardous gases and pollutants in the atmosphere, leading to a cleaner and safer environment

Surface engineering of non-platinum-based electrocatalysts for sustainable hydrogen production: Encapsulation, doping, and decoration approach

The hydrogen evolution reaction's electrocatalytic reduction of water to molecular hydrogen may one day provide a long-term sustainable source of energy. However, the use of precious platinum catalysts makes it difficult to commercialize. So far, all alternatives to platinum are based on non-precious metals and transition metals. Hence, tuning the catalytic activity of nanomaterials through surface engineering might offer significant advantages. Herein, we step-wisely modulate the surface of all carbon fullerene nanomaterial by encapsulation, doping and decoration with alkali and transition metals to produce a hybrid catalyst which demonstrated excellent hydrogen evolution activity with comparable Gibbs free energy with both experimentally developed and theoretically modelled electrocatalyst. The adsorption of H* intermediate on the doped and decorated metal sites has been investigated in comparison with the pristine C24 fullerene structure. The electronic properties, the density of state (PDOS), reaction-free energy (ΔG) and transition states have all been carefully considered at appropriate theoretical levels. The ΔG of hydrogen adsorption on H@IndecNidopMgencC24 was found to be closer to zero (0.0328 eV) because of the concomitant effect of the encapsulation, doping and decoration with transition metals thus, demonstrating the effectiveness of this approach to tuning catalytic activity. The encapsulated metal enhanced the catalyst surface's conductivity and electronic attributes, leading to improved HER activity. The catalytic HER was also found to follow the Volmer-Tafel pathways, resulting in a lower free energy barrier. Overall, this work demonstrates a simple structure-activity relationship between metallic effects and substrate engineering and could open new dimensions for the development of novel non-platinum-based electrocatalysts.Ministry of Education and Science of the Russian Federation24 month embargo; first published 29 October 2023This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Adsorption mechanism of AsH3 pollutant on metal-functionalized coronene C24H12-X (X = Mg, Al, K) quantum dots

Inorganic arsenic compounds are frequently found to occur naturally or as a result of mining in soils, sediments, and groundwater. Organic arsenic exists mainly in fish, shellfish, and other aquatic life and as a result of this, it may be contaminated in edible consumables such as rice and poorly purified drinking water. Exposure to this toxic gas can cause severe lung and skin cancer as well as other related cancer cases. Therefore, the need to develop more efficient sensing/monitoring devices to signal or detect the presence of excessive accumulation of this gas in our atmosphere is highly demanding. This study has effectively employed quantum mechanical approach, utilizing density functional theory (DFT) to investigate the nanosensing efficacy of metal-decorated coronene quantum dot (QD); (CadecQD, AldecQD, KdecQD, and MgdecQD) surface towards the efficient trapping of AsH3 gas molecule in an attempt to effectively detect the presence of the gas molecule which would help in reducing the health risk imposed by the AsH3. The result obtained from the electronic studies reveals that the engineered molecules interacted more favorably at the gas and water phase than other solvents, owing to their varying calculated adsorption energies (Eads). It was observed that the decoration of potassium and aluminum into the QD surface enhanced the adsorption process of AsH3 gas onto KdecQD and AldecQD surfaces with a comparably moderate level of stability exhibited by the said systems, which is evidently shown by the excellent energy gap (Eg) of 6.9599 eV and 7.3313 eV respectively for the aforementioned surfaces

Superconductivity, quantum capacitance, and electronic structure investigation of transition metals (X = Y, Zr, Nb, Mo) encapsulated silicon nanoclusters (Si59X): Intuition from quantum and molecular mechanics

Silicon nanoclusters (SiNCs) have unique structural and electronic properties that make them promising candidates for energy storage devices such as batteries, supercapacitors, and solar cells. This study theoretically investigated the superconducting and capacitance properties of transition metal (TM) doped silicon nanoclusters using density functional theory (DFT) calculations. The electronic and ionic conductivity, as well as the non-linear optic property, of TM-doped silicon nanoclusters herein, were analyzed to determine their potential as capacitor electrodes. The effects of temperature on electronic and ionic conductivity were also studied. The results suggest that TM doping enhances the superconducting and capacitance properties of silicon nanoclusters. The electronic conductivity was found to increase with increasing temperature, while the ionic conductivity showed a nonlinear relationship with temperature. Furthermore, it was observed that the doping of studied certain TM elements, such as Nb and Mo, leads to the formation of metallic states within the HOMO-LUMO energy range, indicating their potential for superconducting behaviour. The HOMO-LUMO analysis also reveals the electronic band structure and the bandgap of TM-doped silicon nanoclusters, showing that the dopants can tune the bandgap, resulting in improved superconductivity capacitance. The NBO analysis reveals the nature of bonding between the dopant atoms and the silicon atoms, indicating that charge transfer between the dopants and the silicon atoms plays a crucial role in enhancing the electronic properties Additionally, the stability of TM-doped silicon nanoclusters was analyzed, and it's found that the doping with TM elements resulted in stable structures. The result strongly suggested that doping with Y, Zr, Nb, and Mo enhances the capacitance at different voltages and conductivity at elevated temperatures especially as the electronic configuration of the d-orbital of the dopant evolves. Overall, this study provides valuable insights into the potential of TM-doped silicon nanoclusters as efficient materials for superconducting and capacitive applications.Ministry of Education and Science of the Russian Federation24 month embargo; first published 04 November 2023This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Investigating the intermolecular interactions in the explicitly solvated complexes of lomustine with water and ethanol

Lomustine is an alkylating chemotherapy drug that is used to treat diverse types of cancer, including brain tumors, Hodgkin's lymphoma, and non-Hodgkin's lymphoma, which works by interfering with the DNA in cancer cells, preventing them from dividing and growing. As such the lipid bilayer of the cell and body fluids provides the environments in which lomustine (lmt) performs its biological function. Chemical reactions involving biological systems occur in the liquid phase, where accurate modeling of the reaction pathways considers the influence of the solvent used. Implicit solvation adequately accounts for these effects but falls short when evaluating solvent-solute interactions. This study aims to explore the structures, thermodynamics, reactivity, UV–vis spectroscopy, energy decomposition analysis, and the interaction energies of lmt with molecules of water and ethanol (n = 1, 2, and 3), using density functional theory (DFT) at the ωB97XD/6–311++G (d, p) level of theory. The thermodynamics results reveal that the polarity of water molecules significantly influences the interaction strength of the studied systems as the interaction observed between lmt with W1, Et1, and Et2 is feasible and spontaneous, compared to others. The stability of the different clusters depends on the intermolecular hydrogen bonds formed between the drug and the polar solvent as explicated by the H-bond interaction distance. Also, the interaction of lmt with each of the solvents causes a slight deformation in the geometry of the lmt, moreover, the reactivity descriptors predicted the interaction of lmt to increase with a corresponding increase in the addition of water molecules

Interaction of 5‑Fluorouracil on the Surfaces of Pristine and Functionalized Ca12O12 Nanocages: An Intuition from DFT

The utilization of nanostructured materials for several biomedical applications has tremendously increased over the last few decades owing to their nanosizes, porosity, large surface area, sensitivity, and efficiency as drug delivery systems. Thus, the incorporation of functionalized and pristine nanostructures for cancer therapy offers substantial prospects to curb the persistent problems of ineffective drug administration and delivery to target sites. The potential of pristine (Ca12O12) and formyl (−CHO)- and amino (−NH2)-functionalized (Ca12O12–CHO and Ca12O12–NH2) derivatives as efficient nanocarriers for 5-fluorouracil (5FU) was studied at the B3LYP-GD3(BJ)/6-311++G(d,p) theoretical level in two electronic media (gas and solvent). To effectively account for all adsorption interactions of the drug on the investigated surfaces, electronic studies as well as topological analysis based on the quantum theory of atoms in molecules (QTAIM) and noncovalent interactions were exhaustively utilized. Interestingly, the obtained results divulged that the 5FU drug interacted favorably with both Ca12O12 and its functionalized derivatives. The adsorption energies of pristine and functionalized nanostructures were calculated to be −133.4, −96.9, and −175.6 kcal/mol, respectively, for Ca12O12, Ca12O12–CHO, and Ca12O12–NH2. Also, both topological analysis and NBO stabilization analysis revealed the presence of interactions among O3–H32, O27–C24, O10–C27, and N24–H32 atoms of the drug and the surface. However, 5FU@Ca12O12–CHO molecules portrayed the least adsorption energy due to considerable destabilization of the molecular complex as revealed by the computed deformation energy. Therefore, 5FU@Ca12O12 and 5FU@Ca12O12–NH2 acted as better nanovehicles for 5FU