bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shaping of microbial phenotypes by trade-offs
Authors: Zhu Manlu , Dai Xiongfeng 
Published: May 2024

AbstractGrowth rate maximization is an important fitness strategy for microbes. However, the wide distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth is often not favored across ecological environments. In many circumstances, there exist trade-offs between growth and other important traits (e.g., adaptability and survival) due to physiological and proteome constraints. Investments on alternative traits could compromise growth rate and microbes need to adopt bet-hedging strategies to improve fitness in fluctuating environments. Here we review the mechanistic role of trade-offs in controlling bacterial growth and further highlight its ecological implications in driving the emergences of many important ecological phenomena such as co-existence, population heterogeneity and oligotrophic/copiotrophic lifestyles.
A reactive neural network framework for water-loaded acidic zeolites
Authors: Erlebach Andreas , Šípka Martin , Saha Indranil , Nachtigall Petr , Heard Christopher J. , Grajciar Lukáš 
Published: May 2024

AbstractUnder operating conditions, the dynamics of water and ions confined within protonic aluminosilicate zeolite micropores are responsible for many of their properties, including hydrothermal stability, acidity and catalytic activity. However, due to high computational cost, operando studies of acidic zeolites are currently rare and limited to specific cases and simplified models. In this work, we have developed a reactive neural network potential (NNP) attempting to cover the entire class of acidic zeolites, including the full range of experimentally relevant water concentrations and Si/Al ratios. This NNP has the potential to dramatically improve sampling, retaining the (meta)GGA DFT level accuracy, with the capacity for discovery of new chemistry, such as collective defect formation mechanisms at the zeolite surface. Furthermore, we exemplify how the NNP can be used as a basis for further extensions/improvements which include data-efficient adoption of higher-level (hybrid) references via Δ-learning and the acceleration of rare event sampling via automatic construction of collective variables. These developments represent a significant step towards accurate simulations of realistic catalysts under operando conditions.
Cerebral microstructural alterations in Post-COVID-condition are related to cognitive impairment, olfactory dysfunction and fatigue
Authors: Hosp Jonas A. , Reisert Marco , Dressing Andrea , Götz Veronika , Kellner Elias , Mast Hansjörg , Arndt Susan , Waller Cornelius F. , Wagner Dirk , Rieg Siegbert , Urbach Horst , Weiller Cornelius , Schröter Nils , Rau Alexander 
Published: May 2024

AbstractAfter contracting COVID-19, a substantial number of individuals develop a Post-COVID-Condition, marked by neurologic symptoms such as cognitive deficits, olfactory dysfunction, and fatigue. Despite this, biomarkers and pathophysiological understandings of this condition remain limited. Employing magnetic resonance imaging, we conduct a comparative analysis of cerebral microstructure among patients with Post-COVID-Condition, healthy controls, and individuals that contracted COVID-19 without long-term symptoms. We reveal widespread alterations in cerebral microstructure, attributed to a shift in volume from neuronal compartments to free fluid, associated with the severity of the initial infection. Correlating these alterations with cognition, olfaction, and fatigue unveils distinct affected networks, which are in close anatomical-functional relationship with the respective symptoms.
Mitochondrial respiratory function is preserved under cysteine starvation via glutathione catabolism in NSCLC
Authors: Ward Nathan P. , Yoon Sang Jun , Flynn Tyce , Sherwood Amanda M. , Olley Maddison A. , Madej Juliana , DeNicola Gina M. 
Published: May 2024

AbstractCysteine metabolism occurs across cellular compartments to support diverse biological functions and prevent the induction of ferroptosis. Though the disruption of cytosolic cysteine metabolism is implicated in this form of cell death, it is unknown whether the substantial cysteine metabolism resident within the mitochondria is similarly pertinent to ferroptosis. Here, we show that despite the rapid depletion of intracellular cysteine upon loss of extracellular cystine, cysteine-dependent synthesis of Fe-S clusters persists in the mitochondria of lung cancer cells. This promotes a retention of respiratory function and a maintenance of the mitochondrial redox state. Under these limiting conditions, we find that glutathione catabolism by CHAC1 supports the mitochondrial cysteine pool to sustain the function of the Fe-S proteins critical to oxidative metabolism. We find that disrupting Fe-S cluster synthesis under cysteine restriction protects against the induction of ferroptosis, suggesting that the preservation of mitochondrial function is antagonistic to survival under starved conditions. Overall, our findings implicate mitochondrial cysteine metabolism in the induction of ferroptosis and reveal a mechanism of mitochondrial resilience in response to nutrient stress.
Combination of UGT1A1 polymorphism and baseline plasma bilirubin levels in predicting the risk of antipsychotic-induced dyslipidemia in schizophrenia patients
Authors: Lin Chenquan , Zhang Shuangyang , Yang Ping , Zhang Bikui , Guo Wenbin , Wu Renrong , Liu Yong , Wang Jianjian , Wu Haishan , Cai Hualin 
Published: May 2024

AbstractThe prolonged usage of atypical antipsychotic drugs (AAPD) among individuals with schizophrenia often leads to metabolic side effects such as dyslipidemia. These effects not only limit one’s selection of AAPD but also significantly reduce compliance and quality of life of patients. Recent studies suggest that bilirubin plays a crucial role in maintaining lipid homeostasis and may be a potential pre-treatment biomarker for individuals with dyslipidemia. The present study included 644 schizophrenia patients from two centers. Demographic and clinical characteristics were collected at baseline and 4 weeks after admission to investigate the correlation between metabolites, episodes, usage of AAPDs, and occurrence of dyslipidemia. Besides, we explored the combined predictive value of genotypes and baseline bilirubin for dyslipidemia by employing multiple PCR targeted capture techniques to sequence two pathways: bilirubin metabolism-related genes and lipid metabolism-related genes. Our results indicated that there existed a negative correlation between the changes in bilirubin levels and triglyceride (TG) levels in patients with schizophrenia. Among three types of bilirubin, direct bilirubin in the baseline (DBIL-bl) proved to be the most effective in predicting dyslipidemia in the ROC analysis (AUC = 0.627, p < 0.001). Furthermore, the odds ratio from multinomial logistic regression analysis showed that UGT1A1*6 was a protective factor for dyslipidemia (ß = −12.868, p < 0.001). The combination of baseline DBIL and UGT1A1*6 significantly improved the performance in predicting dyslipidemia (AUC = 0.939, p < 0.001). Schizophrenia patients with UGT1A1*6 mutation and a certain level of baseline bilirubin may be more resistant to dyslipidemia and have more selections for AAPD than other patients.
Sweet-spot operation of a germanium hole spin qubit with highly anisotropic noise sensitivity
Authors: Hendrickx N. W. , Massai L. , Mergenthaler M. , Schupp F. J. , Paredes S. , Bedell S. W. , Salis G. , Fuhrer A. 
Published: May 2024

AbstractSpin qubits defined by valence band hole states are attractive for quantum information processing due to their inherent coupling to electric fields, enabling fast and scalable qubit control. Heavy holes in germanium are particularly promising, with recent demonstrations of fast and high-fidelity qubit operations. However, the mechanisms and anisotropies that underlie qubit driving and decoherence remain mostly unclear. Here we report the highly anisotropic heavy-hole g-tensor and its dependence on electric fields, revealing how qubit driving and decoherence originate from electric modulations of the g-tensor. Furthermore, we confirm the predicted Ising-type hyperfine interaction and show that qubit coherence is ultimately limited by 1/f charge noise, where f is the frequency. Finally, operating the qubit at low magnetic field, we measure a dephasing time of $${T}_{2}^{* }$$

T

2

*

= 17.6 μs, maintaining single-qubit gate fidelities well above 99% even at elevated temperatures of T > 1 K. This understanding of qubit driving and decoherence mechanisms is key towards realizing scalable and highly coherent hole qubit arrays.
Bidirectional epigenetic editing reveals hierarchies in gene regulation
Authors: Pacalin Naomi M. , Steinhart Zachary , Shi Quanming , Belk Julia A. , Dorovskyi Dmytro , Kraft Katerina , Parker Kevin R. , Shy Brian R. , Marson Alexander , Chang Howard Y. 
Published: May 2024

AbstractCRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants.
Research on trajectory control technology for L-shaped horizontal exploration wells in coalbed methane
Authors: Liu Xiugang , Jiang Zaibing , Wang Yi , Mo Haitao , Li Haozhe , Guo Jianlei 
Published: May 2024

AbstractHorizontal wells have significant advantages in coal bed methane exploration and development blocks. However, its application in new exploration and development blocks could be challenging. Limited geological data, uncertain geological conditions, and the emergence of micro-faults in pre-drilled target coal seams make it hard to accurately control the well trajectory. The well trajectory prior to drilling needs to be optimized to ensure that the drilling trajectory is within the target coal seam and to prevent any reduction in drilling ratio (defined here as the percentage of the drilling trajectory in the entire horizontal section of the well located in the target coal seam) caused by faults. In this study, the well trajectory optimization is achieved by implementing the following process to drill pilot hole, acquire 2D resonance, and azimuthal gamma logging while drilling. The pilot hole drilling can obtain the characteristic parameters of the target coal seam and the top and bottom rock layers in advance, which can provide judgment values for the landing site design and real-time monitoring of whether the wellbore trajectory extends along the target coal seam; 2D resonance exploration can obtain the construction of set orientation before drilling and the development of small faults and formation fluctuations in the horizontal section, which can optimize the well trajectory in advance; the azimuth gamma logging while drilling technology can monitor the layers drilled by the current drill bit in real time, and can provide timely and accurate well trajectory adjustment methods.The horizontal well-Q in the Block-W of the Qinshui Basin was taken as a case study and underwent technical mechanism research and applicability analysis. The implementation of this new innovative process resulted in a successful drilling of a 711 m horizontal section, with a target coal seam drilling rate of 80%. Compared to previous L-type wells, the drilling rate increased by about 20%, and the drilling cycle shortened by 25%. The technical experience gained from this successful case provides valuable insight for low-cost exploration and development of new coalbed methane blocks.
Optimized multi-frequency nonlinear broadband piezoelectric energy harvester designs
Authors: Elgamal Mohamed A. , Elgamal Hassan , Kouritem Sallam A. 
Published: May 2024

AbstractMany electrical devices can be powered and operated by harvesting the wasted energy of the surroundings. This research aims to overcome the challenges of output power with a sharp peak, small bandwidth, and the huge dimensions of the piezoelectric energy harvesters relative to the output power. The aforementioned challenges motivated us to investigate the effect of nonlinearity in the shape (tapered and straight cross-section area) as well as the fixation method (the number of fastened ends) to determine the optimal design with high output power and wide working frequency. This research proposes a novel piezoelectric energy harvester array, where each beam is made up of three fixed beams that are joined together by a center mass. The proposed design produces an output power of 35 mW between 25 and 40 Hz. The output power of the proposed design is 3.24 times more than the conventional designs. The recommended approach is simulated utilizing finite element analysis FEA. Analytical and experimental methods validate the proposed FEA, which exhibits excellent agreement.
Research on multilateral collaboration strategies in agricultural seed quality assurance
Authors: Wang Yanmei , Chen Yusheng 
Published: May 2024

AbstractSeeds, as the initial products in agricultural systems, play a pivotal role in ensuring quality, fundamental to national food security and sustainable agricultural development. This study introduces a concept integrating public governance and evolutionary game theory to construct a quadripartite evolutionary game model involving seed companies, certification agencies, farmers, and governmental departments. It considers the strategic choices of these stakeholders under varying economic motivations and market mechanisms, as well as the influence of external regulation and incentives on game strategies. The existence conditions for evolutionarily stable strategy combinations are determined using the Lyapunov first method, and MATLAB is employed for numerical simulation analysis to validate the game analysis under initial conditions. The simulation results reveal two potential equilibrium points corresponding to different strategic choices among stakeholders. The study finds that producing high-quality seeds and the refusal of certification agencies to engage in rent-seeking are crucial for ensuring seed quality. Additionally, the cost–benefit ratio of seed companies, the speculative cost of certification agencies, and the rights-protection cost of farmers are key determinants in the evolution of seed quality assurance strategies. This research also holds practical significance in enhancing seed quality assurance mechanisms and fostering sustainable development in agriculture.
A privacy-preserving publicly verifiable quantum random number generator
Authors: Islam Tanvirul , Banerji Anindya , Boon Chin Jia , Rui Wang , Reezwana Ayesha , Grieve James A. , Piera Rodrigo , Ling Alexander 
Published: May 2024

AbstractVerifying the quality of a random number generator involves performing computationally intensive statistical tests on large data sets commonly in the range of gigabytes. Limitations on computing power can restrict an end-user’s ability to perform such verification. There are also random number-based applications where an honest user needs to publicly demonstrate that the random bits they are using pass the statistical tests without the bits being revealed. Here, we report the implementation of an entanglement-based protocol that allows a third party to publicly perform statistical tests without compromising the privacy of the random bits.
Damage prediction and improvement method based on cutting mode of circular empty hole
Authors: Qin Huifeng , Zhao Yan , Wang Hailong , Ge Lijie , Tong Xiao 
Published: May 2024

AbstractBased on the theory of empty hole effect of cutting blasting, the Hopkinson effect and Saint–Venant principle are integrated to establish a two-dimensional calculation model of dynamic stress evolution of the holes wall, and then the dynamic fracture mechanism and damage distribution mode of the rock mass in the cutting area under the action of longitudinal waves are predicted. The results of the calculation and numerical simulation are verified by experiments, and the results show that: The time-varying stress function of the circular cavity wall conforms to the periodic dynamic evolution of the trigonometric function, and the theoretical calculation is consistent with the simulation results. Through the calculation of the round holes cut model and the square empty hole cut model, the change of the shape of the holes in the cut area changes the failure form of the surrounding rock mass. The circular empty hole wall is affected by the stress wave to produce "interval ring" destruction, and the effect of the reflected stretch wave is inhibited. The large range of rock mass in the square empty hole wall produces tensile and shear failure, and the rock mass collapses inward under the influence of the second stage stress. Among them, the empty space utilization rate of the square empty hole model is about 8.5 times that of the circular holes model. Vibration monitoring in the center of the cutting area shows that the vibration effect of the circular empty hole is larger than that of the square empty hole, and the proportion of rock breaking energy is lower.
Crowdsourcing with the drift diffusion model of decision making
Authors: Lalvani Shamal , Katsaggelos Aggelos 
Published: May 2024

AbstractCrowdsourcing involves the use of annotated labels with unknown reliability to estimate ground truth labels in datasets. A common task in crowdsourcing involves estimating reliabilities of annotators (such as through the sensitivities and specificities of annotators in the binary label setting). In the literature, beta or dirichlet distributions are typically imposed as priors on annotator reliability. In this study, we investigated the use of a neuroscientifically validated model of decision making, known as the drift-diffusion model, as a prior on the annotator labeling process. Two experiments were conducted on synthetically generated data with non-linear (sinusoidal) decision boundaries. Variational inference was used to predict ground truth labels and annotator related parameters. Our method performed similarly to a state-of-the-art technique (SVGPCR) in prediction of crowdsourced data labels and prediction through a crowdsourced-generated Gaussian process classifier. By relying on a neuroscientifically validated model of decision making to model annotator behavior, our technique opens the avenue of predicting neuroscientific biomarkers of annotators, expanding the scope of what may be learnt about annotators in crowdsourcing tasks.
Prevalence of hepatitis B and C viruses among migrant workers in Qatar
Authors: Nasrallah Gheyath K. , Chemaitelly Hiam , Ismail Ahmed I. A. , Nizamuddin Parveen B. , Al-Sadeq Duaa W. , Shurrab Farah M. , Amanullah Fathima H. , Al-Hamad Tasneem H. , Mohammad Khadija N. , Alabdulmalek Maryam A. , Al Kahlout Reham A. , Al-Shaar Ibrahim , Elshaikh Manal A. , Abouassali Mazen N. , Karimeh Ibrahim W. , Ali Mutaz M. , Ayoub Houssein H. , Abdeen Sami , Abdelkarim Ashraf , Daraan Faisal , Ismail Ahmed Ibrahim Hashim Elhaj , Mostafa Nahid , Sahl Mohamed , Suliman Jinan , Tayar Elias , Kasem Hasan Ali , Agsalog Meynard J. A. , Akkarathodiyil Bassam K. , Alkhalaf Ayat A. , Alakshar Mohamed Morhaf M. H. , Al-Qahtani Abdulsalam Ali A. H. , Al-Shedifat Monther H. A. , Ansari Anas , Ataalla Ahmad Ali , Chougule Sandeep , Gopinathan Abhilash K. K. V. , Poolakundan Feroz J. , Ranbhise Sanjay U. , Saefan Saed M. A. , Thaivalappil Mohamed M. , Thoyalil Abubacker S. , Umar Inayath M. , Al Kuwari Einas , Coyle Peter , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Abdul Rahim Hanan F. , Yassine Hadi M. , Al Thani Asmaa A. , Chaghoury Odette , Al Kuwari Mohamed Ghaith , Farag Elmoubasher , Bertollini Roberto , Al Romaihi Hamad Eid , Al Khal Abdullatif , Al-Thani Mohamed H. , Abu-Raddad Laith J. 
Published: May 2024

AbstractLimited data exist on viral hepatitis among migrant populations. This study investigated the prevalence of current hepatitis B virus (HBV) infection and lifetime hepatitis C virus (HCV) infection among Qatar's migrant craft and manual workers (CMWs), constituting 60% of the country's population. Sera collected during a nationwide COVID-19 population-based cross-sectional survey on CMWs between July 26 and September 9, 2020, underwent testing for HBsAg and HCV antibodies. Reactive samples underwent confirmatory testing, and logistic regression analyses were employed to explore associations with HBV and HCV infections. Among 2528 specimens tested for HBV infection, 15 were reactive, with 8 subsequently confirmed positive. Three samples lacked sufficient sera for confirmatory testing but were included in the analysis through multiple imputations. Prevalence of current HBV infection was 0.4% (95% CI 0.2–0.7%). Educational attainment and occupation were significantly associated with current HBV infection. For HCV infection, out of 2607 specimens tested, 46 were reactive, and 23 were subsequently confirmed positive. Prevalence of lifetime HCV infection was 0.8% (95% CI 0.5–1.2%). Egyptians exhibited the highest prevalence at 6.5% (95% CI 3.1–13.1%), followed by Pakistanis at 3.1% (95% CI 1.1–8.0%). Nationality, geographic location, and occupation were significantly associated with lifetime HCV infection. HBV infection is relatively low among CMWs, while HCV infection falls within the intermediate range, both compared to global and regional levels.
Assessing the efficacy of the ovicidal fungus Mucor circinelloides in reducing coccidia parasitism in peacocks
Authors: Lozano João , Almeida Cristina , Vicente Eduardo , Sebastião Daniela , Palomero Antonio Miguel , Cazapal-Monteiro Cristiana , Arias María Sol , Oliveira Manuela , Carvalho Luís Madeira de , Paz-Silva Adolfo 
Published: May 2024

AbstractThe biological control of gastrointestinal (GI) parasites using predatory fungi has been recently proposed as an accurate and sustainable approach in birds. The current study aimed to assess for the first time the efficacy of using the native ovicidal fungus Mucor circinelloides (FMV-FR1) in reducing coccidia parasitism in peacocks. For this purpose, an in vivo trial was designed in the resident peacock collection (n = 58 birds) of the São Jorge Castle, at Lisbon, Portugal. These animals presented an initial severe infection by coccidia of the genus Eimeria (20106 ± 8034 oocysts per gram of feces, OPG), and thus received commercial feed enriched with a M. circinelloides suspension (1.01 × 108 spores/kg feed), thrice-weekly. Fresh feces were collected every 15 days to calculate the coccidia shedding, using the Mini-FLOTAC technique. The same bird flock served simultaneously as control (t0 days) and test groups (t15–t90 days). The average Eimeria sp. shedding in peacocks decreased up to 92% following fungal administrations, with significant reduction efficacies of 78% (p = 0.004) and 92% (p = 0.012) after 45 and 60 days, respectively. Results from this study suggest that the administration of M. circinelloides spores to birds is an accurate solution to reduce their coccidia parasitism.