bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitive detection of SARS‐CoV‐2 main protease 3CLpro with an engineered ribonuclease zymogen
Authors: Wralstad Evans C. , Raines Ronald T. 
Published: March 2024

AbstractAlongside vaccines and antiviral therapeutics, diagnostic tools are a crucial aid in combating the COVID‐19 pandemic caused by the etiological agent SARS‐CoV‐2. All common assays for infection rely on the detection of viral sub‐components, including structural proteins of the virion or fragments of the viral genome. Selective pressure imposed by human intervention of COVID‐19 can, however, induce viral mutations that decrease the sensitivity of diagnostic assays based on biomolecular structure, leading to an increase in false‐negative results. In comparison, mutations are unlikely to alter the function of viral proteins, and viral machinery is under less selective pressure from vaccines and therapeutics. Accordingly, diagnostic assays that rely on biomolecular function can be more robust than ones that rely on biopolymer structure. Toward this end, we used a split intein to create a circular ribonuclease zymogen that is activated by the SARS‐CoV‐2 main protease, 3CLpro. Zymogen activation by 3CLpro leads to a >300‐fold increase in ribonucleolytic activity, which can be detected with a highly sensitive fluorogenic substrate. This coupled assay can detect low nanomolar concentrations of 3CLpro within a timeframe comparable to that of common antigen‐detection protocols. More generally, the concept of detecting a protease by activating a ribonuclease could be the basis of diagnostic tools for other indications.
RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short‐chain L‐asparaginases
Authors: Zhang Di , Czapinska Honorata , Bochtler Matthias , Wlodawer Alexander , Lubkowski Jacek 
Published: March 2024

AbstractL‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum, reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.
Biochemical and structural characterization reveals Rv3400 codes for β‐phosphoglucomutase in Mycobacterium tuberculosis
Authors: Singh Latika , Karthikeyan Subramanian , Thakur Krishan Gopal 
Published: March 2024

AbstractMycobacterium tuberculosis (Mtb) adapt to various host environments and utilize a variety of sugars and lipids as carbon sources. Among these sugars, maltose and trehalose, also play crucial role in bacterial physiology and virulence. However, some key enzymes involved in trehalose and maltose metabolism in Mtb are not yet known. Here we structurally and functionally characterized a conserved hypothetical gene Rv3400. We determined the crystal structure of Rv3400 at 1.7 Å resolution. The crystal structure revealed that Rv3400 adopts Rossmann fold and shares high structural similarity with haloacid dehalogenase family of proteins. Our comparative structural analysis suggested that Rv3400 could perform either phosphatase or pyrophosphatase or β‐phosphoglucomutase (β‐PGM) activity. Using biochemical studies, we further confirmed that Rv3400 performs β‐PGM activity and hence, Rv3400 encodes for β‐PGM in Mtb. Our data also confirm that Mtb β‐PGM is a metal dependent enzyme having broad specificity for divalent metal ions. β‐PGM converts β‐D‐glucose‐1‐phosphate to β‐D‐glucose‐6‐phosphate which is required for the generation of ATP and NADPH through glycolysis and pentose phosphate pathway, respectively. Using site directed mutagenesis followed by biochemical studies, we show that two Asp residues in the highly conserved DxD motif, D29 and D31, are crucial for enzyme activity. While D29A, D31A, D29E, D31E and D29N mutants lost complete activity, D31N mutant retained about 30% activity. This study further helps in understanding the role of β‐PGM in the physiology of Mtb.
Mechanosensitive channel MscL gating transitions coupling with constriction point shift
Authors: Zhang Mingfeng , Tang Siyang , Wang Xiaomin , Fang Sanhua , Li Yuezhou 
Published: March 2024

AbstractThe mechanosensitive channel of large conductance (MscL) acts as an “emergency release valve” that protects bacterial cells from acute hypoosmotic stress, and it serves as a paradigm for studying the mechanism underlying the transduction of mechanical forces. MscL gating is proposed to initiate with an expansion without opening, followed by subsequent pore opening via a number of intermediate substates, and ends in a full opening. However, the details of gating process are still largely unknown. Using in vivo viability assay, single channel patch clamp recording, cysteine cross‐linking, and tryptophan fluorescence quenching approach, we identified and characterized MscL mutants with different occupancies of constriction region in the pore domain. The results demonstrated the shifts of constriction point along the gating pathway towards cytoplasic side from residue G26, though G22, to L19 upon gating, indicating the closed‐expanded transitions coupling of the expansion of tightly packed hydrophobic constriction region to conduct the initial ion permeation in response to the membrane tension. Furthermore, these transitions were regulated by the hydrophobic and lipidic interaction with the constricting “hot spots”. Our data reveal a new resolution of the transitions from the closed to the opening substate of MscL, providing insights into the gating mechanisms of MscL.
Soil sample storage conditions affect measurements of pH, potassium, and nitrogen
Authors: Sollen‐Norrlin Maya , Rintoul‐Hynes Naomi Laura Jane 
Published: March 2024

AbstractSoil quality monitoring schemes are a useful tool for assessing the potential of soils to perform desired services such as agricultural productivity. When researchers or other stakeholders wish to compare results between different schemes or studies, failure to consider differences in soil sample storage conditions presents a significant potential for error. Here, we compared levels of nitrogen and potassium, as well as pH, in agricultural soil samples stored under three different conditions (refrigerated, frozen, and oven‐dried). All tests were performed after 7 and 24 weeks of storage. Nitrate decreased significantly in dried (p < 0.001) samples. When refrigerated, nitrate first increased (p < 0.01) and then decreased (p < 0.001). Nitrate levels where unchanged at Week 7 in the freezer but decreased significantly at Week 24 (p < 0.001). Nitrite and ammonium increased after drying (p < 0.001) and when frozen (p < 0.001 and p < 0.05) but remained stable when refrigerated. There was no significant difference in potassium levels between the fresh control and Week 7 in the freezer, but potassium had increased at Week 24 (p < 0.05). Potassium concentration increased in refrigerated samples (p < 0.001) and fluctuated up and down in dried samples (p < 0.01). pH measurements fluctuated significantly in refrigerated and frozen samples (p < 0.001 and p < 0.01, respectively) but were unchanged in dried samples. We suggest that soil monitoring schemes standardize their sample storage, and we encourage researchers to clearly report soil sample storage conditions in publications, to improve transparency and reproducibility.
Recent Advancements and Developments in the Biological Importance of 1,3,5‐Triazines
Authors: Rathod Bhagyashri , Pawar Swati , Puri Sachin , Diwan Anupama , Kumar Kapil 
Published: March 2024

AbstractNitrogen‐bearing heterocycles are ubiquitous in landscapes and have a great impact on living nature. Structural motifs are present in diverse natural products like vitamins, antibiotics, and alkaloids, as well as pharmaceuticals. The 1,3,5‐Triazines are the primitive class of heterocyclic motifs and are used in various synthetic and medicinal applications. This review covers an exhaustive exploration of literature reports and describes various synthetic strategies and pharmacological activities of 1,3,5‐triazine moiety. Synthetic strategies include multicomponent reaction, metal catalyst reaction, microwave‐assisted strategy, etc. to construct 1,3,5‐triazine moiety. Pharmacological activities include anticancer, antimalarial, antibacterial, antifungal, antiviral, anti‐tubercular, anti‐leishmanial, anti‐inflammatory, histamine antagonist, serotonin antagonist, etc. For anticancer activity, 1,3,5‐triazine moiety‐containing compounds were tested on different cell lines, and inhibitory activity was also mentioned. The involvement of this scaffold in the treatment of various diseases and disorders makes this scaffold important from a research perspective. Therefore, there is a need to present the combined data of research and reviews to the researchers to develop new molecules. For that reason, the review included information from articles published from 1978 onwards.
Insight of Cadmium Solidification by Mineral‐Based Soil Conditioner
Authors: Liu ShanKe , Liu Jianming , Liu Yanhong , Yuan Yuan 
Published: March 2024

AbstractIn response to the environmental concerns posed by cadmium (Cd) contamination, the application of nano‐submicron mineral‐based soil conditioner (MSC) as a potential soil amendment has garnered interest due to its promising Cd mitigation properties. In this study, we aimed to investigate the solidification capacity and mechanism of Cd in MSC and examine the phase and morphology changes following solidification. Systematic experiments were conducted to assess the solidification capacity of MSC for Cd, revealing an impressive efficiency of nearly 100 % even at Cd concentrations of approximately 800 mg/L. The solidification efficiency was found to be positively correlated with the pH value, significantly declining as the environment shifted from pH>7 to pH<7. Notably, under alkaline conditions (pH>7), Cd solidification in MSC was primarily attributed to the Cd‐OH complex formed on the surface of MSC and aided by cation‐exchange reaction. In contrast, under acidic conditions (pH<7) and exposure to extreme Cd concentrations, Cd(OH)Cl precipitation became the dominant mechanism for solidification. Interestingly, the presence of KCdCl3, a water‐soluble phase, did not significantly contribute to the overall solidification efficiency. These findings provide valuable insights into the solidification mechanism of Cd in MSC and offer potential implications for soil remediation efforts targeting Cd contamination.
Mediated Peroxymonosulfate Activation at the Single Atom Fe‐N3O1 Sites: Synergistic Degradation of Antibiotics by Two Non‐Radical Pathways
Authors: Zeng Yuxi , Deng Jie , Zhou Nan , Xia Wu , Wang Zihao , Song Biao , Wang Ziwei , Yang Yang , Xu Xing , Zeng Guangming , Zhou Chengyun 
Published: March 2024

AbstractThe activation of persulfates to degrade refractory organic pollutants is a hot issue in advanced oxidation right now. Here, it is reported that single‐atom Fe‐incorporated carbon nitride (Fe‐CN‐650) can effectively activate peroxymonosulfate (PMS) for sulfamethoxazole (SMX) removal. Through some characterization techniques and DFT calculation, it is proved that Fe single atoms in Fe‐CN‐650 exist mainly in the form of Fe‐N3O1 coordination, and Fe‐N3O1 exhibited better affinity for PMS than the traditional Fe‐N4 structure. The degradation rate constant of SMX in the Fe‐CN‐650/PMS system reached 0.472 min−1, and 90.80% of SMX can still be effectively degraded within 10 min after five consecutive recovery cycles. The radical quenching experiment and electrochemical analysis confirm that the pollutants are mainly degraded by two non‐radical pathways through 1O2 and Fe(IV)═O induced at the Fe‐N3O1 sites. In addition, the intermediate products of SMX degradation in the Fe‐CN‐650/PMS system show toxicity attenuation or non‐toxicity. This study offers valuable insights into the design of carbon‐based single‐atom catalysts and provides a potential remediation technology for the optimum activation of PMS to disintegrate organic pollutants.
Self–Zincophilic Dual Protection Host of 3D ZnO/Zn⊂CF to Enhance Zn Anode Cyclability
Authors: Lu Huibing , Hua Weimin , Zhang Zhengchunyu , An Xuguang , Feng Jinkui , Xi Baojuan , Xiong Shenglin 
Published: March 2024

AbstractZn dendrite growth and side reactions restrict the practical use of Zn anode. Herein, the design of a novel 3D hierarchical structure is demonstrated with self–zincophilic dual–protection constructed by ZnO and Zn nanoparticles immobilized on carbon fibers (ZnO/Zn⊂CF) as a versatile host on the Zn surface. The unique 3D frameworks with abundant zinc nucleation storage sites can alleviate the structural stress during the plating/stripping process and overpower Zn dendrite growth by moderating Zn2+ flux. Moreover, given the dual protection design, it can reduce the contact area between active zinc and electrolyte, inhibiting hydrogen evolution reactions. Importantly, density functional theory calculations and experimental results confirm that the introduced O atoms in ZnO/Zn⊂CF enhance the interaction between Zn2+ and the host and reduce Zn nucleation overpotential. As expected, the ZnO/Zn⊂CF–Zn electrode exhibits stable Zn plating/stripping with low polarization for 4200 h at 0.2 mA cm−2 and 0.2 mAh cm−2. Furthermore, the symmetrical cell displays a significantly long cycling life of over 1800 h, even at 30 mA cm−2. The fabricated full cells also show impressive cycling performance when coupled with V2O3 cathodes.
The Phase Control of Transition Metallic Elements via Facile Chemical and Physical Syntheses
Authors: Liu Yuhan , Qin Ying , Gao Junyun , Huang Bo 
Published: March 2024

AbstractThe crystal phases of metals are important factors to tune the properties of metals, and therefore received extensive attention. Traditionally, phase control is performed within limited numbers of elements by harsh conditions, such as face‐centered cubic Fe by high temperature. This review summarizes most reports in metal phase control area, including elements of Fe, Co, Ni, Cu, Ru, Pd, Rh, Os and Au. For every metallic element, the facile phase control methods are systematically introduced, such as epitaxial growth, ball milling, chemical reduction, etc. Their corresponding applications and the mechanisms for phase control are thoroughly discussed.
Effect of Bacillus subtilis and Bacillus coagulans spores on induced allergic contact dermatitis in dogs
Authors: Khosravi Mohammad , Avizeh Reza , Zayerzadeh Akram , Gharibi Darioush , Razijalali Mohammad 
Published: March 2024

AbstractBackgroundProbiotic strains have the potential to modulate immune responses, reduce intestinal inflammation, normalize intestinal mucosal function and decrease allergic reactions.ObjectiveThis study aimed to investigate the effect of oral probiotic supplements containing Bacillus subtilis and Bacillus coagulans spores on clinical symptoms, haematological factors and immune responses to allergic contact dermatitis in dogs induced by dinitrochlorobenzene (DNCB).MethodsDNCB was injected subcutaneously into the scapular region of 20 healthy adult dogs of both sexes, divided into four groups, to induce experimental allergic contact dermatitis. Dogs in Group 1 received food without probiotics or medication. Oral prednisolone was administered to Group 2 for 30 days at a dosage of 0.25 mg/kg every other day. The dogs in Group 3 were treated with a combination of oral prednisolone and probiotics. The dogs in Group 4 were fed daily with a mixture of 109 B. subtilis and B. coagulans bacteria for 30 days. The immune system responses and related gene expression were analysed in the treated animals.ResultsThe administration of probiotics for 30 days resulted in a reduction in clinical symptoms and duration of wound repair. The probiotics treatment also significantly increased the serum bactericidal effects against Staphylococcus aureus and Escherichia coli. It enhanced both the classic and alternative activity of the complement, as well as lysozyme activity. Additionally, the probiotics led to higher total immunoglobulin levels and significant reductions in anti‐trypsin and C‐reactive protein levels. Furthermore, the expression of IgE, induction of interferon‐gamma and IL‐4 genes were also reduced.ConclusionsAccording to the results, B. subtilis and B. coagulans can be further investigated as a viable alternative to corticosteroids in treating allergic contact dermatitis in dogs.
Inferior vena cava reconstruction with non‐fascial autologous peritoneum: Retrospective study and literature review
Authors: Delcarro Alessandro , Coubeau Laurent 
Published: March 2024

AbstractBackgroundInferior vena cava (IVC) resection is essential for complete (R0) excision of some malignancies. However, the optimal material for IVC reconstruction remains unclear. Our objective is to demonstrate the efficacy, safety, and advantages of using Non‐Fascial Autologous Peritoneum (NFAP) for IVC reconstruction. To conduct a literature review of surgical strategies for tumors involving the IVC.MethodsWe reviewed all IVC reconstructions performed at our institution between 2015 and 2023. Preoperative, operative, postoperative, and follow‐up data were collected and analyzed.ResultsA total of 33 consecutive IVC reconstructions were identified: seven direct sutures, eight venous homografts (VH), and 18 NFAP. With regard to NFAP, eight tubular (mean length, 12.5 cm) and 10 patch (mean length, 7.9 cm) IVC reconstructions were performed. Resection was R0 in 89% of the cases. Two patients had Clavien–Dindo grade I complications, 2 grade II, 2 grade III and 2 grade V complications. The only graft‐related complication was a case of early partial thrombosis, which was conservatively treated. At a mean follow‐up of 25.9 months, graft patency was 100%. There were seven recurrences and six deaths. Mean overall survival (OS) was 23.4 months and mean disease‐free survival (DFS) was 14.4 months. According to our results, no statistically significant differences were found between NFAP and VH.ConclusionsNFAP is a safe and effective alternative for partial or complete IVC reconstruction and has many advantages over other techniques, including its lack of cost, wide and ready availability, extreme handiness, and versatility. Further comparative studies are required to determine the optimal technique for IVC reconstruction.
Reconciling Deep Learning and Control Theory: Recurrent Neural Networks for Indirect Data-Driven Control
Authors: Bonassi Fabio 
Published: March 2024

AbstractThis Brief aims to discuss the potential of Recurrent Neural Networks (RNNs) for indirect data-driven control. Indeed, while RNNs have long been known to be universal approximators of dynamical systems, their adoption for system identification and control has been limited by the lack of solid theoretical foundations. We here intend to summarize a novel approach to address this gap, which is structured in two contributions. First, a framework for learning safe and robust RNN models is devised, relying on the Incremental Input-to-State Stability ($$\delta $$
δ
ISS) notion. Then, after a $$\delta $$
δ
ISS black-box model of the plant is identified, its use for the design of model-based control laws (such as Nonlinear MPC) with closed-loop performance guarantees is illustrated. Finally, the main open problems and future research directions are outlined.
The minimal massive Majoron Seesaw Model
Authors: de Giorgi Arturo , Merlo Luca , Díaz Xavier Ponce , Rigolin Stefano 
Published: March 2024

Abstract
A convincing explanation of the smallness of neutrino masses is represented by the Type-I Seesaw mechanism, where the two measured neutrino mass differences can be generated by introducing at least two right-handed neutrinos. In an ultraviolet complete model, it is possible to dynamically generate the heavy Majorana scale through the spontaneous symmetry breaking of a global Abelian symmetry and the most economical realisation consists in coupling the two exotic neutral leptons to a singlet complex scalar field. The associated Goldstone boson is often dubbed as Majoron, which may achieve a non-vanishing mass by means of a small term that explicitly breaks the Abelian symmetry. In a generic model, the neutrino and Majoron mass generation mechanisms are completely uncorrelated. In this paper, instead, we reduce the landscape of possible models proposing a unique, minimal and predictive framework in which these two types of masses are strictly tied and arise from the same source. Bounds from various terrestrial and astrophysical experiments are discussed.
Single-cell analysis of age-related changes in leukocytes of diabetic mouse hindpaws
Authors: Nichols James M. , Pham Hoang Vu , Lee Eric F. , Mahalingam Rajasekaran , Shepherd Andrew J. 
Published: March 2024

AbstractComplications associated with Type 1 and Type 2 diabetes, such as diabetic peripheral neuropathy and diabetic foot ulcers, are a growing health-care concern. In addition, this concern increases as diabetic patients age due to their increased susceptibility to complications. To address this growing problem, it is important to understand fluctuations in physiology which lead to pathological changes associated with the metabolic disturbances of diabetes. Our study explores dysregulation of immune cell populations in the hindpaws of healthy and diabetic mice at 12 and 21 weeks of age using single-cell RNA sequencing to provide insight into immune disruptions occurring in the distal limb during chronic diabetes. In 21-week-old Leprdb/db mice, increases were seen in mast cells/basophils, dermal γδ T cells, heterogeneous T cells, and Type 2 innate lymphoid cells. In addition, macrophages represented the largest cluster of immune cells and showed the greatest increase in genes associated with immune-specific pathways. Sub-clustering of macrophages revealed a bias toward angiogenic Lyve1+MHCIIlo macrophages in the hindpaws of 21-week-old diabetic mice, which corresponded to an increase in Lyve1+ macrophages in the hindpaws of 21-week-old diabetic mice on histology. Our results show that in Type 2 diabetes, the immunological function and phenotype of multiple immune cell types shift not only with metabolic disturbance, but also with duration of disease, which may explain the increased susceptibility to pathologies of the distal limb in patients with more chronic diabetes.