bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum error mitigation via quantum-noise-effect circuit groups
Authors: Hama Yusuke , Nishi Hirofumi 
Published: March 2024

AbstractNear-term quantum computers have been built as intermediate-scale quantum devices and are fragile against quantum noise effects, namely, NISQ devices. Traditional quantum-error-correcting codes are not implemented on such devices and to perform quantum computation in good accuracy with these machines we need to develop alternative approaches for mitigating quantum computational errors. In this work, we propose quantum error mitigation (QEM) scheme for quantum computational errors which occur due to couplings with environments during gate operations, i.e., decoherence. To establish our QEM scheme, first we estimate the quantum noise effects on single-qubit states and represent them as groups of quantum circuits, namely, quantum-noise-effect circuit groups. Then our QEM scheme is conducted by subtracting expectation values generated by the quantum-noise-effect circuit groups from those obtained by the quantum circuits for the quantum algorithms under consideration. As a result, the quantum noise effects are reduced, and we obtain approximately the ideal expectation values via the quantum-noise-effect circuit groups and the numbers of elementary quantum circuits composing them scale polynomial with respect to the products of the depths of quantum algorithms and the numbers of register bits. To numerically demonstrate the validity of our QEM scheme, we run noisy quantum simulations of qubits under amplitude damping effects for four types of quantum algorithms. Furthermore, we implement our QEM scheme on IBM Q Experience processors and examine its efficacy. Consequently, the validity of our scheme is verified via both the quantum simulations and the quantum computations on the real quantum devices. Our QEM scheme is solely composed of quantum-computational operations (quantum gates and measurements), and thus, it can be conducted by any type of quantum device. In addition, it can be applied to error mitigation for many other types of quantum noise effects as well as noisy quantum computing of long-depth quantum algorithms.
Description and management of Aspergillus section Nigri causing post-harvest bulbs rot of onion
Authors: El-Dawy Eman G. A. M. , Hussein Mohamed A. , El‑Nahas Safaa 
Published: March 2024

AbstractWhen onions are improperly stored, a post-harvest disease known as black mold of onion bulbs can result in considerable economic losses. Aspergillus section Nigri, one of many species, has been implicated in the development of black mold. In the present study, rot onion bulbs were collected from markets in Qena, Egypt. Thirteen Aspergillus section Nigri isolates were obtained and identified by morphological and molecular characterization. The ochratoxins potential of isolated A. section Nigri was tested, and three isolates were producers at the range of 1.5–15 ppm. For the presence of pks gene, no amplification product was detected. Using the fungal growth inhibition test, the isolates of A. niger were inhibited by eco-friendly materials Cement and Zeolite. Cement exhibited maximum percentage growth inhibition against the tested isolates at 74.7–86.7%. The pathogenicity activity of the A. niger isolates was tested by inoculation of healthy onion bulbs, other onion bulbs covered with Cement and Zeolite before inoculation by A. niger was used. The two treatments significantly reduced bulbs rot disease of onion than untreated bulbs. Seven and nine isolates showed 0% rot on covered bulbs by Cement and Zeolite, respectively as compared with inoculated onions, which exhibited rot ranging from 55 to 80%. Using eco-friendly materials with efficiency against post-harvest bulbs rot of onion was evaluated in this study.
Vibrio natriegens as a superior host for the production of c-type cytochromes and difficult-to-express redox proteins
Authors: Fuchs Helena , Ullrich Sophie R. , Hedrich Sabrina 
Published: March 2024

AbstractC-type cytochromes fulfil many essential roles in both aerobic and anaerobic respiration. Their characterization requires large quantities of protein which can be obtained through heterologous production. Heterologous production of c-type cytochromes in Escherichia coli is hindered since the ccmABCDEFGH genes necessary for incorporation of heme c are only expressed under anaerobic conditions. Different strategies were devised to bypass this obstacle, such as co-expressing the ccm genes from the pEC86 vector. However, co-expression methods restrict the choice of expression host and vector. Here we describe the first use of Vibrio natriegens Vmax X2 for the recombinant production of difficult-to-express redox proteins from the extreme acidophile Acidithiobacillus ferrooxidans CCM4253, including three c-type cytochromes. Co-expression of the ccm genes was not required to produce holo-c-type cytochromes in Vmax X2. E. coli T7 Express only produced holo-c-type cytochromes during co-expression of the ccm genes and was not able to produce the inner membrane cytochrome CycA. Additionally, Vmax X2 cell extracts contained higher portions of recombinant holo-proteins than T7 Express cell extracts. All redox proteins were translocated to the intended cell compartment in both hosts. In conclusion, V. natriegens represents a promising alternative for the production of c-type cytochromes and difficult-to-express redox proteins.
Morphological differences of the neuroretinal rim between temporally tilted and non-tilted optic discs in healthy eyes
Authors: Joo Chan Woong , Choi Youn Joo , Kim Han Ul , Park Sung Pyo , Na Kyeong Ik 
Published: March 2024

AbstractThis study aimed to compare morphological differences of the neuroretinal rim between the temporally tilted and non-tilted optic discs in healthy eyes. We prospectively enrolled participants aged 20–40 years with temporally tilted or non-tilted optic discs. The optic nerve head parameters were analyzed using spectral domain-optical coherence tomography. The angle between the Bruch’s membrane opening (BMO) plane and BMO-minimum rim width (BMO-MRW) was termed “BMO-MRW angle”. Peripapillary retinal nerve fiber layer thickness (pRNFLT) and BMO-based parameters were compared between the temporally tilted and non-tilted disc groups. As a result, 55 temporally tilted disc eyes and 38 non-tilted disc eyes were analyzed. Global pRNFLT, global BMO-MRW, and total BMO-minimum rim area (BMO-MRA) were similar between the two groups (p = 0.138, 0.161, and p = 0.410, respectively). In the sectoral analysis, temporally tilted disc group exhibited thicker BMO-MRW in the temporal sector (p = 0.032) and thinner in the nasal superior and nasal sectors (p = 0.025 and p = 0.002, respectively). Temporally tilted disc group showed larger BMO-MRA in the temporal, temporal superior, and temporal inferior sectors (p < 0.001, p < 0.001, and p < 0.016, respectively), alongside a higher BMO-MRW angle in the temporal sector and lower in the nasal superior and nasal sectors. In conclusion, the neuroretinal rim, represented by BMO-MRW and BMO-MRA, showed morphological differences between temporally tilted and non-tilted optic discs in healthy eyes. BMO-MRW and BMO-MRA showed temporalization in the same manner as pRNFLT in the temporally tilted disc eyes. The BMO-MRW angle showed that in temporally tilted disc eyes, optic nerve fibers met the BMO plane steeply in the nasal sector and gently in the temporal sector than in non-tilted disc eyes, suggesting potential stress region of optic nerve fibers in temporally tilted disc eyes.
Timing of first abdominal operation in Crohn’s disease based on a diagnostic model
Authors: Yang Lichao , Zhang Yawei , Yao Baojia , Wu Qiang , Peng Liangxin , Yuan Lianwen 
Published: March 2024

AbstractThis study aims to develop a clinical diagnostic model for assessing the need for initial abdominal surgery in patients diagnosed with Crohn's disease (CD) and create a nomogram to facilitate clinical decision-making. A total of 164 surgical CD patients and 230 control CD patients were included in this retrospective analysis. Least Absolute Shrinkage and Selection Operator (Lasso) regression and binomial logistic regression were employed to select clinical variables. The 394 CD patients were randomly allocated to a training set and a validation set in a 7:3 ratio. The filtered variables were used to establish a diagnostic model and nomogram in the training set, subsequently validated in the testing set. Decision Curve Analysis (DCA) and clinical impact curve were constructed to validate the clinical applicability of the model. Binomial logistic regression analysis identified seven clinical variables with a p-value less than 0.01, including Biomarker (B), Waist-to-Height Ratio (WHtR), Intestinal obstruction, Albumin (ALB), Crohn's Disease Activity Index (CDAI), Myocardial Flow Index (MFI), and C-reactive protein (CRP). These variables were utilized to establish the diagnostic model. Calibration curves showed good alignment, with a C-index of 0.996 in the training set and 0.990 in the testing set. DCA and clinical impact curve demonstrated that the diagnostic model had good clinical efficiency and could provide clinical benefits. A validated diagnostic model for determining the timing of the first abdominal operation in CD patients was established and evaluated, showing high discriminative ability, calibration, and clinical efficiency. It can be utilized by clinicians to assess the optimal timing for transitioning CD patients from medical treatment to surgical intervention, providing valuable references for individualized treatment decisions for CD patients.
The Impact of Russia-Ukraine geopolitical conflict on the air quality and toxicological properties of ambient PM2.5 in Milan, Italy
Authors: Aghaei Yashar , Badami Mohammad Mahdi , Tohidi Ramin , Subramanian P. S. Ganesh , Boffi Roberto , Borgini Alessandro , De Marco Cinzia , Contiero Paolo , Ruprecht Ario Alberto , Verma Vishal , Chatila Talal , Sioutas Constantinos 
Published: March 2024

AbstractThe geopolitical conflict between Russia and Ukraine has disrupted Europe’s natural gas supplies, driving up gas prices and leading to a shift towards biomass for residential heating during colder months. This study assessed the consequent air quality and toxicological impacts in Milan, Italy, focusing on fine particulate matter (PM2.5, dp < 2.5 μm) emissions. PM2.5 samples were analyzed for their chemical composition and assessed for their oxidative potential using the dithiothreitol (DTT) assay across three periods reflecting residential heating deployment (RHD): pre-RHD, intra-RHD, and post-RHD periods. During the intra-RHD period, PM2.5 levels were significantly higher than those in other periods, with concentrations reaching 57.94 ± 7.57 μg/m3, indicating a deterioration in air quality. Moreover, levoglucosan was 9.2 times higher during the intra-RHD period compared to the pre-RHD period, correlating with elevated levels of elemental carbon (EC) and polycyclic aromatic hydrocarbons (PAHs). These findings were compared with previous local studies before the conflict, underscoring a significant rise in biomass-related emissions. DTT assay levels during the intra-RHD were 2.1 times higher than those observed during the same period in 2022, strongly correlating with biomass burning emissions. Our findings highlight the necessity for policies to mitigate the indirect health effects of increased biomass burning emissions due to the energy crisis triggered by the geopolitical conflict.
Facile synthesis of Fe2O3, Fe2O3@CuO and WO3 nanoparticles: characterization, structure determination and evaluation of their biological activity
Authors: Mohamed Asmaa T. , Hameed Reda Abdel , EL-Moslamy Shahira H. , Fareid Mohamed , Othman Mohamad , Loutfy Samah A. , Kamoun Elbadawy A. , Elnouby Mohamed 
Published: March 2024

AbstractDue to their high specific surface area and its characteristic’s functionalized nanomaterials have great potential in medical applications specialty, as an anticancer. Herein, functional nanoparticles (NPs) based on iron oxide Fe2O3, iron oxide modified with copper oxide Fe2O3@CuO, and tungsten oxide WO3 were facile synthesized for biomedical applications. The obtained nanomaterials have nanocrystal sizes of 35.5 nm for Fe2O3, 7 nm for Fe2O3@CuO, and 25.5 nm for WO3. In addition to octahedral and square nanoplates for Fe2O3, and WO3; respectively. Results revealed that Fe2O3, Fe2O3@CuO, and WO3 NPs showed remarked anticancer effects versus a safe effect on normal cells through cytotoxicity test using MTT-assay. Notably, synthesized NPs e.g. our result demonstrated that Fe2O3@CuO exhibited the lowest IC50 value on the MCF-7 cancer cell line at about 8.876 µg/ml, compared to Fe2O3 was 12.87 µg/ml and WO3 was 9.211 µg/ml which indicate that the modification NPs Fe2O3@CuO gave the highest antiproliferative effect against breast cancer. However, these NPs showed a safe mode toward the Vero normal cell line, where IC50 were monitored as 40.24 µg/ml for Fe2O3, 21.13 µg/ml for Fe2O3@CuO, and 25.41 µg/ml for WO3 NPs. For further evidence. The antiviral activity using virucidal and viral adsorption mechanisms gave practiced effect by viral adsorption mechanism and prevented the virus from replicating inside the cells. Fe2O3@CuO and WO3 NPs showed a complete reduction in the viral load synergistic effect of combinations between the tested two materials copper oxide instead of iron oxide alone. Interestingly, the antimicrobial efficiency of Fe2O3@CuO NPs, Fe2O3NPs, and WO3NPs was evaluated using E. coli, S. aureus, and C. albicans pathogens. The widest microbial inhibition zone (ca. 38.45 mm) was observed with 250 mg/ml of WO3 NPs against E. coli, whereas using 40 mg/ml of Fe2O3@CuO NPS could form microbial inhibition zone ca. 32.86 mm against S. aureus. Nevertheless, C. albicans was relatively resistant to all examined NPs. The superior biomedical activities of these nanostructures might be due to their unique features and accepted evaluations.
Pathogenic mutations in UBQLN2 exhibit diverse aggregation propensity and neurotoxicity
Authors: Safren Nathaniel , Dao Thuy P. , Mohan Harihar Milaganur , Huang Camellia , Trotter Bryce , Castañeda Carlos A. , Paulson Henry , Barmada Sami , Sharkey Lisa M. 
Published: March 2024

AbstractThe ubiquitin-adaptor protein UBQLN2 promotes degradation of several aggregate-prone proteins implicated in neurodegenerative diseases. Missense UBQLN2 mutations also cause X-linked amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Previously we demonstrated that the liquid-like properties of UBQLN2 molecular assemblies are altered by a specific pathogenic mutation, P506T, and that the propensity of UBQLN2 to aggregate correlated with neurotoxicity. Here, we systematically assess the effects of multiple, spatially distinct ALS/FTD-linked missense mutations on UBQLN2 aggregation propensity, neurotoxicity, phase separation, and autophagic flux. In contrast to what we observed for the P506T mutation, no other tested pathogenic mutant exhibited a clear correlation between aggregation propensity and neurotoxicity. These results emphasize the unique nature of pathogenic UBQLN2 mutations and argue against a generalizable link between aggregation propensity and neurodegeneration in UBQLN2-linked ALS/FTD.
Enhancing coevolutionary signals in protein–protein interaction prediction through clade-wise alignment integration
Authors: Fang Tao , Szklarczyk Damian , Hachilif Radja , von Mering Christian 
Published: March 2024

AbstractProtein–protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates—thus reducing false positives as well as computation time.
Research on driving mechanism and prediction of electric power carbon emission in Gansu Province under dual-carbon target
Authors: Qiao Fuwei , Yang Qinzhe , Shi Wei , Yang Xuedi , Ouyang Guanwen , Zhao Lulu 
Published: March 2024

AbstractThe electric power industry is a key industry for the country to achieve the double carbon target. Its low carbon development has a double effect on this industry and helps other industries to achieve the carbon peak target. This paper firstly uses the IPCC inventory method to calculate carbon emissions in the production phase of the power industry in Gansu Province from 2000 to 2019, followed by the ridge regression method and the STIRPAT model to analyse the quantitative impact of six major drivers on carbon emissions, and finally, the scenario analysis method is used to forecast carbon emissions in this phase. The results show that the carbon emissions of Gansu Province show a trend of rising and then falling, and reached a peak of 65.66 million tons in 2013. For every 1% increase in population effect, urbanisation level, affluence, clean energy generation share, technology level and industrial structure, carbon emissions will grow by 4.939%, 0.625%, 0.224%, − 0.259%, 0.063% and 0.022% respectively. Because of the clean energy advantage in Gansu Province, the low-carbon development scenario will continue to have low carbon emissions during the scenario cycle, which can be reduced to 53.454 million tons in 2030; the baseline scenario will achieve a carbon peak in 2025, with a peak of 62.627 million tons; the economic development scenario has not achieved carbon peak during the scenario cycle, and carbon emissions will increase to 73.223 million tons in 2030.
Exploring cell-free assays for COVID-19 serosurvey
Authors: Inchauste Lucia , Nurtop Elif , Brisbarre Nadège , Ninove Laetitia , Gallian Pierre , de Lamballerie Xavier , Priet Stéphane 
Published: March 2024

AbstractSerosurveys to monitor immunity toward COVID-19 in the population are primarily performed using an ELISA to screen samples for SARS-CoV-2 antibodies, followed by confirmation by a virus neutralization test, which is considered the Gold Standard. However, virus neutralization test may not be feasible for some laboratories because of the requirement for specific facilities and trained personnel. In an attempt to address this limitation, we evaluated three cell-free methods as potential alternatives for assessing SARS-CoV-2 seroprevalence in human population from plasma. We report the establishment of two inhibition ELISAs designed to detect anti-Spike RBD IgG antibodies and a microsphere quantitative suspension array technology assay, based on the Luminex xMAP platform, to measure the presence of antibodies against various SARS-CoV-2 antigens, including anti-RBD. These methods were also compared to a commercial chemiluminescent immunoassay designed for anti-RBD antibodies detection and to the combined ELISA + virus neutralization test strategy. These cell-free assays performed equally to estimate the percentage of positive and negative samples and could be used to determine the prevalence of SARS-CoV-2 antibodies in human population, at least in cohort with high-expected prevalence, without the use of seroneutralization assay.
Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease
Authors: Martinelli Filippo , Heinken Almut , Henning Ann-Kristin , Ulmer Maria A. , Hensen Tim , González Antonio , Arnold Matthias , Asthana Sanjay , Budde Kathrin , Engelman Corinne D. , Estaki Mehrbod , Grabe Hans-Jörgen , Heston Margo B. , Johnson Sterling , Kastenmüller Gabi , Martino Cameron , McDonald Daniel , Rey Federico E. , Kilimann Ingo , Peters Olive , Wang Xiao , Spruth Eike Jakob , Schneider Anja , Fliessbach Klaus , Wiltfang Jens , Hansen Niels , Glanz Wenzel , Buerger Katharina , Janowitz Daniel , Laske Christoph , Munk Matthias H. , Spottke Annika , Roy Nina , Nauck Matthias , Teipel Stefan , Knight Rob , Kaddurah-Daouk Rima F. , Bendlin Barbara B. , Hertel Johannes , Thiele Ines 
Published: March 2024

AbstractIn this study, we aimed to understand the potential role of the gut microbiome in the development of Alzheimer's disease (AD). We took a multi-faceted approach to investigate this relationship. Urine metabolomics were examined in individuals with AD and controls, revealing decreased formate and fumarate concentrations in AD. Additionally, we utilised whole-genome sequencing (WGS) data obtained from a separate group of individuals with AD and controls. This information allowed us to create and investigate host-microbiome personalised whole-body metabolic models. We predicted microbial formate as well as other microbial metabolites, which could alter urine formate production in the host-microbiome personalised models. Additionally, we identified specific reactions responsible for the production of formate in the host, and interestingly, these reactions were linked to genes that have correlations with AD. This study suggests formate as a possible early AD marker and highlights genetic and microbiome contributions to its production. The reduced formate secretion and its genetic associations point to a complex connection between gut microbiota and AD. This holistic understanding might pave the way for novel diagnostic and therapeutic avenues in AD management.
Novel pheromone-mediated reproductive behaviour in the stag beetle, Lucanus cervus
Authors: Harvey Deborah J. , Vuts József , Hooper Antony , Caulfield John C. , Finch Paul , Woodcock Christine M. , Gange Alan C. , Chapman Jason W. , Birkett Michael A. , Pickett John A. 
Published: March 2024

AbstractThe iconic European stag beetle (Lucanus cervus) (Coleoptera: Lucanidae) is one of the largest terrestrial beetles in Europe. Due to decreasing population numbers, thought to be a consequence of habitat loss, this beetle has become a near-threatened species across much of Europe, and a reliable monitoring system is required to measure its future population trends. As part of a programme aimed at conserving UK populations, we have investigated the chemical ecology of the beetle, with a view to developing an efficient semiochemical-based monitoring system. Such a scheme will be beneficial not only in the UK but across the European range of the species, where the beetle is of conservation concern. Here, we report on a surprising discovery of a male-produced pheromone, which provokes initial sexual receptivity in females, and which has not been previously identified in the animal kingdom. Furthermore, we assign sex pheromone function to a previously described female-specific compound.