bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulating adsorption performance of zeolites by pre-activation in electric fields
Authors: Chen Kaifei , Yu Zhi , Mousavi Seyed Hesam , Singh Ranjeet , Gu Qinfen , Snurr Randall Q. , Webley Paul A. , Li Gang Kevin 
Published: September 2023

AbstractWhile multiple external stimuli (e.g., temperature, light, pressure) have been reported to regulate gas adsorption, limited studies have been conducted on controlling molecular admission in nanopores through the application of electric fields (E-field). Here we show gas adsorption capacity and selectivity in zeolite molecular sieves can be regulated by an external E-field. Through E-field pre-activation during degassing, several zeolites exhibited enhanced CO2 adsorption and decreased CH4 and N2 adsorptions, improving the CO2/CH4 and CO2/N2 separation selectivity by at least 25%. The enhanced separation performance of the zeolites pre-activated by E-field was maintained in multiple adsorption/desorption cycles. Powder X-ray diffraction analysis and ab initio computational studies revealed that the cation relocation and framework expansion induced by the E-field accounted for the changes in gas adsorption capacities. These findings demonstrate a regulation approach to sharpen the molecular sieving capability by E-fields and open new avenues for carbon capture and molecular separations.
Methylene blue accelerates liquid-to-gel transition of tau condensates impacting tau function and pathology
Authors: Huang Yongqi , Wen Jitao , Ramirez Lisa-Marie , Gümüşdil Eymen , Pokhrel Pravin , Man Viet H. , Ye Haiqiong , Han Yue , Liu Yunfei , Li Ping , Su Zhengding , Wang Junmei , Mao Hanbin , Zweckstetter Markus , Perrett Sarah , Wu Si , Gao Meng 
Published: September 2023

AbstractPreventing tau aggregation is a potential therapeutic strategy in Alzheimer’s disease and other tauopathies. Recently, liquid–liquid phase separation has been found to facilitate the formation of pathogenic tau conformations and fibrillar aggregates, although many aspects of the conformational transitions of tau during the phase transition process remain unknown. Here, we demonstrate that the tau aggregation inhibitor methylene blue promotes tau liquid–liquid phase separation and accelerates the liquid-to-gel transition of tau droplets independent of the redox activity of methylene blue. We further show that methylene blue inhibits the conversion of tau droplets into fibrils and reduces the cytotoxicity of tau aggregates. Although gelation slows down the mobility of tau and tubulin, it does not impair microtubule assembly within tau droplets. These findings suggest that methylene blue inhibits tau amyloid fibrillization and accelerates tau droplet gelation via distinct mechanisms, thus providing insights into the activity of tau aggregation inhibitors in the context of phase transition.
In-situ X-ray monitoring of solidification and related processes of metal alloys
Authors: Reinhart G. , Browne D. J. , Kargl F. , García-Moreno F. , Becker M. , Sondermann E. , Binder K. , Mullen J. S. , Zimmermann G. , Mathiesen R. H. , Sillekens W. H. , Nguyen-Thi H. 
Published: September 2023

AbstractX-ray radioscopy enables the in-situ monitoring of metal alloy processes and then gives access to crucial information on the dynamics of the underlying phenomena. In the last decade, the utilisation of this powerful imaging technique has been adapted to microgravity platforms such as sounding rockets and parabolic flights. The combination of microgravity experimentation with X-ray radioscopy has resulted in a leap in the understanding of fundamental science and has opened new paths in the fields of materials science. The present review focuses on the short history of this research, which includes facility developments, microgravity experiments and results obtained by partners of the XRMON (In-situ X-Ray MONitoring of advanced metallurgical processes under microgravity and terrestrial conditions) research project in the framework of the MAP (Microgravity Application Promotion) programme of the European Space Agency. Three illustrative research topics that were advanced significantly through the use of X-ray radioscopy will be detailed: solidification of metal alloys, metallic foam formation and diffusion in melts.
Ensuring equity with pre-clinical planning for chlamydia vaccines
Authors: Collar Amanda L. , Clarke Tegan N. , Jamus Andzoa N. , Frietze Kathryn M. 
Published: September 2023

AbstractChlamydia trachomatis (Ct) remains the most common bacterial sexually transmitted pathogen worldwide, causing significant morbidity particularly among women, including pelvic inflammatory disease, ectopic pregnancy, and infertility. Several vaccines are advancing through pre-clinical and clinical development, and it is likely that one or more vaccines will progress into human efficacy trials soon. In this Perspective, we present a case for considering the challenges of Ct vaccine development through a lens of equity and justice. These challenges include the need to protect against multiple serovars, in both females and males, at multiple anatomic sites, and in resource poor areas of the world. We propose that early consideration of vaccine implementation by conducting community-engaged research will ensure that a scientifically sound chlamydia vaccine promotes equity, justice, and shared-gendered responsibility for STI prevention.
Development of an integrated and inferenceable RDF database of glycan, pathogen and disease resources
Authors: Arakawa Koichi , Ono Tamiko , Aoki-Kinoshita Kiyoko F. , Yamamoto Yasunori 
Published: September 2023

AbstractGlycans are known to play extremely important roles in infections by viruses and pathogens. In fact, the SARS-CoV-2 virus has been shown to have evolved due to a single change in glycosylation. However, data resources on glycans, pathogens and diseases are not well organized. To accurately obtain such information from these various resources, we have constructed a foundation for discovering glycan and virus interaction data using Semantic Web technologies to be able to semantically integrate such heterogeneous data. Here, we created an ontology to encapsulate the semantics of virus-glycan interactions, and used Resource Description Framework (RDF) to represent the data we obtained from non-RDF related databases and data associated with literature. These databases include PubChem, SugarBind, and PSICQUIC, which made it possible to refer to other RDF resources such as UniProt and GlyTouCan. We made these data publicly available as open data and provided a service that allows anyone to freely perform searches using SPARQL. In addition, the RDF resources created in this study are available at the GlyCosmos Portal.
A new class of anticancer activity with computational studies for a novel bioactive aminophosphonates based on pyrazole moiety
Authors: Baren Mohamed H. , Ibrahim Seham A. , Al-Rooqi Munirah M. , Ahmed Saleh A. , El-Gamil Mohammed M. , Hekal Hend A. 
Published: September 2023

AbstractThe present study involves synthesis a new series of α-aminophosphonates 2a-f and 4a-d derivatives in good yield with a simple workup via Kabachnik-Fields reaction in the presence of lithium perchlorate as Lewis acid catalyst. All the newly synthesized compounds were confirmed using various physical, spectroscopic, and analytical data. The in vitro anticancer activities of each compound were evaluated against colorectal carcinoma Colon cancer (HCT-116) and Epdermoid carcinoma (HEP2) and also Human lung fibroblast normal cell line (WI38) compared with Doxorubicin. The results showed that Compounds 2a, 4b and 4d exhibited more potent inhibitory activity for Epdermoid Carcinoma (HEP2) compared with doxorubicin. For colon carcinoma cells (HCT-116) Compounds 2a, 2d and 4b gave the strongest activity among all compounds compared with doxorubicin. Moreover, all designed structures were docked into the active site of VEGFR2 and FGFR1 proteins. The result reveals that compound 2b and have the strongest inhibitory activity of the VEGFR2 and FGFR1 proteins indicating that these substances might conceivably operate as VEGFR2 and FGFR1 inhibitors and hence might take role in anticancer activities with various binding interactions. The 3D-QSAR models produced strong statistical results since they were defined by PLS factors 4 and confirmed by parameters as R2, R2 CV, Stability, F-value, P-value, RMSE, Q2, and Pearson-r.
Simplified 3D hydrodynamic flow focusing for lab-on-chip single particle study
Authors: Storti Filippo , Bonfadini Silvio , Criante Luigino 
Published: September 2023

AbstractAccurately control of the position of a fluid and particle within lab-on-a-chip platform is a critical prerequisite for many downstream analysis processes, such as detection, trapping and separation, moving the sensing at the single-particle level. With the development of microfluidic fabrication technology, particle/cell focusing has shifted from two to three dimensions. 3D hydrodynamic focusing, which sorts and aligns the incoming cloud of particles so that they pass through the interrogation area one by one, enables new possibilities and breakthroughs in the single-cell analysis system. Despite the excellent results shown in literature, there is still a lack of a device that can simultaneously fulfilling the requirements of high throughput, compactness, high integrability, and ease of use operation to become a widely accepted work center for biomedical research and clinical applications. Here, we proposed a unique 3D flow focusing microfluidic device buried in fused silica substrate that potentially combines all this advantages. By designing a sample channel suspended inside a larger buffer channel, manufactured by exploiting the laser-assisted micromachine technique, a not size-dependent focusing capability is shown. A spatially and temporally stable central flow of a mixture of 15 μm and 6 μm PS particles to a 1 μm PS microsphere solution has been obtained with high accuracy. Finally, to test the achievable focusing resolution, the chip was tested for the detection of Escherichia Coli bacteria in water solution as proof of concept of biological application.
Osteological, multi-isotope and proteomic analysis of poorly-preserved human remains from a Dutch East India Company burial ground in South Africa
Authors: Olszewski Judyta , Hall Rachael A. , Kootker Lisette M. , Oldham Neil J. , Layfield Robert , Shaw Barry , Derksen Leon , Manders Martijn , Hart Tim , Schrader Sarah A. 
Published: September 2023

AbstractSkeletal remains discovered in Simon’s Town, South Africa, were hypothesised as being associated with a former Dutch East India Company (VOC) hospital. We report a novel combined osteological and biochemical approach to these poorly-preserved remains. A combined strontium (87Sr/86Sr), oxygen (δ18OVPDB) and carbon (δ13CVPDB) isotope analysis informed possible childhood origins and diet, while sex-specific amelogenin enamel peptides revealed biological sex. Osteological analyses presented evidence of residual rickets, a healed trauma, dental pathological conditions, and pipe notches. The combined isotope analyses yielded results for 43 individuals which suggested a diverse range of geological origins, including at least 16% of the population being non-local. The inclusion of δ13CVPDB had intriguing implications for three individuals who likely did not have origins in the Cape Town region nor in Europe. Peptide analysis on the dental enamel of 25 tested individuals confirmed they were all biologically male. We suggest that isolated enamel may provide crucial information about individuals’ pathological conditions, geographical origins, diet, and biological sex. These data further demonstrated that a combined approach using multiple osteological and biochemical methods is advantageous for human remains which are poorly preserved and can contextualise a site with little direct evidence.
A new time-varying coefficient regression approach for analyzing infectious disease data
Authors: Liu Juxin , Bellows Brandon , Hu X. Joan , Wu Jianhong , Zhou Zhou , Soteros Chris , Wang Lin 
Published: September 2023

AbstractSince the beginning of the global pandemic of Coronavirus (SARS-COV-2), there has been many studies devoted to predicting the COVID-19 related deaths/hospitalizations. The aim of our work is to (1) explore the lagged dependence between the time series of case counts and the time series of death counts; and (2) utilize such a relationship for prediction. The proposed approach can also be applied to other infectious diseases or wherever dynamics in lagged dependence are of primary interest. Different from the previous studies, we focus on time-varying coefficient models to account for the evolution of the coronavirus. Using two different types of time-varying coefficient models, local polynomial regression models and piecewise linear regression models, we analyze the province-level data in Canada as well as country-level data using cumulative counts. We use out-of-sample prediction to evaluate the model performance. Based on our data analyses, both time-varying coefficient modeling strategies work well. Local polynomial regression models generally work better than piecewise linear regression models, especially when the pattern of the relationship between the two time series of counts gets more complicated (e.g., more segments are needed to portray the pattern). Our proposed methods can be easily and quickly implemented via existing R packages.
Tracing the birth of structural domains from loops during protein evolution
Authors: Aziz M. Fayez , Mughal Fizza , Caetano-Anollés Gustavo 
Published: September 2023

AbstractThe structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop prototypes combine to form folded structures in protein domain evolution. Phylogenomic data-driven chronologies reoriented a bipartite network of loops and domains (and its projections) into ‘waterfalls’ depicting an evolving ‘elementary functionome’ (EF). Two primordial waves of functional innovation involving founder ‘p-loop’ and ‘winged-helix’ domains were accompanied by an ongoing emergence and reuse of structural and functional novelty. Metabolic pathways expanded before translation functionalities. A dual hourglass recruitment pattern transferred scale-free properties from loop to domain components of the EF network in generative cycles of hierarchical modularity. Modeling the evolutionary emergence of the oldest P-loop and winged-helix domains with AlphFold2 uncovered rapid convergence towards folded structure, suggesting that a folding vocabulary exists in loops for protein fold repurposing and design.
HIV-1 Vpu protein forms stable oligomers in aqueous solution via its transmembrane domain self-association
Authors: Majeed Saman , Dang Lan , Islam Md Majharul , Ishola Olamide , Borbat Peter P. , Ludtke Steven J. , Georgieva Elka R. 
Published: September 2023

AbstractWe report our findings on the assembly of the HIV-1 protein Vpu into soluble oligomers. Vpu is a key HIV-1 protein. It has been considered exclusively a single-pass membrane protein. Previous observations show that this protein forms stable oligomers in aqueous solution, but details about these oligomers still remain obscure. This is an interesting and rather unique observation, as the number of proteins transitioning between soluble and membrane embedded states is limited. In this study we made use of protein engineering, size exclusion chromatography, cryoEM and electron paramagnetic resonance (EPR) spectroscopy to better elucidate the nature of the soluble oligomers. We found that Vpu oligomerizes via its N-terminal transmembrane domain (TM). CryoEM suggests that the oligomeric state most likely is a hexamer/heptamer equilibrium. Both cryoEM and EPR suggest that, within the oligomer, the distal C-terminal region of Vpu is highly flexible. Our observations are consistent with both the concept of specific interactions among TM helices or the core of the oligomers being stabilized by hydrophobic forces. While this study does not resolve all of the questions about Vpu oligomers or their functional role in HIV-1 it provides new fundamental information about the size and nature of the oligomeric interactions.
Chemo-enzymatic total synthesis of the spirosorbicillinols
Authors: Milzarek Tobias M. , Gulder Tobias A. M. 
Published: September 2023

AbstractThe natural product class of the sorbicillinoids is composed of structurally diverse molecules with many strong, biomedically relevant biological activities. Owing to their complex structures, the synthesis of sorbicillinoids is a challenging task. Here we show the first total synthesis of the fungal sorbicillinoids spirosorbicillinols A–C. The convergent route comprises the chemo-enzymatic transformation of sorbicillin to the highly reactive sorbicillinol and the assembly of scytolide and isomers starting from shikimic and quinic acid analogs. The key step in the total synthesis is the fusion of both building blocks in a Diels-Alder cycloaddition leading to the straightforward formation of the characteristic sorbicillinoid bicyclo[2.2.2]octane backbone. This work provides unifying access to all natural spirosorbicillinols and unnatural diastereomers.
Intravenous ferric carboxymaltose and ferric derisomaltose alter the intestinal microbiome in female iron-deficient anemic mice
Authors: Rieg Timo , Xue Jianxiang , Stevens Monica , Thomas Linto , White James R. , Dominguez Rieg Jessica A. 
Published: September 2023

Abstract
Iron deficiency anemia (IDA) is a leading global health concern affecting approximately 30% of the population. Treatment for IDA consists of replenishment of iron stores, either by oral or intravenous (IV) supplementation. There is a complex bidirectional interplay between the gut microbiota, the host’s iron status, and dietary iron availability. Dietary iron deficiency and supplementation can influence the gut microbiome; however, the effect of IV iron on the gut microbiome is unknown. We studied how commonly used IV iron preparations, ferric carboxymaltose (FCM) and ferric derisomaltose (FDI), affected the gut microbiome in female iron-deficient anemic mice. At the phylum level, vehicle-treated mice showed an expansion in Verrucomicrobia, mostly because of the increased abundance of Akkermansia muciniphila, along with contraction in Firmicutes, resulting in a lower Firmicutes/Bacteroidetes ratio (indicator of dysbiosis). Treatment with either FCM or FDI restored the microbiome such that Firmicutes and Bacteroidetes were the dominant phyla. Interestingly, the phyla Proteobacteria and several members of Bacteroidetes (e.g., Alistipes) were expanded in mice treated with FCM compared with those treated with FDI. In contrast, several Clostridia class members were expanded in mice treated with FDI compared with FCM (e.g., Dorea spp., Eubacterium). Our data demonstrate that IV iron increases gut microbiome diversity independently of the iron preparation used; however, differences exist between FCM and FDI treatments. In conclusion, replenishing iron stores with IV iron preparations in clinical conditions, such as inflammatory bowel disease or chronic kidney disease, could affect gut microbiome composition and consequently contribute to an altered disease outcome.
Auditory, Lexical, and Multitasking Demands Interactively Impact Listening Effort
Authors: Kuchinsky Stefanie E. , Razeghi Niki , Pandža Nick B. 
Published: September 2023

Purpose:
This study examined the extent to which acoustic, linguistic, and cognitive task demands interactively impact listening effort.

Method:
Using a dual-task paradigm, on each trial, participants were instructed to perform either a single task or two tasks. In the primary word recognition task, participants repeated Northwestern University Auditory Test No. 6 words presented in speech-shaped noise at either an easier or a harder signal-to-noise ratio (SNR). The words varied in how commonly they occur in the English language (lexical frequency). In the secondary visual task, participants were instructed to press a specific key as soon as a number appeared on screen (simpler task) or one of two keys to indicate whether the visualized number was even or odd (more complex task).

Results:
Manipulation checks revealed that key assumptions of the dual-task design were met. A significant three-way interaction was observed, such that the expected effect of SNR on effort was only observable for words with lower lexical frequency and only when multitasking demands were relatively simpler.

Conclusions:
This work reveals that variability across speech stimuli can influence the sensitivity of the dual-task paradigm for detecting changes in listening effort. In line with previous work, the results of this study also suggest that higher cognitive demands may limit the ability to detect expected effects of SNR on measures of effort. With implications for real-world listening, these findings highlight that even relatively minor changes in lexical and multitasking demands can alter the effort devoted to listening in noise.
An Exploratory Study of Walking, Listening, and Remembering in Younger and Middle-Aged Adults
Authors: Helfer Karen S. , van Emmerik Richard , Freyman Richard L. , Banks Jacob J. 
Published: September 2023

Purpose:
The purpose of this study was to assess how needing to listen and remember information while walking affects speech perception, memory task performance, and gait in younger and middle-aged adults.

Method:
Four gait parameters (stride duration, step variability, whole-body center of mass acceleration, and mediolateral head acceleration) were measured when younger and middle-aged participants stood or walked on a treadmill while they simultaneously completed a speech-on-speech perception task and a preload memory task, singly and in combination.

Results:
Speech perception was significantly poorer for middle-aged than for younger participants. Performance on the speech perception measure did not differ significantly between walking and standing for either group of participants, but the additional cognitive load of the memory task reduced performance on the speech perception task. Memory task performance was significantly poorer when combined with the speech perception task than when measured in isolation for both participant groups, but no further declines were noted when participants were also walking. Mediolateral head acceleration, which has been linked to loss of balance, was significantly greater during multitask trials, as compared to when participants were only walking without being required to listen or remember. Post hoc analysis showed that dual- and multitask influences on mediolateral head acceleration were more prominent for middle-aged than for younger participants. Stride duration was longer in the multitask condition than when participants were only walking.

Conclusions:
Results of this exploratory study indicate that gait may be impacted when individuals (both younger and middle-aged) are listening and remembering while walking. Data also substantiate prior findings of early age-related declines in the perception of speech in the presence of understandable speech maskers.
Consensus control of multi‐agent systems with switched linear dynamics
Authors: Zhu Yan 
Published: September 2023

AbstractIn this work, the consensus problem of multi‐agent systems is addressed whose agent dynamics are described by the switched linear system, and the interaction topology is a directed graph. Two cases are considered: For completely controllable agent dynamics, a novel construct method of control law and switching signal are proposed to derive sufficient conditions to solve the finite‐time consensus problem. When the controllability of the agent system is incomplete, it is proven that the uncontrollable sub‐mode of agent dynamics is consistently asymptotically stabilizable is a key condition to achieve consistency for multi‐agent systems. Finally, numerical examples are provided to demonstrate the effectiveness of the theoretical results obtained in this paper.