bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed characterization of the complete mitochondrial genome of the oceanic whitetip shark Carcharhinus longimanus (Poey, 1861)
Authors: Kamal Sadia A. , Baeza J. Antonio 
Published: July 2024

Abstract

Background
The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as “vulnerable” throughout its range and “critically endangered” in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail.

Methods and results
The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical ‘cloverleaf’ secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus.

Conclusions
The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean.
Exploring a New Geometric-mechanical Artefact for Calculus
Authors: Maschietto Michela , Milici Pietro 
Published: July 2024

AbstractWe introduce a geometric-mechanical artefact designed for laboratory activities related to Calculus topics (3D models and construction instructions are freely available online). With new capabilities and a new design, this instrument adopts some mechanisms historically introduced to solve inverse tangent problems (that analytically correspond to solving differential equations). By such an instrument, besides materially revealing the tangent to a curve (tangent mode), it is possible to trace the graph of exponential functions and parabolas starting from the geometrical properties of their tangent (curvigraph mode). Furthermore, one can perform transformations as derivatives and integrals (transformation mode). Our research project aims to study the use of this artefact mainly for secondary school students. In this paper, we present the analysis of its semiotic potential, referring to the instrumental approach and the Theory of Semiotic Mediation. We also focus on a secondary school teacher manipulating the artefact to identify exploration processes and gestures of usage. The analysis supports the choice of starting the exploration in the tangent mode and suggests that the artefact fosters the emergence of the idea of the tangent line.
Body composition and aging: cross-sectional results from the INSPIRE study in people 20 to 93 years old
Authors: Briand Marguerite , Raffin Jeremy , Gonzalez-Bautista Emmanuel , Ritz Patrick , Abellan Van Kan Gabor , Pillard Fabien , Faruch-Bilfeld Marie , Guyonnet Sophie , Dray Cédric , Vellas Bruno , de Souto Barreto Philipe , Rolland Yves 
Published: July 2024

AbstractAging is characterized by several major changes, including altered body composition, which is associated with numerous negative clinical consequences such as sarcopenia, osteoporosis, and frailty. The study is to evaluate body composition parameters depending on age and sex in a population ranging from the young adult to the very old, and to identify break points in the association between body composition and age. In this cross-sectional study, we included the enrolment population of the French INSPIRE-T prospective cohort, accounting for 915 subjects (62% female). Age ranged from 20 to 93 years, median age (years) was 63 (IQR 27). Body composition (lean mass, fat mass, and bone mineral content) was assessed with dual-X-ray absorptiometry (DXA). Different break points in the relationship between age and body composition variables in males and females were identified using a segmented regression analysis adjusted on physical activity, nutritional status, educational level, and comorbidities. Lean mass decreased from the age of 55 years for males (CI 95% 44–66) and 31 years for females (CI 95% 23–39). For fat mass, we observed a trend towards an increase with age for males. For females, we observed an increase with age up to age 75 (CI 95% 62–86), followed by a decreasing trend. In this study, we described the relationship between body composition and age as a function of sex, establishing a foundation for further studies on predictive biomarkers of age-related body composition alteration.
Zinc Deficiency Causes Glomerulosclerosis and Renal Interstitial Fibrosis Through Oxidative Stress and Increased Lactate Metabolism in Rats
Authors: Huang Zixuan , Liao Yajie , Zheng Yunxi , Ye Shang , Zhang Qianyu , Yu Xiaohong , Liu Xiaoxin , Li Ningxu 
Published: July 2024

AbstractChronic kidney disease (CKD) is a highly prevalent condition characterized by renal fibrosis as its ultimate manifestation. Zinc deficiency is closely associated with CKD, evidenced by its link to renal fibrosis. Recently, local lactic acidosis has been demonstrated to promote renal fibrosis. Under zinc-deficient conditions, mitochondrial function is compromised and abnormal lactate metabolism might be induced potentially. However, it remains unclear whether zinc deficiency leads to renal fibrosis through local lactic acidosis. Zinc deficiency rat models were successfully established by feeding zinc-deficient diet. Western blot, qPCR, IHC, and other experiments were employed to investigate the key markers and molecular mechanisms of glomerulosclerosis and renal interstitial fibrosis. Our results indicate that zinc deficiency reduces specific markers of podocytes (podocalyxin, WT1, and nephrin) and activates the Wnt3a/β-catenin pathway, a key pathway in podocyte injury. Concurrently, glomerulosclerosis is indicated by increased urinary microalbumin and serum creatinine levels along with histological alteration observed through PAS and Masson staining in zinc-deficient rats. Furthermore, various degrees of upregulation for several markers of interstitial fibrosis including α-SMA, FN1 and collagen III are also revealed. These findings were further confirmed by Masson staining and IHC. Additionally, alterations in four markers in the EMT process, N-cadherin, E-cadherin, Vimentin, and snail, were consistent with expectations. We then confirmed the activation of the non-canonical TGF-β1 pathway known as the PI3K/AKT/mTOR pathway. An elevation in renal ROS levels accompanied by increased mitochondrial marker cytochrome C expression as well as an elevated NADH/NAD + ratio is also observed within the kidneys. Furthermore, the activity of both MMP/TIMP system and fibrinolytic system was abnormally enhanced under zinc deficiency conditions. Finally, we find zinc supplementation could significantly ameliorate relevant pathological alterations induced by zinc deficiency. These results collectively point that zinc deficiency causes podocyte damage ultimately resulting in glomerulosclerosis via accumulation of ROS and induces interstitial fibrosis via lactic acidosis.
Online news ecosystem dynamics: supply, demand, diffusion, and the role of disinformation
Authors: Gravino Pietro , Prevedello Giulio , Brugnoli Emanuele 
Published: July 2024

AbstractThe digital age provides new challenges as information travels more quickly in a system of increasing complexity. But it also offers new opportunities, as we can track and study the system more efficiently. Several studies individually addressed different digital tracks, focusing on specific aspects like disinformation production or content-sharing dynamics. In this work, we propose to study the news ecosystem as an information market by analysing three main metrics: Supply, Demand, and Diffusion of information. Working on a dataset relative to Italy from December 2019 to August 2020, we validate the choice of the metrics, proving their static and dynamic relations, and their potential in describing the whole system. We demonstrate that these metrics have specific equilibrium relative levels. We reveal the strategic role of Demand in leading a non-trivial network of causal relations. We show how disinformation news Supply and Diffusion seem to cluster among different social media platforms. Disinformation also appears to be closer to information Demand than the general news Supply and Diffusion, implying a potential danger to the health of the public debate. Finally, we prove that the share of disinformation in the Supply and Diffusion of news has a significant linear relation with the gap between Demand and Supply/Diffusion of news from all sources. This finding allows for a real-time assessment of disinformation share in the system. It also gives a glimpse of the potential future developments in the modelisation of the news ecosystem as an information market studied through its main drivers.
Simulation and reconstruction of particle trajectories in the CEPC drift chamber
Authors: Liu Meng-Yao , Li Wei-Dong , Huang Xing-Tao , Zhang Yao , Lin Tao , Yuan Ye 
Published: July 2024

AbstractThe circular electron-positron collider (CEPC) is designed to precisely measure the properties of the Higgs boson, study electroweak interactions at the Z-boson peak, and search for new physics beyond the Standard Model. As a component of the $$4^{\text {th}}$$

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conceptual CEPC detector, the drift chamber facilitates the measurement of charged particles. This study implemented a Geant4-based simulation and track reconstruction for the drift chamber. For the simulation, detector construction and response were implemented and added to the CEPC simulation chain. The development of track reconstruction involves track finding using the combinatorial Kalman filter method and track fitting using the tool of GenFit. Using the simulated data, the tracking performance was studied. The results showed that both the reconstruction resolution and tracking efficiency satisfied the requirements of the CEPC experiment.
Sandstone mounds from the Ordovician of the Central Iberian Zone, Spain
Authors: Jensen Sören 
Published: July 2024

AbstractSandstone mounds (sensu Bradshaw in Sedimentology 7:149–154, 1966) are sedimentary structures formed by fluid erosion of sands consisting of systems of variously shaped mounds, ridges and gullies preserved on the upper surface of sandstone beds. Sandstone mounds are here reported from the Armorican Quartzite Formation and Marjaliza beds, Extremadura, and the Pochico Formation of Ciudad Real. These are the first reports of this sedimentary structure from the Ordovician of the Central Iberian Zone, southwest Spain, adding to the scarce global record of this sedimentary structure. A literature review reveals no reports of sandstone mounds from rocks younger than the Devonian Period, with the majority coming from Ordovician rocks located on the Gondwanan margin of the Rheic Ocean. It is probable that sandstone mounds exist in younger rocks but secular changes in sediment properties and favourable shelf configuration are alternative explanations for this pattern.
Bacterial community composition of Hungarian salt-affected soils under different land uses
Authors: Gangwar Ravi Kumar , Táncsics András , Makádi Marianna , Farkas Milán , Cserháti Mátyás , Michéli Erika , Fuchs Márta , Szegi Tamás 
Published: July 2024

AbstractSalinization and sodification are serious and worldwide growing threats to healthy soil functions. Although plants developed a plethora of traits to cope with high salinity, soil bacteria are also essential players of the adaptation process. However, there is still lack of knowledge on how other biotic and abiotic factors, such as land use or different soil properties, affect the bacterial community structure of these soils. Therefore, besides soil chemical and physical investigations, bacterial communities of differently managed salt-affected soils were analysed through 16S rRNA gene Illumina amplicon sequencing and compared. Results have shown that land use and soil texture were the main drivers in shaping the bacterial community structure of the Hungarian salt-affected soils. It was observed that at undisturbed pasture and meadow sites, soil texture and the ratio of vegetation cover were the determinative factors shaping the bacterial community structures, mainly at the level of phylum Acidobacteriota. Sandy soil texture promoted the high abundance of members of the class Blastocatellia, while at the slightly disturbed meadow soil showing high clay content was dominated by members of the class Acidobacteriia. The OTUs belonging to the class Ktedonobacteria, which were reported mostly in geothermal sediments, reached a relatively high abundance in the meadow soil.
Confronting the effects of climate change through development plans
Authors: Mahvash Mohammadi Zahra , Barakpour Naser 
Published: July 2024

AbstractIn recent years, climate change as a consequence of global warming, has garnered significant attention. Therefore, serious measures must be considered in the development planning process to adapt to and reduce effects of climate change. This research evaluates six development plans in Isfahan, Iran in the face of climate change effects using a framework consisting of three components of the analytical Awareness-Analysis-Action (A-A-A) approach and using quantitative and qualitative content analysis methods. In fact, the evaluation of the level of attention of the development plans from the perspective of the level of reflection and attention to raising awareness about the issues of climate change, the ability to analyze the available climate information in a useful way to support planning decisions and the level of special actions to deal with these changes. Finally, out of the three elements of the approach, the highest amount of attention in the plans is related to the element of action with 67/70% and the lowest is related to the element of awareness with 39/10%. The overall evaluation of the development plans shows that their role in integrating climate change issues into urban planning in Iran is still limited and insufficient. On the other hand, air pollution and climate change are closely related, as chemicals that cause air quality deterioration often enter together with greenhouse gases. Therefore, it can be said that although indicators of the transportation dimension (A3-J) with 80.66%, resource management have been given special attention under the action component, but carbon sequestration dimension (A2-F) with 14.63%, under the analysis component that seeks to evaluate the amount of air pollutants, classification of the type and sources of emission of pollutants could not reflect more than half of the total percentage in all development plans.
Water Exchange Through the Upper and Middle Luzon Strait Using the Sigma–Pi Diagram
Authors: Zheng Hua , Zhu Xiao‐Hua 
Published: July 2024

AbstractWater exchange in the Luzon Strait (LS) is critical for layered circulation in the South China Sea (SCS); however, observational evidence of sandwich‐like water exchange is scarce. This study presents a comprehensive analysis of the meridional and zonal spatial patterns of water exchange in the upper and middle LS, along with its seasonal variations in a sigma–pi diagram using Argo profiles. As observed viewed from the perspective of SCS, inflow and outflow occur in the upper and middle layers, respectively. Upper‐layer Kuroshio intrudes into the SCS primarily in the northern and central regions of the LS, extending along the continental shelf into the inner SCS. A significant middle‐layer eastward outflow is evident at 26.7–27.56 kg/m3 (500–1,500 m) in the northern part of the strait, extending to 123°E. The Kuroshio intrusion intensifies during the winter, whereas the middle‐layer outflow is most pronounced in the autumn.
Metasurface-integrated elliptically polarized laser-pumped SERF magnetometers
Authors: Liang Zihua , Hu Jinsheng , Zhou Peng , Liu Lu , Hu Gen , Wang Ankang , Ye Mao 
Published: July 2024

AbstractThe emergence of biomagnetism imaging has led to the development of ultrasensitive and compact spin-exchange relaxation-free (SERF) atomic magnetometers that promise high-resolution magnetocardiography (MCG) and magnetoencephalography (MEG). However, conventional optical components are not compatible with nanofabrication processes that enable the integration of atomic magnetometers on chips, especially for elliptically polarized laser-pumped SERF magnetometers with bulky optical systems. In this study, an elliptical-polarization pumping beam (at 795 nm) is achieved through a single-piece metasurface, which results in an SERF magnetometer with a high sensitivity reaching 10.61 fT/Hz1/2 by utilizing a 87Rb vapor cell with a 3 mm inner diameter. To achieve the optimum theoretical polarization, our design combines a computer-assisted optimization algorithm with an emerging metasurface design process. The metasurface is fabricated with 550 nm thick silicon-rich silicon nitride on a 2 × 2 cm2 SiO2 substrate and features a 22.17° ellipticity angle (a deviation from the target polarization of less than 2%) and more than 80% transmittance. This study provides a feasible approach for on-chip polarization control of future all-integrated atomic magnetometers, which will further pave the way for high-resolution biomagnetism imaging and portable atomic sensing applications.
Metabolic activity of CYP2C19 and CYP2D6 on antidepressant response from 13 clinical studies using genotype imputation: a meta-analysis
Authors: Li Danyang , Pain Oliver , Fabbri Chiara , Wong Win Lee Edwin , Lo Chris Wai Hang , Ripke Stephan , Cattaneo Annamaria , Souery Daniel , Dernovsek Mojca Z. , Henigsberg Neven , Hauser Joanna , Lewis Glyn , Mors Ole , Perroud Nader , Rietschel Marcella , Uher Rudolf , Maier Wolfgang , Baune Bernhard T. , Biernacka Joanna M. , Bondolfi Guido , Domschke Katharina , Kato Masaki , Liu Yu-Li , Serretti Alessandro , Tsai Shih-Jen , Weinshilboum Richard ,   the GSRD Consortium, the Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, McIntosh Andrew M. , Lewis Cathryn M. 
Published: July 2024

AbstractCytochrome P450 enzymes including CYP2C19 and CYP2D6 are important for antidepressant metabolism and polymorphisms of these genes have been determined to predict metabolite levels. Nonetheless, more evidence is needed to understand the impact of genetic variations on antidepressant response. In this study, individual clinical and genetic data from 13 studies of European and East Asian ancestry populations were collected. The antidepressant response was clinically assessed as remission and percentage improvement. Imputed genotype was used to translate genetic polymorphisms to metabolic phenotypes (poor, intermediate, normal, and rapid+ultrarapid) of CYP2C19 and CYP2D6. CYP2D6 structural variants cannot be imputed from genotype data, limiting the determination of metabolic phenotypes, and precluding testing for association with response. The association of CYP2C19 metabolic phenotypes with treatment response was examined using normal metabolizers as the reference. Among 5843 depression patients, a higher remission rate was found in CYP2C19 poor metabolizers compared to normal metabolizers at nominal significance but did not survive after multiple testing correction (OR = 1.46, 95% CI [1.03, 2.06], p = 0.033, heterogeneity I2 = 0%, subgroup difference p = 0.72). No metabolic phenotype was associated with percentage improvement from baseline. After stratifying by antidepressants primarily metabolized by CYP2C19, no association was found between metabolic phenotypes and antidepressant response. Metabolic phenotypes showed differences in frequency, but not effect, between European- and East Asian-ancestry studies. In conclusion, metabolic phenotypes imputed from genetic variants using genotype were not associated with antidepressant response. CYP2C19 poor metabolizers could potentially contribute to antidepressant efficacy with more evidence needed. Sequencing and targeted pharmacogenetic testing, alongside information on side effects, antidepressant dosage, depression measures, and diverse ancestry studies, would more fully capture the influence of metabolic phenotypes.
Bidirectional microwave-optical transduction based on integration of high-overtone bulk acoustic resonators and photonic circuits
Authors: Blésin Terence , Kao Wil , Siddharth Anat , Wang Rui N. , Attanasio Alaina , Tian Hao , Bhave Sunil A. , Kippenberg Tobias J. 
Published: July 2024

AbstractCoherent interconversion between microwave and optical frequencies can serve as both classical and quantum interfaces for computing, communication, and sensing. Here, we present a compact microwave-optical transducer based on monolithic integration of piezoelectric actuators on silicon nitride photonic circuits. Such an actuator couples microwave signals to a high-overtone bulk acoustic resonator defined by the silica cladding of the optical waveguide core, suspended to enhance electromechanical and optomechanical couplings. At room temperature, this triply resonant piezo-optomechanical transducer achieves an off-chip photon number conversion efficiency of 1.6 × 10−5 over a bandwidth of 25 MHz at an input pump power of 21 dBm. The approach is scalable in manufacturing and does not rely on superconducting resonators. As the transduction process is bidirectional, we further demonstrate the synthesis of microwave pulses from a purely optical input. Capable of leveraging multiple acoustic modes for transduction, this platform offers prospects for frequency-multiplexed qubit interconnects and microwave photonics at large.
Light-induced Kondo-like exciton-spin interaction in neodymium(II) doped hybrid perovskite
Authors: Xiao Xudong , Latt Kyaw Zin , Gong Jue , Kim Taewoo , Connell Justin G. , Liu Yuzi , Fry H. Christopher , Pearson John E. , Wostoupal Owen S. , Li Mengyuan , Soldan Calvin , Yang Zhenzhen , Schaller Richard D. , Diroll Benjamin T. , Hla Saw Wai , Xu Tao 
Published: July 2024

AbstractTuning the properties of a pair of entangled electron and hole in a light-induced exciton is a fundamentally intriguing inquiry for quantum science. Here, using semiconducting hybrid perovskite as an exploratory platform, we discover that Nd2+-doped CH3NH3PbI3 (MAPbI3) perovskite exhibits a Kondo-like exciton-spin interaction under cryogenic and photoexcitation conditions. The feedback to such interaction between excitons in perovskite and the localized spins in Nd2+ is observed as notably prolonged carrier lifetimes measured by time-resolved photoluminescence, ~10 times to that of pristine MAPbI3 without Nd2+ dopant. From a mechanistic standpoint, such extended charge separation states are the consequence of the trap state enabled by the antiferromagnetic exchange interaction between the light-induced exciton and the localized 4 f spins of the Nd2+ in the proximity. Importantly, this Kondo-like exciton-spin interaction can be modulated by either increasing Nd2+ doping concentration that enhances the coupling between the exciton and Nd2+ 4 f spins as evidenced by elongated carrier lifetime, or by using an external magnetic field that can nullify the spin-dependent exchange interaction therein due to the unified orientations of Nd2+ spin angular momentum, thereby leading to exciton recombination at the dynamics comparable to pristine MAPbI3.