bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the novel-binding site of RPA2 on Menin and predicting the effect of point mutation of Menin through protein–protein interactions
Authors: Kaur Gurjeet , Prajapat Manisha , Singh Harvinder , sarma Phulen , Bhadada Sanjay kumar , Shekhar Nishant , Sharma Saurabh , Sinha Shweta , kumar Subodh , Prakash Ajay , Medhi Bikash 
Published: June 2023

AbstractProtein–protein interactions (PPIs) play a critical role in all biological processes. Menin is tumor suppressor protein, mutated in multiple endocrine neoplasia type 1 syndrome and has been shown to interact with multiple transcription factors including (RPA2) subunit of replication protein A (RPA). RPA2, heterotrimeric protein required for DNA repair, recombination and replication. However, it’s still remains unclear the specific amino acid residues that have been involved in Menin-RPA2 interaction. Thus, accurately predicting the specific amino acid involved in interaction and effects of MEN1 mutations on biological systems is of great interests. The experimental approaches for identifying amino acids in menin-RPA2 interactions are expensive, time-consuming, and challenging. This study leverages computational tools, free energy decomposition and configurational entropy scheme to annotate the menin-RPA2 interaction and effect on menin point mutation, thereby proposing a viable model of menin-RPA2 interaction. The menin–RPA2 interaction pattern was calculated on the basis of different 3D structures of menin and RPA2 complexes, constructed using homology modeling and docking strategy, generating three best-fit models: Model 8 (− 74.89 kJ/mol), Model 28 (− 92.04 kJ/mol) and Model 9 (− 100.4 kJ/mol). The molecular dynamic (MD) was performed for 200 ns and binding free energies and energy decomposition analysis were calculated using Molecular Mechanics Poisson–Boltzmann Surface Area (MM/PBSA) in GROMACS. From binding free energy change, model 8 of Menin-RPA2 exhibited most negative binding energy of − 205.624 kJ/mol, followed by model 28 of Menin-RPA2 with − 177.382 kJ/mol. After S606F point mutation in Menin, increase of BFE (ΔGbind) by − 34.09 kJ/mol in Model 8 of mutant Menin-RPA2 occurs. Interestingly, we found a significant reduction of BFE (ΔGbind) and configurational entropy by − 97.54 kJ/mol and − 2618 kJ/mol in mutant model 28 as compared the o wild type. Collectively, this is the first study to highlight the configurational entropy of protein–protein interactions thereby strengthening the prediction of two significant important interaction sites in menin for the binding of RPA2. These predicted sites could be vulnerable for structural alternation in terms of binding free energy and configurational entropy after missense mutation in menin.
Climatic niche convergence through space and time for a potential archaeophyte (Acacia caven) in South America
Authors: Velasco Nicolás , Andrade Nicolás , Smit Christian , Bustamante Ramiro 
Published: June 2023

AbstractBased on the niche conservatism hypothesis, i.e. the idea that niches remain unchanged over space and time, climatic niche modelling (CNM) is a useful tool for predicting the spread of introduced taxa. Recent advances have extended such predictions deeper in time for plant species dispersed by humans before the modern era. The latest CNMs successfully evaluate niche differentiation and estimate potential source areas for intriguing taxa such as archaeophytes (i.e., species introduced before 1492 AD). Here, we performed CNMs forAcacia caven, a common Fabaceae tree in South America, considered an archaeophyte west of the Andes, in Central Chile. Accounting for the infraspecific delimitation of the species, our results showed that even when climates are different, climatic spaces used by the species overlap largely between the eastern and western ranges. Despite slight variation, results were consistent when considering one, two, or even three-environmental dimensions, and in accordance with the niche conservatism hypothesis. Specific distribution models calibrated for each region (east vs west) and projected to the past, indicate a common area of occupancy available in southern Bolivia—northwest Argentina since the late Pleistocene, which could have acted as a source-area, and this signal becomes stronger through the Holocene. Then, in accordance with a taxon introduced in the past, and comparing regional vs continental distribution models calibrated at the infraspecific or species level, the western populations showed their spread status to be mostly in equilibrium with the environment. Our study thus indicates how niche and species distribution models are useful to improve our knowledge related to taxa introduced before the modern era.
HighAltitudeOmicsDB, an integrated resource for high-altitude associated genes and proteins, networks and semantic-similarities
Authors: Gupta Apoorv , Pathak Sandhya , Varshney Rajeev , Ahmad Yasmin , Khurana Pankaj 
Published: June 2023

AbstractMillions of people worldwide visit, live or work in the hypoxic environment encountered at high altitudes and it is important to understand the biomolecular responses to this stress. This would help design mitigation strategies for high altitude illnesses. In spite of a number of studies spanning over 100 years, still the complex mechanisms controlling acclimatization to hypoxia remain largely unknown. To identify potential diagnostic, therapeutic and predictive markers for HA stress, it is important to comprehensively compare and analyse these studies. Towards this goal, HighAltitudeOmicsDB is a unique resource that provides a comprehensive, curated, user-friendly and detailed compilation of various genes/proteins which have been experimentally validated to be associated with various HA conditions, their protein–protein interactions (PPIs) and gene ontology (GO) semantic similarities. For each database entry, HighAltitudeOmicsDB additionally stores the level of regulation (up/down-regulation), fold change, study control group, duration and altitude of exposure, tissue of expression, source organism, level of hypoxia, method of experimental validation, place/country of study, ethnicity, geographical location etc. The database also collates information on disease and drug association, tissue-specific expression level, GO and KEGG pathway associations. The web resource is a unique server platform that offers interactive PPI networks and GO semantic similarity matrices among the interactors.These unique features help to offer mechanistic insights into the disease pathology. Hence, HighAltitudeOmicsDBis a unique platform for researchers working in this area to explore, fetch, compare and analyse HA-associated genes/proteins, their PPI networks, and GO semantic similarities. The database is available at http://www.altitudeomicsdb.in.
Single-machine scheduling with periodic maintenance and learning effect
Authors: Wu Hui , Zheng Hongmei 
Published: June 2023

AbstractThis paper discusses a single-machine scheduling problem with periodic maintenance activities and position-based learning effect to minimize the makespan. To obtain exact solutions of small-scale problems, one new two-stage binary integer programming model is formulated. In addition, a branch and bound algorithm combining boundary method and pruning rules is also proposed. According to the property of the optimal solution, a special search neighborhood is constructed. A hybrid genetic-tabu search algorithm based on genetic mechanism with tabu technique as an operator is proposed to solve medium-scale and large-scale problems. Moreover, to improve the efficiency of genetic algorithm and hybrid genetic-tabu search algorithm, Taguchi method is used for parameter tuning. Furthermore, computational experiments are carried out to compare the efficiency and performance of these algorithms.
Agricultural adaptations to mid-late Holocene climate change in western Türkiye
Authors: Maltas Tom , Şahoğlu Vasıf , Erkanal Hayat 
Published: June 2023

AbstractThe period around the mid-late Holocene transition (c. 2200bc) saw major societal developments across the eastern Mediterranean. At the same time, the region experienced a shift to more arid climatic conditions. This included punctuated episodes of rapid climate change such as the ‘4.2 ka event’, which has been implicated in widespread societal ‘collapse’ at the end of the Early Bronze Age. The ways in which societies adapted agricultural production to cope with a drying climate are poorly understood. We begin to rectify this through stable isotope analysis of archaeobotanical remains from the Aegean region of western Türkiye, conducted to reveal changes in agricultural decision making across the mid-late Holocene transition. We find that Bronze Age farmers adapted agricultural production strategies by investing in drought-tolerant cereals cultivated on drier fields with water management strategies redirected towards pulses. Despite this, we find no evidence for pronounced drought stress in cereals grown during the period of the 4.2 ka event. This raises the potential for alternative explanations for societal disruptions visible across the Anatolian Plateau during this time, such as the breakdown of long-distance trade networks.
Design of phononic crystal using open resonators as harmful gases sensor
Authors: Zaky Zaky A. , Mohaseb M. A. , Hendy Ahmed S. , Aly Arafa H. 
Published: June 2023

AbstractThis paper investigates the ability to use a finite one-dimensional phononic crystal composed of branched open resonators with a horizontal defect to detect the concentration of harmful gases such as CO2. This research investigates the impact of periodic open resonators, defect duct at the center of the structure, and geometrical parameters such as cross-sections and length of the primary waveguide and resonators on the model's performance. As far as we know, this research is unique in the sensing field. Furthermore, these simulations show that the investigated finite one-dimensional phononic crystal composed of branched open resonators with a horizontal defect is a promising sensor.
A set of vectors and strains for chromosomal integration in fission yeast
Authors: Matsuyama Akihisa , Hashimoto Atsushi , Nishimura Shinichi , Yoshida Minoru 
Published: June 2023

AbstractThe expression of heterologous genes is an important technique in yeast genetics. In fission yeast, the leu1 and ura4 genes have been used mainly as selectable markers for heterologous expression. To expand the repertoire of selection markers available for heterologous expression of genes, here we developed new host-vector systems employing lys1 and arg3. By employing genome editing with the CRISPR/Cas9 system, we isolated several alleles of lys1 and arg3, each having a critical mutation in the ORF region. In parallel, we developed a set of vectors that complement the amino acid auxotrophy of lys1 and arg3 mutants when integrated into each locus. Using these vectors in combination with the previously developed integration vector pDUAL, we successfully observed the localization of three proteins in a cell simultaneously by fusing them with different fluorescent proteins. Thus, these vectors enable combinatorial expression of heterologous genes, which addresses increasingly diverse experimental challenges.
Assessing the impacts of dam/weir operation on streamflow predictions using LSTM across South Korea
Authors: Kwon Yongsung , Cha YoonKyung , Park Yeonjeong , Lee Sangchul 
Published: June 2023

AbstractRecently, weather data have been applied to one of deep learning techniques known as “long short-term memory (LSTM)” to predict streamflow in rainfall-runoff relationships. However, this approach may not be suitable for regions with artificial water management structures such as dams and weirs. Therefore, this study aims to evaluate the prediction accuracy of LSTM for streamflow depending on the availability of dam/weir operational data across South Korea. Four scenarios were prepared for 25 streamflow stations. Scenarios #1 and #2 used weather data and weather and dam/weir operational data, respectively, with the same LSTM model conditions for all stations. Scenarios #3 and #4 used weather data and weather and dam/weir operational data, respectively, with the different LSTM models for individual stations. The Nash–Sutcliffe efficiency (NSE) and the root mean squared error (RMSE) were adopted to assess the LSTM’s performance. The results indicated that the mean values of NSE and RMSE were 0.277 and 292.6 (Scenario #1), 0.482 and 214.3 (Scenario #2), 0.410 and 260.7 (Scenario #3), and 0.592 and 181.1 (Scenario #4), respectively. Overall, the model performance was improved by the addition of dam/weir operational data, with an increase in NSE values of 0.182–0.206 and a decrease in RMSE values of 78.2–79.6. Surprisingly, the degree of performance improvement varied according to the operational characteristics of the dam/weir, and the performance tended to increase when the dam/weir with high frequency and great amount of water discharge was included. Our findings showed that the overall LSTM prediction of streamflow was improved by the inclusion of dam/weir operational data. When using dam/weir operational data to predict streamflow using LSTM, understanding of their operational characteristics is important to obtain reliable streamflow predictions.
All green sulfolane-based solvent enhanced electrical conductivity and rigidity of perovskite crystalline layer
Authors: Siripraparat Akarapitch , Mittanonsakul Pimolrat , Pansa-Ngat Pimsuda , Seriwattanachai Chaowaphat , Kumnorkaew Pisist , Kaewprajak Anusit , Kanjanaboos Pongsakorn , Pakawatpanurut Pasit 
Published: June 2023

AbstractIndustrial commercialization of perovskite solar cells not only depends on sufficient device performance, but also requires complete elimination of hazardous solvents in the fabrication process to enable sustainable development of the technology. This work reports a new solvent system based on sulfolane,$$\gamma$$γ-butyrolactone (GBL), and acetic acid (AcOH) as a significantly greener alternative to common but more hazardous solvents. Interestingly, this solvent system not only resulted in densely-packed perovskite layer of bigger crystal size and better crystallinity, the grain boundaries were found to be more rigid and highly conductive to electrical current. The physical changes at the grain boundaries were due to the sulfolane-infused crystal interfaces, which were expected to facilitate better charge transfer and provide stronger barrier to moisture within the perovskite layer, yielding higher current density and longer performance of the device as a result. In fact, by using a mixed solvent system consisting of sulfolane, GBL, and AcOH in the volume ratio of 70.0:27.5:2.5, the device stability was better and the photovoltaic performance was statistically comparable with those prepared using DMSO-based solvent. Our report reflects unprecedented findings of enhanced electrical conductivity and rigidity of the perovskite layer simply by using an appropriate choice of the all-green solvent.
A comparative multi-level toxicity assessment of carbon-based Gd-free dots and Gd-doped nanohybrids from coffee waste: hematology, biochemistry, histopathology and neurobiology study
Authors: Kuznietsova Halyna , Dziubenko Natalia , Paliienko Konstantin , Pozdnyakova Natalia , Krisanova Natalia , Pastukhov Artem , Lysenko Tetiana , Dudarenko Marina , Skryshevsky Valeriy , Lysenko Vladimir , Borisova Tatiana 
Published: June 2023

AbstractHere, a comparative toxicity assessment of precursor carbon dots from coffee waste (cofCDs) obtained using green chemistry principles and Gd-doped nanohybrids (cofNHs) was performed using hematological, biochemical, histopathological assays in vivo (CD1 mice, intraperitoneal administration, 14 days), and neurochemical approach in vitro (rat cortex nerve terminals, synaptosomes). Serum biochemistry data revealed similar changes in cofCDs and cofNHs-treated groups, i.e. no changes in liver enzymes' activities and creatinine, but decreased urea and total protein values. Hematology data demonstrated increased lymphocytes and concomitantly decreased granulocytes in both groups, which could evidence inflammatory processes in the organism and was confirmed by liver histopathology; decreased red blood cell-associated parameters and platelet count, and increased mean platelet volume, which might indicate concerns with platelet maturation and was confirmed by spleen histopathology. So, relative safety of both cofCDs and cofNHs for kidney, liver and spleen was shown, whereas there were concerns about platelet maturation and erythropoiesis. In acute neurotoxicity study, cofCDs and cofNHs (0.01 mg/ml) did not affect the extracellular level of L-[14C]glutamate and [3H]GABA in nerve terminal preparations. Therefore, cofNHs demonstrated minimal changes in serum biochemistry and hematology assays, had no acute neurotoxicity signs, and can be considered as perspective biocompatible non-toxic theragnostic agent.
Using pressure to unravel the structure–dynamic-disorder relationship in metal halide perovskites
Authors: Xu Kai , Pérez-Fidalgo Luis , Charles Bethan L. , Weller Mark T. , Alonso M. Isabel , Goñi Alejandro R. 
Published: June 2023

AbstractThe exceptional optoelectronic properties of metal halide perovskites (MHPs) are presumed to arise, at least in part, from the peculiar interplay between the inorganic metal-halide sublattice and the atomic or molecular cations enclosed in the cage voids. The latter can exhibit a roto-translative dynamics, which is shown here to be at the origin of the structural behavior of MHPs as a function of temperature, pressure and composition. The application of high hydrostatic pressure allows for unraveling the nature of the interaction between both sublattices, characterized by the simultaneous action of hydrogen bonding and steric hindrance. In particular, we find that under the conditions of unleashed cation dynamics, the key factor that determines the structural stability of MHPs is the repulsive steric interaction rather than hydrogen bonding. Taking as example the results from pressure and temperature-dependent photoluminescence and Raman experiments on MAPbBr$$_3$$3but also considering the pertinent MHP literature, we provide a general picture about the relationship between the crystal structure and the presence or absence of cationic dynamic disorder. The reason for the structural sequences observed in MHPs with increasing temperature, pressure, A-site cation size or decreasing halide ionic radius is found principally in the strengthening of the dynamic steric interaction with the increase of the dynamic disorder. In this way, we have deepened our fundamental understanding of MHPs; knowledge that could be coined to improve performance in future optoelectronic devices based on this promising class of semiconductors.
Thickness of hydrogel for nitrifying biomass entrapment determines the free ammonia susceptibility differently in batch and continuous modes
Authors: Song Minsu , Yuan Meng , Jeong Sanghyun , Bae Hyokwan 
Published: June 2023

AbstractHydrogels immobilizing nitrifying bacteria with different thicknesses of 0.55 and 1.13 cm (HG-0.55 and HG-1.13, respectively) were produced. It was recognized that the thickness of media is a crucial parameter that affects both the stability and efficiency of wastewater treatment. Batch mode experiments were conducted to quantify specific oxygen uptake rate (SOUR) values at various total ammonium nitrogen (TAN) concentrations and pH levels. In the batch test, HG-0.55 exhibited 2.4 times higher nitrifying activity than HG-1.13, with corresponding SOUR values of 0.00768 and 0.00317 mg-O2/L mL-PVA min, respectively. However, HG-0.55 was more susceptible to free ammonia (FA) toxicity than HG-1.13, resulting in a reduction of 80% and 50% in SOUR values for HG-0.55 and -1.13, respectively, upon increasing the FA concentration from 15.73 to 118.12 mg-FA/L. Continuous mode experiments were conducted to assess the partial nitritation (PN) efficiency in practical applications, where continuous wastewater inflow maintains low FA toxicity through high ammonia-oxidizing rates. With step-wise TAN concentration increases, HG-0.55 experienced a gentler increase in FA concentration compared to HG-1.13. At a nitrogen loading rate of 0.78–0.95 kg-N/m3 day, the FA increase rate for HG-0.55 was 0.0179 kg-FA/m3 day, while that of HG-1.13 was 0.0516 kg-FA/m3 day. In the batch mode, where wastewater is introduced all at once, the high accumulation of FA posed a disadvantage for the FA-susceptible HG-0.55, which made it unsuitable for application. However, in the continuous mode, the thinner HG-0.55, with its larger surface area and high ammonia oxidation activity, proved to be suitable and demonstrated its effectiveness. This study provides valuable insights and a framework for the utilization strategy of immobilized gels in addressing the toxic effects of FA in practical processes.
Primary mouse myoblast metabotropic purinoceptor profiles and calcium signalling differ with their muscle origin and are altered in mdx dystrophinopathy
Authors: Róg Justyna , Oksiejuk Aleksandra , Górecki Dariusz C. , Zabłocki Krzysztof 
Published: June 2023

AbstractMortality of Duchenne Muscular Dystrophy (DMD) is a consequence of progressive wasting of skeletal and cardiac muscle, where dystrophinopathy affects not only muscle fibres but also myogenic cells. Elevated activity of P2X7 receptors and increased store-operated calcium entry have been identified in myoblasts from the mdx mouse model of DMD. Moreover, in immortalized mdx myoblasts, increased metabotropic purinergic receptor response was found. Here, to exclude any potential effects of cell immortalization, we investigated the metabotropic response in primary mdx and wild-type myoblasts. Overall, analyses of receptor transcript and protein levels, antagonist sensitivity, and cellular localization in these primary myoblasts confirmed the previous data from immortalised cells. However, we identified significant differences in the pattern of expression and activity of P2Y receptors and the levels of the “calcium signalling toolkit” proteins between mdx and wild-type myoblasts isolated from different muscles. These results not only extend the earlier findings on the phenotypic effects of dystrophinopathy in undifferentiated muscle but, importantly, also reveal that these changes are muscle type-dependent and endure in isolated cells. This muscle-specific cellular impact of DMD may not be limited to the purinergic abnormality in mice and needs to be taken into consideration in human studies.
Retreatment of oval-shaped root canals filled with TotalFill bioceramic or AH plus sealer
Authors: Jamleh Ahmed , Nassar Mohannad , Alfadley Abdulmohsen , Alanazi Azhar , Alotiabi Hadeel , Alghilan Maryam , Alfouzan Khalid 
Published: June 2023

AbstractThis study investigated retreatment of oval canals filled with gutta-percha and different sealers using WaveOne Gold (WOG). Single oval canals were prepared to size 30, 0.04 and obturated with gutta percha and AH Plus (AHP) or TotalFill bioceramic (TFBC) sealer. After 6-month incubation, the canals were retreated with WOG Primary (25, 0.07) under simulated body temperature, and the developed load and torque were simultaneously measured. The time and regaining the apical patency were checked. Micro-computed tomography scanning was performed to calculate the remaining obturating materials. An independent t-test and chi-square test were performed at a 95% confidence level. A shorter retreatment time was needed in TFBC than in AHP (P = 0.003). However, a higher maximum apical load was reported with AHP (P = 0.000). Meanwhile, comparable maximum coronal load and maximum torque values were observed. Apical patency was regained in all TFBC roots and only 75% of the AHP samples (P = 0.217). The remaining obturating materials were comparable in TFBC (13.02 ± 8.12%) and AHP (10.11 ± 8.46%) (P = 0.398). WOG was able to remove 89.89% and 86.98% of obturating materials in TFBC and AHP, respectively. The TFBC presented lower apical loads and faster retreatment compared to AHP.