bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermo‐responsive polymer to clean fouled forward osmosis membrane after wastewater treatment: Excellent flux recovery
Authors: Rai Mayank , Pandey Aaditya , Singh Satish Kumar , Maiti Abhijit
Published: March 2024

Thermally responsive polymers (TRPs) have gained significant attention in the past decade due to their unique phase transition behavior, those exhibiting changes in properties with temperature variations. In water, hydrophilic block copolymers form helical structures that can transform into hydrophobic globules above the lower critical solution temperature (LCST). Fouling is one of the limiting issues for the forward osmosis (FO) process in wastewater treatment. In this work, after the treatment of wastewater from the paper and pulp industries, foulants were removed from the surface of the commercial polyamide thin‐film composite membrane of the FO process using polyvinyl methyl ether (PVME), a TRP with an LCST of 35–37°C. PVME was mixed with different aqueous solutions to form cleaning solutions. Foulant cleaning experiments utilized a 1% PVME (w/v) solution in 300 mL of de‐ionized (DI) water, while 1 M NaCl solution served as the draw solution (DS) in the FO process. Comparing the water flux (J) and change in membrane hydraulic resistance (Rf) among pristine, fouled, and cleaned membranes revealed a 56.67% increase in water flux and a 51.68% decrease in membrane resistance after PVME mixed with DI water cleaning solution showcasing its effectiveness in improving membrane performance and reducing fouling. The cleaning efficiency of two solutions, that is, 1% PVME mixed in DI water and 1% PVME mixed in 1 M aqueous urea solution, is compared. Results showed that the former cleaning solution helped to obtain 32.62% higher water flux and 56.05% less membrane resistance. Various membrane characterizations are performed, such as field emission scanning electron microscopy (FE‐SEM), which characterizes the membrane's pore structure and surface morphology, while a contact angle analyzer assesses hydrophilicity. This research highlights the use of TRPs as effective cleaning agents, enhancing membrane performance by effectively removing foulants on the membrane surface. Investigating alternative cleaning solutions also provides insights for optimizing water treatment processes.

Highlights

Cleaning of fouled thin‐film composite membrane using thermal‐responsive polymers (TRPs).

Polyvinyl methyl ether, a TRP with an lower critical solution temperature of 35–37°C used as a cleaning agent.

60% increase in water flux was observed after the single‐step cleaning process.

Multiple uses of TRP for cleaning performed with no membrane damage.
New role of ionic liquid as accelerator activator in rubber compounds and its influence on curing and mechanical properties
Authors: Hanumanthrao Sushmitha , Chanda Jagannath , Dolui Tuhin , Banerjee Shib Shankar , Das Gupta Saikat , Ghosh Prasenjit , Mukhopadhyay Rabindra
Published: March 2024

This study focuses on the effect of ionic liquids (ILs) on the cure characteristics and filler dispersion of natural rubber (NR) and styrene‐butadiene rubber (SBR) gum and filled compounds. The complexation of ionic liquid with zinc oxide (ZnO) increases the activity of ZnO and the cure rate together with improved filler dispersion. This has also increased the rubber filler interaction. Imidazolium and chloride based ionic liquids with different cationic groups were compared and characterized by thermogravimetric analysis, Fourier transform infrared spectroscopy, and differential scanning calorimetry to understand the thermal and chemical behavior of the compounds. Interestingly, it was found that the ionic liquid can act as an activator and is able to accelerate the vulcanization rate with improved rubber filler interaction. The complexes formed by IL‐Zn were shown to be much more reactive than Zn‐stearic acid complexes. The dispersion of carbon black in the NR and SBR compounds was studied by using Field Emission Scanning Electron Microscope and Transmission Electron Microscope and the results demonstrate that ILs could significantly improve the filler dispersion. Thus, this study has revealed the multifunctional role of ionic liquids in rubber compounds.

Highlights

This article describes the dual role of the ionic liquid (IL) in rubber compounds.

It can act both as an accelerator‐activator as well as an efficient dispersing aid.

The complexation of IL with zinc oxide (ZnO) plays a crucial role in enhancing the activity of ZnO.

As a result, the physico‐mechanical properties of both natural rubber and styrene‐butadiene rubber based compounds are significantly improved.
A review on natural fiber composites: Polymer matrices, fiber surface treatments, fabrication methods, properties, and applications
Authors: Mylsamy Bhuvaneshwaran , Shanmugam Senthil Kumar Marudhamuthu , Aruchamy Karthik , Palanisamy Sivasubramanian , Nagarajan Rajini , Ayrilmis Nadir
Published: March 2024

High performance and durability are essential for goods to satisfy the needs of the expanding worldwide market. Wood plastic composites (WPCs) are materials made from a combination of wood, polymers, and additives. WPCs can be extruded, injected, compressed, or thermoformed. Presently, WPCs are manufactured using sophisticated processes including as laser sintering, fused layer modeling, and additive manufacturing. Properly managing the melt temperature and pressure is crucial in the manufacturing process of WPCs to ensure effective polymer incorporation. Natural fibers have distinct benefits for polymer composites, but they also have some serious drawbacks, like lower strength properties—especially lower impact strength than synthetic fibers—poor compatibility with hydrophobic polymers, poorer dimensional stability and moisture absorption due to hydroxly groups, a maximum processing temperature that is limited, thermal degradation above 200–220°C, and lower biological durability. The modification of the surface of the fibers improves the mentioned disadvantages of the natural fibers. High‐quality WPCs require the application of chemical or physical treatment to the wood fibers. This extensive review focused on the modification techniques applied to the surface of wood, manufacturing processes, and properties and applications of WPCs.

Highlights

Modification methods used in surface treatment of natural fibers was explained.

Properties and recent applications of wood polymer composites were given.

Optimum requirements of natural fibers and polymer matrices are given.

Fabrication methods of natural fiber composites are extensively given.
Investigation of sound absorption on a polymeric acoustic metamaterial using 3D printing process
Authors: Shah Saliq Shamim , Singh Daljeet , Saini J. S. , Garg Naveen , Gautam Chitra
Published: March 2024

This paper presents the design and characterization of DENORMS (Designs for Noise‐Reducing Materials and Structures) cell‐based acoustic metamaterial developed using a 3D printing technique. The metamaterial's acoustic absorption properties were investigated through experimental testing and numerical simulations. The experimental testing of the acoustic metamaterial was conducted in an impedance tube using a two‐microphone method. The numerical simulations were carried out using a thermoviscous module. The simulations allowed for a deeper understanding of the influence of geometric parameters on the absorption coefficient, providing valuable insights for optimizing the design. It was observed that upon increasing the spherical diameter while maintaining the same cylindrical diameter and cylindrical length resulted in an increase in the absorption coefficient throughout the frequency range. It was also observed that upon increasing the cylindrical diameter, there was a significant decrement of absorption coefficient, and upon increasing the length of the cylinder, there was a shift of response toward lower frequency. The augmentation in cell count from 9 to 24 led to a rise in the absorption coefficient and a shift of the response toward lower frequencies. The findings highlight the significance of photopolymer 3D printing in tailoring complex geometries for enhanced performance of the acoustic metamaterial.

Highlights

Photopolymeric resin used for DENORMS cell‐based acoustic metamaterial.

High cleanability and accuracy of digital light processing 3D printing technique.

Usage of thermoviscous model for simulation of sound absorption behavior.

Use of two microphone impedance tube to determine sound absorption coefficient.

Geometric parameters significantly affect the absorption coefficient.
Dyeability and mechanical properties of banana fiber reinforced polypropylene composite
Authors: Brahma Shuvo , Raafi Sk. Mohammad , Arju Sharfun Nahar , Rehman Junaid ur
Published: March 2024

Banana fibers being highly strong and biodegradable, have always been an interesting aspect of polymer science. The research examines the pretreatment process to enhance the dyeability of banana fibers with synthetic dyes, followed by the preparation of polypropylene (PP) composites with dyed fibers to explore their mechanical properties. Raw banana fibers were extracted from the pseudo stems of banana plants for pretreating with sodium hydroxide and hydrogen peroxide and further dyed in the exhaust method using direct, basic, reactive, and vat dyes. Despite a decrease in fiber strength, the scoured‐bleached fibers appeared whiter and lustrous compared to untreated fibers. Direct dye exhibited a higher color strength (K/S) value of 20.7 and better wash fastness on average of 4‐3 rating compared to basic dye. Later polypropylene sheets were prepared using a Hot Plate Molding Machine, and composite specimens were fabricated by sandwiching the fibers between PP sheets and hot pressing. Fourier Transform Infrared Spectroscopy (FTIR) analysis revealed minor bond formations between the dyed fibers and polypropylene matrix in composites showing significant bonding at NH, CH, and OH regions. The composites containing dyed fibers showed slight improvements in tensile strength and modulus which is at best 2% than that of untreated fiber.

Highlights

Direct and basic dyes were determined as the most suitable synthetic dyes.

FTIR analysis revealed minimal bond formation between the fiber and PP matrix.

Composites having dyed banana fiber showed little better mechanical features.
Self‐standing gelatin‐ methacryloyl 3D structure using Carbopol‐embedded printing
Authors: Villata Simona , Frascella Francesca , Gaglio Cesare Gabriele , Nastasi Giuliana , Petretta Mauro , Pirri Candido Fabrizio , Baruffaldi Désirée
Published: March 2024

Gelatin‐methacryloyl (GelMA) hydrogel has gained huge success in the last decades thanks to its versatilities in many applications. Notably, one of them is 3D bioprinting, as GelMA physical‐mechanical properties and biocompatibility of uncured formulation perfectly suit the requirements of a bioink. Nevertheless, before the photopolymerization, the hydrogel shows weak mechanical properties and long recovery time after stress application, which results in the inability to obtain complex and self‐standing forms due to structure collapse. In this work, Carbopol ETD 2020 NF, dissolved in cell culture medium, was used as supporting bath to optimize GelMA bioprinting and overcome its stability limitations. The achieved results demonstrated the possibility of printing shapes containing hollows with lumens or non‐planar surfaces, also by using nozzles with larger inner diameter, which reduced cell death during printing process, but were usually avoid because of low resolution. Moreover, constructs' extraction was easier when Carbopol solution was prepared in culture medium rather than in water, reducing sample handling. In conclusion, thanks to this supporting bath, it was possible to print cellularized scaffold, with channels that were then seeded, obtaining inner structure. Further, this Carbopol formulation could be considered an eligible candidate as a supporting bath to obtain GelMA 3D self‐standing‐shaped and vascularized scaffold.
What is the relationship between body image and the quality of life of women who underwent surgery for breast cancer? A scoping review
Authors: Battistello Camila Zanella , da Silva Nathália Weschenfelder , Remor Eduardo
Published: March 2024

Purpose

This review aimed to identify, characterize, map, and summarize existing knowledge about the relationship of perceived body image with the quality of life (QoL) of women who have undergone surgical treatment for breast cancer.

Methods

A scoping review was conducted following the PRISMA‐ScR guidelines. PubMed, PsycINFO and Scopus databases were searched, and articles published until August 2022 were included.

Results

The search resulted in 796 records, and 51 articles were included for analysis. A significant negative impact on body image perception and QoL after surgical treatment for breast cancer was found in the majority of studies. Sociodemographic variables such as age, education, socioeconomic status, unstable attachment styles and time after the surgery may have an effect on a worsening of the overall body image and QoL score of women. It was found that there was greater dissatisfaction with body image in women who underwent mastectomy compared to those who underwent conservative surgery.

Conclusion

Evidence has shown that breast cancer surgery affects the perceived body image and QoL of patients worldwide. Age, education, socioeconomic status, and the type of surgery are potential factors influencing these outcomes. It is worth noting that the review encompassed articles from various countries, reflecting a significant cultural diversity among the studied populations. However, most of these articles did not delve into an analysis of these cultural disparities. This review also indicated insufficient details regarding the assessment instruments used to assess perceived body image.
Lung and diaphragm ultrasound as predictors of successful weaning from nasal continuous positive airway pressure in preterm infants
Authors: Nour Basma Ahmed , El‐Rahman Ashraf Mohamed Abd , Hameed Suzy Abd Elmabood Abd El , Mohsen Nada , Mohamed Adel , El‐Bayoumi Mohammed Attia , Abdel‐Hady Hesham Elsayed
Published: March 2024

Objective

Assessment of the utility of lung and diaphragm ultrasound in the prediction of successful weaning from nasal continuous positive airway pressure (NCPAP) in preterm infants.

Study Design

This prospective cohort study was conducted on preterm infants who were considered ready for weaning off NCPAP. Lung and diaphragm ultrasound were performed just before and 3 h after weaning off NCPAP. The primary outcome was to evaluate the accuracy of lung ultrasound (LUS) in predicting successful weaning from NCPAP.

Results

Out of 65 enrolled preterm infants, 30 (46.2%) were successfully weaned from NCPAP to room air. The successful weaning group had higher gestational ages, lower incidences of previous invasive mechanical ventilation, and treated hemodynamically significant patent ductus arteriosus before the trial weaning. A LUS score of ≤6, measured before discontinuation of NCPAP, exhibited a predictive sensitivity of 80% and specificity of 75% for successful weaning (Area under the curve (AUC) = 0.865,  ≤.001). When the LUS score was assessed 3 h after weaning from NCPAP, a cutoff point of ≤7 predicted successful weaning with a sensitivity and specificity of 90% and 60% respectively (AUC = 0.838, p ≤ .001). The diaphragmatic thickness fraction (DTF) was significantly lower in the successful weaning group. After adjustment for various factors, LUS score remained the only independent predictor of successful weaning.

Conclusion

LUS score before weaning from NCPAP has a good sensitivity and specificity for predicting successful weaning from NCPAP in preterm infants. Diaphragmatic excursion and DTF were not good predictors.
Inpatient education reduces length of outpatient oxygen therapy in bronchopulmonary dysplasia: A quality improvement project
Authors: Berlin Kathryn E. K. , Lagatta Joanne , Dawson Sara , Malnory Margaret , Scott William , Sprecher Alicia
Published: March 2024

Background

Patients discharged on home oxygen therapy (HOT) for bronchopulmonary dysplasia (BPD) often receive months of this therapy. A previous trial comparing two methods of HOT weaning showed that increased parent involvement in HOT weaning decreased HOT duration. Our outpatient team uses a standard protocol for outpatient HOT weaning, starting at the first clinic visit 4–6 weeks after discharge.

Aim

To shorten HOT duration by teaching parents the outpatient HOT weaning process before neonatal intensive care unit (NICU) discharge.

Methods

We launched a quality improvement program in April 2021 for preterm infants with BPD without significant comorbidities who were stable on ≤0.5 L nasal cannula. Eligible infants started the outpatient HOT weaning protocol while inpatient, with education for parents and nurses. The outcome measure was the duration of HOT after discharge. Process measures focused on protocol adherence. Balancing measures included NICU length of stay and appropriateness of parent‐directed HOT weaning.

Results

During the study period, there were a total of 133 eligible patients discharged on home oxygen, with 75 in the baseline group and 58 in the intervention group. Forty‐five (78%) participated in the HOT weaning protocol while inpatient. HOT was reduced from an average of 27 to 12 weeks after May 2021. We observed no change in NICU length of stay or inappropriate HOT weaning.

Conclusion

Early introduction of HOT weaning with a focus on caregiver education is associated with a decreased duration of HOT.
Xplor‐NIH: Better parameters and protocols for NMR protein structure determination
Authors: Bermejo Guillermo A. , Tjandra Nico , Clore G. Marius , Schwieters Charles D.
Published: March 2024

The present work describes an update to the protein covalent geometry and atomic radii parameters in the Xplor‐NIH biomolecular structure determination package. In combination with an improved treatment of selected non‐bonded interactions between atoms three bonds apart, such as those involving methyl hydrogens, and a previously developed term that affects the system's gyration volume, the new parameters are tested using structure calculations on 30 proteins with restraints derived from nuclear magnetic resonance data. Using modern structure validation criteria, including several formally adopted by the Protein Data Bank, and a clear measure of structural accuracy, the results show superior performance relative to previous Xplor‐NIH implementations. Additionally, the Xplor‐NIH structures compare favorably against originally determined NMR models.
Examining evolutionary scale modeling‐derived different‐dimensional embeddings in the antimicrobial peptide classification through a KNIME workflow
Authors: Martínez‐Mauricio Karla L. , García‐Jacas César R. , Cordoves‐Delgado Greneter
Published: March 2024

Molecular features play an important role in different bio‐chem‐informatics tasks, such as the Quantitative Structure–Activity Relationships (QSAR) modeling. Several pre‐trained models have been recently created to be used in downstream tasks, either by fine‐tuning a specific model or by extracting features to feed traditional classifiers. In this regard, a new family of Evolutionary Scale Modeling models (termed as ESM‐2 models) was recently introduced, demonstrating outstanding results in protein structure prediction benchmarks. Herein, we studied the usefulness of the different‐dimensional embeddings derived from the ESM‐2 models to classify antimicrobial peptides (AMPs). To this end, we built a KNIME workflow to use the same modeling methodology across experiments in order to guarantee fair analyses. As a result, the 640‐ and 1280‐dimensional embeddings derived from the 30‐ and 33‐layer ESM‐2 models, respectively, are the most valuable  since statistically better performances were achieved by the QSAR models built from them. We also fused features of the different ESM‐2 models, and it was concluded that the fusion contributes to getting better QSAR models than using features of a single ESM‐2 model. Frequency studies revealed that only a portion of the ESM‐2 embeddings is valuable for modeling tasks since between 43% and 66% of the features were never used. Comparisons regarding state‐of‐the‐art deep learning (DL) models confirm that when performing methodologically principled studies in the prediction of AMPs, non‐DL based QSAR models yield comparable‐to‐superior performances to DL‐based QSAR models. The developed KNIME workflow is available‐freely at https://github.com/cicese-biocom/classification-QSAR-bioKom. This workflow can be valuable to avoid unfair comparisons regarding new computational methods, as well as to propose new non‐DL based QSAR models.
Dual‐wield NTPases: A novel protein family mined from AlphaFold DB
Authors: Sakuma Koya , Koike Ryotaro , Ota Motonori
Published: March 2024

AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against AlphaFold DB and discovered an uncharacterized P‐loop NTPase family. The structure of the protein family was surprisingly novel, showing an atypical topology for P‐loop NTPases, noticeable twofold symmetry, and two pairs of independent putative active sites. Our findings show that structural data mining is a powerful approach to identifying undiscovered protein families.
The structural landscape of the immunoglobulin fold by large‐scale de novo design
Authors: Roel‐Touris Jorge , Carcelén Lourdes , Marcos Enrique
Published: March 2024

De novo designing immunoglobulin‐like frameworks that allow for functional loop diversification shows great potential for crafting antibody‐like scaffolds with fully customizable structures and functions. In this work, we combined de novo parametric design with deep‐learning methods for protein structure prediction and design to explore the structural landscape of 7‐stranded immunoglobulin domains. After screening folding of nearly 4 million designs, we have assembled a structurally diverse library of ~50,000 immunoglobulin domains with high‐confidence AlphaFold2 predictions and structures diverging from naturally occurring ones. The designed dataset enabled us to identify structural requirements for the correct folding of immunoglobulin domains, shed light on β‐sheet–β‐sheet rotational preferences and how these are linked to functional properties. Our approach eliminates the need for preset loop conformations and opens the route to large‐scale de novo design of immunoglobulin‐like frameworks.
A cellulosomal double‐dockerin module from Clostridium thermocellum shows distinct structural and cohesin‐binding features
Authors: Chen Chao , Yang Hongwu , Dong Sheng , You Cai , Moraïs Sarah , Bayer Edward A. , Liu Ya‐Jun , Xuan Jinsong , Cui Qiu , Mizrahi Itzhak , Feng Yingang
Published: March 2024

Cellulosomes are intricate cellulose‐degrading multi‐enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear. In this study, we characterized the structure and mode of assembly of a tandem bimodular double‐dockerin, which is connected to a putative S8 protease in the cellulosome‐producing bacterium, Clostridium thermocellum. Crystal and NMR structures of the double‐dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double‐dockerin displays a preference for binding to the cell‐wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual‐binding mode, while the second dockerin module was unable to bind to any of the tested cohesins. Surprisingly, the double‐dockerin showed a much higher affinity to a cohesin from the CipC scaffoldin of Clostridium cellulolyticum than to the resident cohesins from C. thermocellum. These results contribute valuable insights into the structure and assembly of the double‐dockerin module, and provide the basis for further functional studies on multiple‐dockerin modules and cellulosomal proteases, thus highlighting the complexity and diversity of cellulosomal components.
Labile assembly of a tardigrade protein induces biostasis
Authors: Sanchez‐Martinez S. , Nguyen K. , Biswas S. , Nicholson V. , Romanyuk A. V. , Ramirez J. , Kc S. , Akter A. , Childs C. , Meese E. K. , Usher E. T. , Ginell G. M. , Yu F. , Gollub E. , Malferrari M. , Francia F. , Venturoli G. , Martin E. W. , Caporaletti F. , Giubertoni G. , Woutersen S. , Sukenik S. , Woolfson D. N. , Holehouse A. S. , Boothby T. C.
Published: March 2024

Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self‐assembly of labile CAHS gels.
Engineering of IF1‐susceptive bacterial F1‐ATPase
Authors: Hatasaki Yuichiro C. , Kobayashi Ryohei , Watanabe Ryo R. , Hara Mayu , Ueno Hiroshi , Noji Hiroyuki
Published: March 2024

IF1, an inhibitor protein of mitochondrial ATP synthase, suppresses ATP hydrolytic activity of F1. One of the unique features of IF1 is the selective inhibition in mitochondrial F1 (MF1); it inhibits catalysis of MF1 but does not affect F1 with bacterial origin despite high sequence homology between MF1 and bacterial F1. Here, we aimed to engineer thermophilic Bacillus F1 (TF1) to confer the susceptibility to IF1 for elucidating the molecular mechanism of selective inhibition of IF1. We first examined the IF1‐susceptibility of hybrid F1s, composed of each subunit originating from bovine MF1 (bMF1) or TF1. It was clearly shown that only the hybrid with the β subunit of mitochondrial origin has the IF1‐susceptibility. Based on structural analysis and sequence alignment of bMF1 and TF1, the five non‐conserved residues on the C‐terminus of the β subunit were identified as the candidate responsible for the IF1‐susceptibility. These residues in TF1 were substituted with the bMF1 residues. The resultant mutant TF1 showed evident IF1‐susceptibility. Reversely, we examined the bMF1 mutant with TF1 residues at the corresponding sites, which showed significant suppression of IF1‐susceptibility, confirming the critical role of these residues. We also tested additional three substitutions with bMF1 residues in α and γ subunits that further enhanced the IF1‐susceptibility, suggesting the additive role of these residues. We discuss the molecular mechanism by which IF1 specifically recognizes F1 with mitochondrial origin, based on the present result and the structure of F1‐IF1 complex. These findings would help the development of the inhibitors targeting bacterial F1.
HadBD dehydratase from Mycobacterium tuberculosis fatty acid synthase type II: A singular structure for a unique function
Authors: Bories Pascaline , Rima Julie , Tranier Samuel , Marcoux Julien , Grimoire Yasmina , Tomaszczyk Mathilde , Launay Anne , Fata Karine , Marrakchi Hedia , Burlet‐Schiltz Odile , Mourey Lionel , Ducoux‐Petit Manuelle , Bardou Fabienne , Bon Cécile , Quémard Annaïk
Published: March 2024

Worldwide, tuberculosis is the second leading infectious killer and multidrug resistance severely hampers disease control. Mycolic acids are a unique category of lipids that are essential for viability, virulence, and persistence of the causative agent, Mycobacterium tuberculosis (Mtb). Therefore, enzymes involved in mycolic acid biosynthesis represent an important class of drug targets. We previously showed that the (3R)‐hydroxyacyl‐ACP dehydratase (HAD) protein HadD is dedicated mainly to the production of ketomycolic acids and plays a determinant role in Mtb biofilm formation and virulence. Here, we discovered that HAD activity requires the formation of a tight heterotetramer between HadD and HadB, a HAD unit encoded by a distinct chromosomal region. Using biochemical, structural, and cell‐based analyses, we showed that HadB is the catalytic subunit, whereas HadD is involved in substrate binding. Based on HadBDMtb crystal structure and substrate‐bound models, we identified determinants of the ultra‐long‐chain lipid substrate specificity and revealed details of structure–function relationship. HadBDMtb unique function is partly due to a wider opening and a higher flexibility of the substrate‐binding crevice in HadD, as well as the drastically truncated central α‐helix of HadD hotdog fold, a feature described for the first time in a HAD enzyme. Taken together, our study shows that HadBDMtb, and not HadD alone, is the biologically relevant functional unit. These results have important implications for designing innovative antivirulence molecules to fight tuberculosis, as they suggest that the target to consider is not an isolated subunit, but the whole HadBD complex.
Flattening the curve—How to get better results with small deep‐mutational‐scanning datasets
Authors: Wirnsberger Gregor , Pritišanac Iva , Oberdorfer Gustav , Gruber Karl
Published: March 2024

Proteins are used in various biotechnological applications, often requiring the optimization of protein properties by introducing specific amino‐acid exchanges. Deep mutational scanning (DMS) is an effective high‐throughput method for evaluating the effects of these exchanges on protein function. DMS data can then inform the training of a neural network to predict the impact of mutations. Most approaches use some representation of the protein sequence for training and prediction. As proteins are characterized by complex structures and intricate residue interaction networks, directly providing structural information as input reduces the need to learn these features from the data. We introduce a method for encoding protein structures as stacked 2D contact maps, which capture residue interactions, their evolutionary conservation, and mutation‐induced interaction changes. Furthermore, we explored techniques to augment neural network training performance on smaller DMS datasets. To validate our approach, we trained three neural network architectures originally used for image analysis on three DMS datasets, and we compared their performances with networks trained solely on protein sequences. The results confirm the effectiveness of the protein structure encoding in machine learning efforts on DMS data. Using structural representations as direct input to the networks, along with data augmentation and pretraining, significantly reduced demands on training data size and improved prediction performance, especially on smaller datasets, while performance on large datasets was on par with state‐of‐the‐art sequence convolutional neural networks. The methods presented here have the potential to provide the same workflow as DMS without the experimental and financial burden of testing thousands of mutants. Additionally, we present an open‐source, user‐friendly software tool to make these data analysis techniques accessible, particularly to biotechnology and protein engineering researchers who wish to apply them to their mutagenesis data.
Reliability assessment models for competing failure processes with two types of correlative thresholds
Authors: Song Qingbiao , Tang Jiayin , Wei Honglei , Li Yong
Published: March 2024

The two dependent competing risks are soft failure due to aging degradation and fragmentation caused by shocks and hard failure due to spring breakage caused by the same shock process. Considering the complexity of the product itself and the instability of the working environment, this study proposed a generalized reliability model for systems experiencing dependent competing failure processes (DCFPs) of degradation and random shocks, which considered two kinds of DCFP: (1) shock process could affect soft failure thresholds; (2) degradation process could affect hard failure thresholds. In case (1), we considered the effect that a cumulative number of shocks above a certain magnitude could have on the change in the soft failure threshold. In case (2), we considered not only the shock process's impact on the soft failure threshold but also the total degradation (including continuous degradation and sudden degradation caused by shock) on the hard failure threshold. The model captures the features that the shocks experienced by the system affect the degradation process, accelerating the system degradation and causing soft failures; the degradation process of the system affects the shock process, making the system more susceptible to failure from external shocks. Finally, an example using micro‐electro‐mechanical systems devices illustrates the effectiveness of the proposed approach with sensitivity analysis.
Model‐free learning‐based distributed cooperative tracking control of human‐in‐the‐loop multi‐agent systems
Authors: Mei Di , Sun Jian , Xu Yong , Dou Lihua
Published: March 2024

This article studies the model‐free learning‐based distributed cooperative tracking control of human‐in‐the‐loop multi‐agent systems in the presence of an active leader. The core role of human‐in‐the‐loop is to use the ground station to send control commands to the non‐zero control input of the leader, and then directly or indirectly control a group of agents to complete complex tasks. Meanwhile, three essential demands including the completely unknown system model, the control objective obtained optimally, as well as no initial admissible control strategy requirement, are satisfied simultaneously. It is worth emphasizing that the relevant results only satisfy one or two demands at most, which are essentially not applicable to this problem. In this article, a model‐based human‐in‐the‐loop learning algorithm is first presented to achieve the optimal tracking control, as well as the convergence of the proposed learning algorithm is proved. Then, a bias‐based data‐driven learning algorithm is proposed, which provides the potential opportunities to overcome the difficulties caused by the above‐mentioned three demands. Finally, the validity of theoretical results is testified by a numerical example.
Low Risk Squamous Cell Carcinoma and Appropriate Follow up
Authors: Goodman Dáire , Fenn Gary , Pierce Brian , Thuillier Rhona , Glavin Hannah , Dolan Roisin
Published: March 2024

A recent article in the BJD postulated that it may be “Time to reconsider skin cancer-related follow-up visits”. In our unit, we too have been seeing too many patient’s unnecessarily and we put in place measures to reduce the numbers of outpatient appointments thereby diverting the resources saved into professional development.
Discovery of Benzoxazepines as a New Class of PIM1 Kinase Inhibitors Through Structure Based Virtual Screening, Biochemical Evaluation and Cytotoxicity Studies
Authors: Sharma Omprakash , Srivastava Shubham , Sharma Manish , Malik Ruchi
Published: March 2024

PIM kinase is a serine/threonine protein kinase implicated in human cancers because it promotes cell proliferation while inhibiting apoptosis and is a crucial target for malignancy. In the present study, we used 700000 commercially available Chembridge small molecules library for structure‐based drug discovery to identify novel potent PIM1 kinase inhibitors. Based on the virtual screening results, ten compounds were chosen and screened enzymatically at 10 μM. Out of ten compounds, only two compounds, 22876894 (61 %) and 58626268 (63 %), inhibited PIM1 kinase. Subsequently, the enzymatic IC50 value for compounds 22876894 and 58626268 was calculated and found to be 0.8 μM and 3.9 μM. Cell viability was evaluated on human malignant cell lines HCT‐116 (colorectal carcinoma), U‐2OS (osteosarcoma), and non‐cancerous hTERT‐RPE‐1. It was found that compound 22876894 possessed significant inhibitory activity against HCT‐116 (IC50=12.1 μM), U‐2OS (IC50=23.2 μM), and hTERT‐RPE‐1 (IC50=12.7 μM) cell lines. The compound 58626268 possessed significant inhibitory activities against HCT‐116 (IC50=28.1 μM), U‐2OS (IC50=23.5 μM), and hTERT‐RPE‐1 (IC50=21 μM) cell lines. Further, the molecular dynamics simulation of identified compounds (22876894 and 58626268) was performed. Based on kinase profiling, cytotoxicity studies, and molecular dynamics simulation results, we claim 5‐{[7‐(1‐benzothien‐3‐yl)‐9‐hydroxy‐2,3‐dihydro‐1,4‐benzoxazepin‐4(5H)‐yl]carbonyl}pyridin‐2(1H)‐one (22876894) and 4‐(2‐aminoisonicotinoyl)‐7‐(1‐benzothien‐3‐yl)‐2,3,4,5‐tetrahydro‐1,4‐benzoxazepin‐9‐ol (58626268) as a selective and potential PIM1 kinase inhibitors.
A New Model for Specific Heat Capacity of Real Gas
Authors: Cui Xiuyun , Zhu Bing , Ni Henmei
Published: March 2024

Based on the new thermodynamic theory, a new model was suggested to calculate the specific heat capacities of monoatomic gas, He, and diatomic gas, O2. The theory suggests a portion of gas molecules with the highest kinetic energy affords the heat exchange to sustain the state equilibrium by inelastically colliding and liquefying on the container walls, whereas the rest elastically colliding with walls creates pressure. Accordingly, a general equation of specific heat capacity is established on the density of liquid and gas. Given
at isobar and
at isochore, Cp and Cv at any temperature can be calculated with the densities of gas and liquid (or solid). Employing the available data of He and O2 issued by NIST, Cps, and Cvs are calculated. The results fit the reference data well.
MgnBu2 Catalyzed the Hydroalkoxylation of Carbodiimides
Authors: Han Luming , Yan Ben , Ni Congjian , Pang Ziyuan , Ma Xiaoli , Yang Zhi
Published: March 2024

The commercially available alkaline earth‐metal compound MgnBu2 can act as a highly efficient pre‐catalyst under mild conditions for the catalytic addition of alcohols to carbodiimides. To the best of our knowledge, it has not been reported in alkaline earth‐metal catalyzing reactions. A possible mechanistic pathway is proposed based on the stoichiometric experiments and the previously published literature.
Synthesis and Properties of a Triphenylamine‐Based Fluorescent Probe for the Continuous Detection of Cu2+ and EDTA
Authors: Hu Hao , Yao Yelin , Deng Linlong , Wang Haibin , Xue Lei
Published: March 2024

A fluorescent probe NS was successfully developed using triphenylamine aldehyde and 1‐hydroxy‐2‐naphthaldehyde. NS demonstrated selective recognition of Cu2+ in a DMSO/H2O solution, forming a stable 1 : 1 complex that led to fluorescence quenching. The addition of EDTA resulted in fluorescence recovery. The fluorescent intensity of NS showed a linear correlation with Cu2+ concentration within the range of 2~14 μmol ⋅ L−1, with a detection limit of 39 nmol ⋅ L−1 and a binding constant of 1.56×103 L mol−1. Additionally, the detection limit of the NS‐Cu2+ complex for EDTA was calculated to be 187 nmol ⋅ L−1. NS also displayed promising applications in the environmental and alcoholic drinks for detecting Cu2+ in water, wine, and Chinese Baijiu samples.
Access to 2,3‐Unsubstituted Imidazo[2,1‐b][1,3]benzothiazole Using Ethylene Glycol as a C2 Precursor and Subsequent Regioselective C3 Functionalization
Authors: Maity Sujit , Panda Niranjan
Published: March 2024

Synthesis of imidazo[2,1‐b][1,3]benzothiazoles by oxidative coupling of 2‐aminobenzothiazoles with vicinal diol was reported. Expectedly, a combination of potassium persulfate and TEMPO oxidized ethylene glycol to α‐hydroxy acetaldehyde, which coupled with 2‐aminobenzothiazole to afford 2,3‐unsubstituted imidazo[2,1‐b][1,3]benzothiazoles. The later was exploited as a reliable handle to access 3‐substituted imidazo[2,1‐b][1,3]benzothiazoles regioselectively.
Regio‐ and Chemoselectivity of Tandem N‐Ketoalkylation/Cyclization of 2‐Thioxoimidazoline‐4‐One
Authors: Dorofeev Ivan A. , Zhilitskaya Larisa V. , Yarosh Nina O. , Shainyan Bagrat A. , Larina Lyudmila I.
Published: March 2024

The reaction of 2‐thioxoimidazolidin‐4‐one (thiohydantoin) with aliphatic, aromatic and heteroaromatic α‐iodomethylketones has been investigated in the absence of bases or catalysts. The reaction proceeds as N‐alkylation with subsequent intramolecular dehydrative cyclization. A series of new mono‐ and fused bicyclic iodide and triiodide salts was obtained based on the 5‐oxo‐2‐thioxoimidazolidin‐1‐ium and imidazo[2,1‐b]thiazolium cations. The observed regioselectivity has been rationalized and the mechanism was proposed.
Cation Bimetallic MOF Anchored Carbon Fiber for Highly Efficient Microwave Absorption
Authors: Zhang Feng , Li Nan , Shi Jun‐Feng , Wang Yue‐Yi , Yan Ding‐Xiang , Li Zhong‐Ming
Published: March 2024

Carbon fiber (CF) is a potential microwave absorption (MA) material due to the strong dielectric loss. Nevertheless, owing to the high conductivity, poor impedance matching of carbon‐based  materials results in limited MA performance. How to solve this problem and achieve excellent MA performance remains a principal challenge. Herein, taking full advantage of CF and excellent impedance matching of bimetallic metal–organic frameworks (MOF) derivatives layer, an excellent microwave absorber based on micron‐scale 1D CF and NiCoMOF (CF@NiCoMOF‐800) is developed. After adjusting the oxygen vacancies of the bimetallic MOF, the resultant microwave absorber presented excellent MA properties including the minimum reflection loss (RLmin) of −80.63 dB and wide effective absorption bandwidth (EAB) of 8.01 GHz when its mass percent is only 5 wt.% and the thickness is 2.59 mm. Simultaneously, the mechanical properties of the epoxy resin (EP)‐based coating with this microwave absorber are effectively improved. The hardness (H), elastic modulus (E), bending strength, and compressive strength of CF@NiCoMOF‐800/EP coating are 334 MPa, 5.56 GPa, 82.2 MPa, and 135.8 MPa, which is 38%, 15%, 106% and 53% higher than EP coating. This work provides a promising solution for carbon materials achieving excellent MA properties and mechanical properties.
Ultralow‐Friction at Cryogenic Temperature Induced by Hydrogen Correlated Quantum Effect
Authors: Chen Weiqi , Wang Kang , Miao Xinran , Zhang Jie , Song Aisheng , Chen Xinchun , Luo Jianbin , Ma Tianbao
Published: March 2024

Temperature is one of the governing factors affecting friction of solids. Undesired high friction state has been generally reported at cryogenic temperatures due to the prohibition of thermally activated processes, following conventional Arrhenius equation. This has brought huge difficulties to lubrication at extremely low temperatures in industry. Here, the study uncovers a hydrogen‐correlated sub‐Arrhenius friction behavior in hydrogenated amorphous carbon (a‐C:H) film at cryogenic temperatures, and a stable ultralow‐friction over a wide temperature range (103–348 K) is achieved. This is attributed to hydrogen‐transfer‐induced mild structural ordering transformation, confirmed by machine‐learning‐based molecular dynamics simulations. The anomalous sub‐Arrhenius temperature dependence of structural ordering transformation rate is well‐described by a quantum mechanical tunneling (QMT) modified Arrhenius model, which is correlated with quantum delocalization of hydrogen in tribochemical reactions. This work reveals a hydrogen‐correlated friction mechanism overcoming the Arrhenius temperature dependence and provides a new pathway for achieving ultralow friction under cryogenic conditions.
Construction of Cobalt Porphyrin‐Modified Cu2O Nanowire Array as a Tandem Electrocatalyst for Enhanced CO2 Reduction to C2 Products
Authors: Min Shihao , Xu Xiao , He Jiaxin , Sun Miao , Lin Wenlie , Kang Longtian
Published: March 2024

Here, the molecule‐modified Cu‐based array is first constructed as the self‐supporting tandem catalyst for electrocatalytic CO2 reduction reaction (CO2RR) to C2 products. The modification of cuprous oxide nanowire array on copper mesh (Cu2O@CM) with cobalt(II) tetraphenylporphyrin (CoTPP) molecules is achieved via a simple liquid phase method. The systematical characterizations confirm that the formation of axial coordinated Co‐O‐Cu bond between Cu2O and CoTPP can significantly promote the dispersion of CoTPP molecules on Cu2O and the electrical properties of CoTPP‐Cu2O@CM heterojunction array. Consequently, as compared to Cu2O@CM array, the optimized CoTPP‐Cu2O@CM sample as electrocatalyst can realize the 2.08‐fold C2 Faraday efficiency (73.2% vs 35.2%) and the 2.54‐fold current density (‒52.9 vs ‒20.8 mA cm–2) at ‒1.1 V versus RHE in an H‐cell. The comprehensive performance is superior to most of the reported Cu‐based materials in the H‐cell. Further study reveals that the CoTPP adsorption on Cu2O can restrain the hydrogen evolution reaction, improve the coverage of *CO intermediate, and maintain the existence of Cu(I) at low potential.
Efficient Tin–Lead Perovskite Solar Cells with a Ultrawide Usage Windows of Precursor Solution Opened by SnF2
Authors: Wan Xiaoyun , Xu Cunyun , Wang Hao , Jiang Zezhuan , Li Fuling , Xu Gaobo , Dai Zhongjun , He Xiaofeng , Song Qunliang
Published: March 2024

High quality tin–lead perovskite solar cells (Sn─Pb PSCs) can be fabricated via simple solution processing methods. However, the instability of precursor solutions and their narrow usage windows still pose challenges in manufacturing efficient and reproducible Sn─Pb PSCs, hindering the commercialization of PSCs. Fluorine tin (SnF2) is widely used as an antioxidant to improve the crystallinity of perovskite. In this study, another role of SnF2 as a stabilizer is found to restrain the deprotonation of methylammonium iodide (MAI) in the precursor solution, which improves their stability and expands their usage windows. Due to the inhibition of SnF2 on oxidation and deprotonation, stable large‐sized colloidal clusters form gradually in perovskite precursor solution during aging, leading to uniform nucleation/crystallization during film growth, significantly reducing the roughness and defect density in the films. Because of the competitive deprotonation and oxidation process of Sn2+, the benefit of larger cluster maximizes after about ten days storage of precursor solution. The champion efficiency of Sn─Pb PSCs prepared with 10 days aged precursor solution is 22.00%. High performance of devices fabricated with precursor solution stored for even ≈40 days discloses the wide usage windows of precursor solution with SnF2 additive.