bluuebunny/crossref_metadata_2025 huggingface dataset:
Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule
Authors: Qin Chuan , Graf Leonie G. , Striska Kilian , Janetzky Markus , Geist Norman , Specht Robin , Schulze Sabrina , Palm Gottfried J. , Girbardt Britta , Dörre Babett , Berndt Leona , Kemnitz Stefan , Doerr Mark , Bornscheuer Uwe T. , Delcea Mihaela , Lammers Michael
Published: July 2024

The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5′-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.
Footprint of sustained poleward warm water flow within East Antarctic submarine canyons
Authors: Donda Federica , Rebesco Michele , Kovacevic Vedrana , Silvano Alessandro , Bensi Manuel , De Santis Laura , Rosenthal Yair , Torricella Fiorenza , Baradello Luca , Gei Davide , Leventer Amy , Post Alix , Leitchenkov German , Noble Taryn , Zgur Fabrizio , Cova Andrea , O’Brien Philip , Romeo Roberto
Published: July 2024

The intrusion of relatively warm water onto the continental shelf is widely recognized as a threat to Antarctic ice shelves and glaciers grounded below sea level, as enhanced ocean heat increases their basal melt. While the circulation of warm water has been documented on the East Antarctic continental shelf, the modes of warm water transport from the deep ocean onto the shelf are still uncertain. This makes predicting the future responses of major East Antarctic marine-grounded glaciers, such as Totten and Ninnis glaciers, particularly challenging. Here, we outline the key role of submarine canyons to convey southward flowing currents that transport warm Circumpolar Deep Water toward the East Antarctic shelf break, thus facilitating warm water intrusion on the continental shelf. Sediment drifts on the eastern flank of the canyons provide evidence for sustained southward-directed flows. These morpho-sedimentary features thus highlight areas potentially prone to enhanced ocean heat transport toward the continental shelf, with repercussions for past, present, and future glacial melting and consequent sea level rise.
Node-layer duality in networked systems
Authors: Presigny Charley , Corsi Marie-Constance , De Vico Fallani Fabrizio
Published: July 2024

Real-world networks typically exhibit several aspects, or layers, of interactions among their nodes. By permuting the role of the nodes and the layers, we establish a new criterion to construct the dual of a network. This approach allows to examine connectivity from either a node-centric or layer-centric viewpoint. Through rigorous analytical methods and extensive simulations, we demonstrate that nodewise and layerwise connectivity measure different but related aspects of the same system. Leveraging node-layer duality provides complementary insights, enabling a deeper comprehension of diverse networks across social science, technology and biology. Taken together, these findings reveal previously unappreciated features of complex systems and provide a fresh tool for delving into their structure and dynamics.
Asymmetric Ru-In atomic pairs promote highly active and stable acetylene hydrochlorination
Authors: Fan Yurui , Xu Haomiao , Gao Guanqun , Wang Mingming , Huang Wenjun , Ma Lei , Yao Yancai , Qu Zan , Xie Pengfei , Dai Bin , Yan Naiqiang
Published: July 2024

Ru single-atom catalysts have great potential to replace toxic mercuric chloride in acetylene hydrochlorination. However, long-term catalytic stability remains a grand challenge due to the aggregation of Ru atoms caused by over-chlorination. Herein, we synthesize an asymmetric Ru-In atomic pair with vinyl chloride monomer yield (>99.5%) and stability (>600 h) at a gas hourly space velocity of 180 h−1, far surpassing those of the Ru single-atom counterparts. A combination of experimental and theoretical techniques reveals that there is a strong d-p orbital interaction between Ru and In atoms, which not only enables the selective adsorption of acetylene and hydrogen chloride at different atomic sites but also optimizes the electron configuration of Ru. As a result, the intrinsic energy barrier for vinyl chloride generation is lowered, and the thermodynamics of the chlorination process at the Ru site is switched from exothermal to endothermal due to the change of orbital couplings. This work provides a strategy to prevent the deactivation and depletion of active Ru centers during acetylene hydrochlorination.
The impact of insect herbivory on biogeochemical cycling in broadleaved forests varies with temperature
Authors: Hwang Bernice C. , Giardina Christian P. , Adu-Bredu Stephen , Barrios-Garcia M. Noelia , Calvo-Alvarado Julio C. , Dargie Greta C. , Diao Haoyu , Duboscq-Carra Virginia G. , Hemp Andreas , Hemp Claudia , Huasco Walter Huaraca , Ivanov Aleksandr V. , Johnson Nels G. , Kuijper Dries P. J. , Lewis Simon L. , Lobos-Catalán Paulina , Malhi Yadvinder , Marshall Andrew R. , Mumladze Levan , Ngute Alain Senghor K. , Palma Ana C. , Petritan Ion Catalin , Rordriguez-Cabal Mariano A. , Suspense Ifo A. , Zagidullina Asiia , Andersson Tommi , Galiano-Cabrera Darcy F. , Jiménez-Castillo Mylthon , Churski Marcin , Gage Shelley A. , Filippova Nina , Francisco Kainana S. , Gaglianese-Woody Morgan , Iankoshvili Giorgi , Kaswamila Mgeta Adidas , Lyatuu Herman , Mampouya Wenina Y. E. , Materu Brayan , Mbemba M. , Moritz Ruslan , Orang Karma , Plyusnin Sergey , Puma Vilca Beisit L. , Rodríguez-Solís Maria , Šamonil Pavel , Stępniak Kinga M. , Walsh Seana K. , Xu Han , Metcalfe Daniel B.
Published: July 2024

Herbivorous insects alter biogeochemical cycling within forests, but the magnitude of these impacts, their global variation, and drivers of this variation remain poorly understood. To address this knowledge gap and help improve biogeochemical models, we established a global network of 74 plots within 40 mature, undisturbed broadleaved forests. We analyzed freshly senesced and green leaves for carbon, nitrogen, phosphorus and silica concentrations, foliar production and herbivory, and stand-level nutrient fluxes. We show more nutrient release by insect herbivores at non-outbreak levels in tropical forests than temperate and boreal forests, that these fluxes increase strongly with mean annual temperature, and that they exceed atmospheric deposition inputs in some localities. Thus, background levels of insect herbivory are sufficiently large to both alter ecosystem element cycling and influence terrestrial carbon cycling. Further, climate can affect interactions between natural populations of plants and herbivores with important consequences for global biogeochemical cycles across broadleaved forests.
Anti-distortion bioinspired camera with an inhomogeneous photo-pixel array
Authors: Choi Changsoon , Hinton Henry , Seung Hyojin , Chang Sehui , Kim Ji Su , You Woosang , Kim Min Sung , Hong Jung Pyo , Lim Jung Ah , Hwang Do Kyung , Lee Gil Ju , Jang Houk , Song Young Min , Kim Dae-Hyeong , Ham Donhee
Published: July 2024

The bioinspired camera, comprising a single lens and a curved image sensor—a photodiode array on a curved surface—, was born of flexible electronics. Its economical build lends itself well to space-constrained machine vision applications. The curved sensor, much akin to the retina, helps image focusing, but the curvature also creates a problem of image distortion, which can undermine machine vision tasks such as object recognition. Here we report an anti-distortion single-lens camera, where 4096 silicon photodiodes arrayed on a curved surface in a nonuniform pattern assimilated to the distorting optics are the key to anti-distortion engineering. That is, the photo-pixel distribution pattern itself is warped in the same manner as images are warped, which correctively reverses distortion. Acquired images feature no appreciable distortion across a 120° horizontal view, as confirmed by their neural-network recognition accuracies. This distortion correction via photo-pixel array reconfiguration is a form of in-sensor computing.
Seed dispersal by Martu peoples promotes the distribution of native plants in arid Australia
Authors: Bliege Bird Rebecca , Bird Douglas W. , Martine Christopher T. , McGuire Chloe , Greenwood Leanne , Taylor Desmond , Williams Tanisha M. , Veth Peter M.
Published: July 2024

Commensal relationships between wild plants and their dispersers play a key ecological and evolutionary role in community structure and function. While non-human dispersers are often considered critical to plant recruitment, human dispersers have received much less attention, especially when it comes to non-domesticated plants. Australia, as a continent historically characterized by economies reliant on non-domesticated plants, is thus a key system for exploring the ecological role of people as seed dispersers in the absence of agriculture. Here, we utilize a controlled observation research design, employing ecological surveys and ethnographic observations to examine how seed dispersal and landscape burning by Martu Aboriginal people affects the distribution of three preferred plants and one (edible, but non-preferred) control species. Using an information theoretic approach, we find that the three preferred plants show evidence of human dispersal, with the strongest evidence supporting anthropogenic dispersal for the wild bush tomato, Solanum diversiflorum.
How molecular architecture defines quantum yields
Authors: Pashley-Johnson Fred , Munaweera Rangika , Hossain Sheikh I. , Gauci Steven C. , Delafresnaye Laura , Frisch Hendrik , O’Mara Megan L. , Du Prez Filip E. , Barner-Kowollik Christopher
Published: July 2024

Understanding the intricate relationship between molecular architecture and function underpins most challenges at the forefront of chemical innovation. Bond-forming reactions are particularly influenced by the topology of a chemical structure, both on small molecule scale and in larger macromolecular frameworks. Herein, we elucidate the impact that molecular architecture has on the photo-induced cyclisations of a series of monodisperse macromolecules with defined spacers between photodimerisable moieties, and examine the relationship between propensity for intramolecular cyclisation and intermolecular network formation. We demonstrate a goldilocks zone of maximum reactivity between the sterically hindered and entropically limited regimes with a quantum yield of intramolecular cyclisation that is nearly an order of magnitude higher than the lowest value. As a result of the molecular design of trifunctional macromolecules, their quantum yields can be deconvoluted into the formation of two different cyclic isomers, as rationalised with molecular dynamics simulations. Critically, we visualise our solution-based studies with light-based additive manufacturing. We formulate four photoresists for microprinting, revealing that the precise positioning of functional groups is critical for resist performance, with lower intramolecular quantum yields leading to higher-quality printing in most cases.
Learning interpretable dynamics of stochastic complex systems from experimental data
Authors: Gao Ting-Ting , Barzel Baruch , Yan Gang
Published: July 2024

Complex systems with many interacting nodes are inherently stochastic and best described by stochastic differential equations. Despite increasing observation data, inferring these equations from empirical data remains challenging. Here, we propose the Langevin graph network approach to learn the hidden stochastic differential equations of complex networked systems, outperforming five state-of-the-art methods. We apply our approach to two real systems: bird flock movement and tau pathology diffusion in brains. The inferred equation for bird flocks closely resembles the second-order Vicsek model, providing unprecedented evidence that the Vicsek model captures genuine flocking dynamics. Moreover, our approach uncovers the governing equation for the spread of abnormal tau proteins in mouse brains, enabling early prediction of tau occupation in each brain region and revealing distinct pathology dynamics in mutant mice. By learning interpretable stochastic dynamics of complex systems, our findings open new avenues for downstream applications such as control.
Turning copper into an efficient and stable CO evolution catalyst beyond noble metals
Authors: Xue Jing , Dong Xue , Liu Chunxiao , Li Jiawei , Dai Yizhou , Xue Weiqing , Luo Laihao , Ji Yuan , Zhang Xiao , Li Xu , Jiang Qiu , Zheng Tingting , Xiao Jianping , Xia Chuan
Published: July 2024

Using renewable electricity to convert CO2 into CO offers a sustainable route to produce a versatile intermediate to synthesize various chemicals and fuels. For economic CO2-to-CO conversion at scale, however, there exists a trade-off between selectivity and activity, necessitating the delicate design of efficient catalysts to hit the sweet spot. We demonstrate here that copper co-alloyed with isolated antimony and palladium atoms can efficiently activate and convert CO2 molecules into CO. This trimetallic single-atom alloy catalyst (Cu92Sb5Pd3) achieves an outstanding CO selectivity of 100% (±1.5%) at −402 mA cm−2 and a high activity up to −1 A cm−2 in a neutral electrolyte, surpassing numerous state-of-the-art noble metal catalysts. Moreover, it exhibits long-term stability over 528 h at −100 mA cm−2 with an FECO above 95%. Operando spectroscopy and theoretical simulation provide explicit evidence for the charge redistribution between Sb/Pd additions and Cu base, demonstrating that Sb and Pd single atoms synergistically shift the electronic structure of Cu for CO production and suppress hydrogen evolution. Additionally, the collaborative interactions enhance the overall stability of the catalyst. These results showcase that Sb/Pd-doped Cu can steadily carry out efficient CO2 electrolysis under mild conditions, challenging the monopoly of noble metals in large-scale CO2-to-CO conversion.
Reversible modulation of superconductivity in thin-film NbSe2 via plasmon coupling
Authors: Cheng Guanghui , Lin Meng-Hsien , Chen Hung-Ying , Wang Dongli , Wang Zheyan , Qin Wei , Zhang Zhenyu , Zeng Changgan
Published: July 2024

In recent years, lightwave has stood out as an ultrafast, non-contact control knob for developing compact superconducting circuitry. However, the modulation efficiency is limited by the low photoresponse of superconductors. Plasmons, with the advantages of strong light-matter interaction, present a promising route to overcome the limitations. Here we achieve effective modulation of superconductivity in thin-film NbSe2 via near-field coupling to plasmons in gold nanoparticles. Upon resonant plasmon excitation, the superconductivity of NbSe2 is substantially suppressed. The modulation factor exceeds 40% at a photon flux of 9.36 × 1013 s−1mm−2, and the effect is significantly diminished for thicker NbSe2 samples. Our observations can be theoretically interpreted by invoking the non-equilibrium electron distribution in NbSe2 driven by the plasmon-associated evanescent field. Finally, a reversible plasmon-driven superconducting switch is realized in this system. These findings highlight plasmonic tailoring of quantum states as an innovative strategy for superconducting electronics.
Maternal preconceptional and prenatal exposure to El Niño Southern Oscillation levels and child mortality: a multi-country study
Authors: Xu Hongbing , Zhuang Castiel Chen , Oddo Vanessa M. , Malembaka Espoir Bwenge , He Xinghou , Zhang Qinghong , Huang Wei
Published: July 2024

El Niño Southern Oscillation (ENSO) has been shown to relate to the epidemiology of childhood infectious diseases, but evidence for whether they increase child deaths is limited. Here, we investigate the impact of mothers’ ENSO exposure during and prior to delivery on child mortality by constructing a retrospective cohort study in 38 low- and middle-income countries. We find that high levels of ENSO indices cumulated over 0–12 lagged months before delivery are associated with significant increases in risks of under-five mortality; with the hazard ratio ranging from 1.33 (95% confidence interval [CI], 1.26, 1.40) to 1.89 (95% CI, 1.78, 2.00). Child mortality risks are particularly related to maternal exposure to El Niño-like conditions in the 0th–1st and 6th–12th lagged months. The El Niño effects are larger in rural populations and those with unsafe sources of drinking water and less education. Thus, preventive interventions are particularly warranted for the socio-economically disadvantaged.
Exploration on the potential efficacy and mechanism of methyl salicylate glycosides in the treatment of schizophrenia based on bioinformatics, molecular docking and dynamics simulation
Authors: Wang Xiuhuan , Ma Jiamu , Dong Ying , Ren Xueyang , Li Ruoming , Yang Guigang , She Gaimei , Tan Yunlong , Chen Song
Published: July 2024

The etiological and therapeutic complexities of schizophrenia (SCZ) persist, prompting exploration of anti-inflammatory therapy as a potential treatment approach. Methyl salicylate glycosides (MSGs), possessing a structural parent nucleus akin to aspirin, are being investigated for their therapeutic potential in schizophrenia. Utilizing bioinformation mining, network pharmacology, molecular docking and dynamics simulation, the potential value and mechanism of MSGs (including MSTG-A, MSTG-B, and Gaultherin) in the treatment of SCZ, as well as the underlying pathogenesis of the disorder, were examined. 581 differentially expressed genes related to SCZ were identified in patients and healthy individuals, with 349 up-regulated genes and 232 down-regulated genes. 29 core targets were characterized by protein-protein interaction (PPI) network, with the top 10 core targets being BDNF, VEGFA, PVALB, KCNA1, GRIN2A, ATP2B2, KCNA2, APOE, PPARGC1A and SCN1A. The pathogenesis of SCZ primarily involves cAMP signaling, neurodegenerative diseases and other pathways, as well as regulation of ion transmembrane transport. Molecular docking analysis revealed that the three candidates exhibited binding activity with certain targets with binding affinities ranging from −4.7 to −109.2 kcal/mol. MSTG-A, MSTG-B and Gaultherin show promise for use in the treatment of SCZ, potentially through their ability to modulate the expression of multiple genes involved in synaptic structure and function, ion transport, energy metabolism. Molecular dynamics simulation revealed good binding abilities between MSTG-A, MSTG-B, Gaultherin and ATP2B2. It suggests new avenues for further investigation in this area.
Mechanical release of homogenous proteins from supramolecular gels
Authors: Bianco Simona , Hasan Muhammad , Ahmad Ashfaq , Richards Sarah-Jane , Dietrich Bart , Wallace Matthew , Tang Qiao , Smith Andrew J. , Gibson Matthew I. , Adams Dave J.
Published: July 2024

A long-standing challenge is how to formulate proteins and vaccines to retain function during storage and transport and to remove the burdens of cold-chain management. Any solution must be practical to use, with the protein being released or applied using clinically relevant triggers. Advanced biologic therapies are distributed cold, using substantial energy, limiting equitable distribution in low-resource countries and placing responsibility on the user for correct storage and handling. Cold-chain management is the best solution at present for protein transport but requires substantial infrastructure and energy. For example, in research laboratories, a single freezer at −80 °C consumes as much energy per day as a small household1. Of biological (protein or cell) therapies and all vaccines, 75% require cold-chain management; the cost of cold-chain management in clinical trials has increased by about 20% since 2015, reflecting this complexity. Bespoke formulations and excipients are now required, with trehalose2, sucrose or polymers3 widely used, which stabilize proteins by replacing surface water molecules and thereby make denaturation thermodynamically less likely; this has enabled both freeze-dried proteins and frozen proteins. For example, the human papilloma virus vaccine requires aluminium salt adjuvants to function, but these render it unstable against freeze–thaw4, leading to a very complex and expensive supply chain. Other ideas involve ensilication5 and chemical modification of proteins6. In short, protein stabilization is a challenge with no universal solution7,8. Here we designed a stiff hydrogel that stabilizes proteins against thermal denaturation even at 50 °C, and that can, unlike present technologies, deliver pure, excipient-free protein by mechanically releasing it from a syringe. Macromolecules can be loaded at up to 10 wt% without affecting the mechanism of release. This unique stabilization and excipient-free release synergy offers a practical, scalable and versatile solution to enable the low-cost, cold-chain-free and equitable delivery of therapies worldwide.
Psilocybin desynchronizes the human brain
Authors: Siegel Joshua S. , Subramanian Subha , Perry Demetrius , Kay Benjamin P. , Gordon Evan M. , Laumann Timothy O. , Reneau T. Rick , Metcalf Nicholas V. , Chacko Ravi V. , Gratton Caterina , Horan Christine , Krimmel Samuel R. , Shimony Joshua S. , Schweiger Julie A. , Wong Dean F. , Bender David A. , Scheidter Kristen M. , Whiting Forrest I. , Padawer-Curry Jonah A. , Shinohara Russell T. , Chen Yong , Moser Julia , Yacoub Essa , Nelson Steven M. , Vizioli Luca , Fair Damien A. , Lenze Eric J. , Carhart-Harris Robin , Raison Charles L. , Raichle Marcus E. , Snyder Abraham Z. , Nicol Ginger E. , Dosenbach Nico U. F.
Published: July 2024

A single dose of psilocybin, a psychedelic that acutely causes distortions of space–time perception and ego dissolution, produces rapid and persistent therapeutic effects in human clinical trials1–4. In animal models, psilocybin induces neuroplasticity in cortex and hippocampus5–8. It remains unclear how human brain network changes relate to subjective and lasting effects of psychedelics. Here we tracked individual-specific brain changes with longitudinal precision functional mapping (roughly 18 magnetic resonance imaging visits per participant). Healthy adults were tracked before, during and for 3 weeks after high-dose psilocybin (25 mg) and methylphenidate (40 mg), and brought back for an additional psilocybin dose 6–12 months later. Psilocybin massively disrupted functional connectivity (FC) in cortex and subcortex, acutely causing more than threefold greater change than methylphenidate. These FC changes were driven by brain desynchronization across spatial scales (areal, global), which dissolved network distinctions by reducing correlations within and anticorrelations between networks. Psilocybin-driven FC changes were strongest in the default mode network, which is connected to the anterior hippocampus and is thought to create our sense of space, time and self. Individual differences in FC changes were strongly linked to the subjective psychedelic experience. Performing a perceptual task reduced psilocybin-driven FC changes. Psilocybin caused persistent decrease in FC between the anterior hippocampus and default mode network, lasting for weeks. Persistent reduction of hippocampal-default mode network connectivity may represent a neuroanatomical and mechanistic correlate of the proplasticity and therapeutic effects of psychedelics.
Normative longitudinal EEG recordings during sleep stage II in the first year of age
Authors: Harmony Thalía , Otero-Ojeda Gloria , Aubert-Vázquez Eduardo , Fernández Thalía , Cubero-Rego Lourdes
Published: July 2024

The electroencephalogram (EEG) is a fundamental diagnostic procedure that explores brain function. This manuscript describes the characteristics of a sample of healthy at-term infants. One hundred and three (103) infants from Mexico between 15 days and 12.5 months of age were recorded during physiological sleep. Referential EEG recordings were obtained using linked ear lobes as reference. The amplifier gain was 10,000, the bandwidth was set between 0.3 and 30 Hz, and the sample rate was 200 Hz. Sample windows of 2.56 s were marked for later quantitative analysis. To our knowledge, this is the first dataset of normal infants during the first year of age.
A diffusion MRI tractography atlas for concurrent white matter mapping across Eastern and Western populations
Authors: Li Yijie , Zhang Wei , Wu Ye , Yin Li , Zhu Ce , Chen Yuqian , Cetin-Karayumak Suheyla , Cho Kang Ik K. , Zekelman Leo R. , Rushmore Jarrett , Rathi Yogesh , Makris Nikos , O’Donnell Lauren J. , Zhang Fan
Published: July 2024

The study of brain differences across Eastern and Western populations provides vital insights for understanding potential cultural and genetic influences on cognition and mental health. Diffusion MRI (dMRI) tractography is an important tool in assessing white matter (WM) connectivity and brain tissue microstructure across different populations. However, a comprehensive investigation into WM fiber tracts between Eastern and Western populations is challenged due to the lack of a cross-population WM atlas and the large site-specific variability of dMRI data. This study presents a dMRI tractography atlas, namely theEast-West WM Atlas, for concurrent WM mapping between Eastern and Western populations and creates a large, harmonized dMRI dataset (n=306) based on the Human Connectome Project and the Chinese Human Connectome Project. The curated WM atlas, as well as subject-specific data including the harmonized dMRI data, the whole brain tractography data, and parcellated WM fiber tracts and their diffusion measures, are publicly released. This resource is a valuable addition to facilitating the exploration of brain commonalities and differences across diverse cultural backgrounds.
A Multi-Center, Multi-Parametric MRI Dataset of Primary and Secondary Brain Tumors
Authors: Gong Zhenyu , Xu Tao , Peng Nan , Cheng Xing , Niu Chen , Wiestler Benedikt , Hong Fan , Li Hongwei Bran
Published: July 2024

Brain metastases (BMs) and high-grade gliomas (HGGs) are the most common and aggressive types of malignant brain tumors in adults, with often poor prognosis and short survival. As their clinical symptoms and image appearances on conventional magnetic resonance imaging (MRI) can be astonishingly similar, their accurate differentiation based solely on clinical and radiological information can be very challenging, particularly for “cancer of unknown primary”, where no systemic malignancy is known or found. Non-invasive multiparametric MRI and radiomics offer the potential to identify these distinct biological properties, aiding in the characterization and differentiation of HGGs and BMs. However, there is a scarcity of publicly available multi-origin brain tumor imaging data for tumor characterization. In this paper, we introduce a multi-center, multi-origin brain tumor MRI (MOTUM) imaging dataset obtained from 67 patients: 29 with high-grade gliomas, 20 with lung metastases, 10 with breast metastases, 2 with gastric metastasis, 4 with ovarian metastasis, and 2 with melanoma metastasis. This dataset includes anonymized DICOM files alongside processed FLAIR, T1-weighted, contrast-enhanced T1-weighted, T2-weighted sequences images, segmentation masks of two tumor regions, and clinical data. Our data-sharing initiative is to support the benchmarking of automated tumor segmentation, multi-modal machine learning, and disease differentiation of multi-origin brain tumors in a multi-center setting.
Chromosome-level genome assembly of Aquilaria yunnanensis
Authors: Li Meifei , Zhang Yingmin , Wang Yi , Yin Yue , Zhou Meijun , Zhang Yonghong
Published: July 2024

Aquilaria yunnanensis is an endangered agarwood-producing tree currently listed on the IUCN Red List of Threatened Species. The agarwood it produces has important medicinal and economic value, but its population has sharply declined due to human destruction and habitat reduction. Therefore, obtaining genomic information on A. yunnanensis is beneficial for its protection work. We assembled a chromosome-level reference genome of A. yunnanensis by using BGI short reads, PacBio HiFi long reads, coupled with Hi-C technology. The final genome assembly of A. yunnanensis is 847.04 Mb, with N50 size of 99.68 Mb, in which 805.49 Mb of the bases were anchored on eight pseudo-chromosomes. Two gapless pseudo-chromosomes were detected in the assembly. A total of 27,955 protein-coding genes as well as 74.65% repetitive elements were annotated. These findings may provide valuable resources in conservation, functional genomics, and molecular breeding of A. yunnanensis, as well as the molecular phylogenetics and evolutionary patterns in Aquilaria.
Trends in hepatitis C virus seroprevalence and associated risk factors among msm in Pakistan: insights from a community-based study
Authors: Tirmizi Raza , Munir Rimsha , Zaidi Nousheen
Published: July 2024

Pakistan bears a substantial burden of hepatitis C virus (HCV) infection, with the second-highest prevalence globally. This community-based cross-sectional study, conducted from January to December 2022 in Punjab, Pakistan, investigates the seroprevalence of HCV among the men who have sex with men (MSM) population. The study identifies demographic and behavioral risk factors associated with HCV infection within this population group. Among the 501 participants, the study found an HCV seroprevalence of 14.86%. The association between demographic characteristics and seroprevalence is assessed by calculating the percentage of positive cases, revealing notable associations with age, education level, and self-identified sexual orientation. Furthermore, the study identified several behavioral risk factors positively associated with HCV seroprevalence, including sharing personal items such as razors and toothbrushes, histories of surgery, blood transfusion, dental procedures, intravenous drug use, and therapeutic injection histories. These risk factors were identified through structured interviews, and the prevalence of HCV seropositivity among the exposed groups was calculated accordingly. Interestingly, a lower HCV positivity rate was observed among self-reported HIV-positive individuals, contradicting previous research. The findings underscore the need for comprehensive, targeted prevention strategies such as risk factor awareness campaigns and educational programs tailored for the MSM population in Pakistan. Further research is warranted to validate these findings and better understand the complex interplay of factors contributing to HCV seroprevalence in this high-risk population.
Thymoquinone’ potent impairment of multidrug-resistant Staphylococcus aureus NorA efflux pump activity
Authors: Ahmad Adel Attia M. , Abdelgalil Sara Y. , Khamis Tarek , Abdelwahab Ashraf M. O. , Atwa Dina Nader , Elmowalid Gamal A.
Published: July 2024

The drug efflux pump is a crucial mechanism implicated in resistance to multiple antimicrobials. Thymoquinone (TQ) has evidently demonstrated multiple activities, antibacterial being the most effective. Knowledge about TQ activity against multidrug-resistant Staphylococcus aureus is very scarce. Therefore, the present study was conducted to investigate TQ resistance modulation in ciprofloxacin (CIP) and doxycycline (DO) multidrug-resistant S. aureus. Forty-seven samples were collected from different sources, and S. aureus was isolated and identified. Then, S. aureus resistance profiles to antimicrobials, N. sativa essential oil, and TQ; the correlation between TQ-MIC readings and disc diffusion; cartwheel and ethidium bromide (EtBr) accumulation assays; and norA gene expression were all described within silico molecular docking for TQ interactions with norA efflux pump protein. TQ-MICs ranged from 5–320 µg/ml. TQ down-regulated norA gene expression, resulting in a drop in efflux pump activity of 77.5–90.6% in the examined strains, comparable to that observed with verapamil. Exposure of S. aureus strains to CIP and DO raises the initial basal efflux pumping expression to 34.2 and 22.9 times, respectively. This induced efflux pumping overexpression was substantially reduced by 97.7% when TQ was combined with CIP or DO. There was a significant reduction of MICs of CIP and DO MICs by 2–15 and 2–4 folds, respectively, after treatment with 0.5XMIC-TQ in resistance modulation assays. These results refer to TQ ligand inhibitory interactions with NorA protein in molecular docking. Interpretations of inhibition zone diameters (IZDs) of disc diffusion and TQ-MICs exhibit independence of MICs from IZDs, as indicated by invalid linear regression analysis. TQ significantly reduced efflux pumping S. aureus induced by CIP and DO, but further investigations are needed to improve TQ-pharmacokinetics to restore CIP and DO activity and suppress fluoroquinolone and doxycycline-resistant S. aureus selection in clinical and animal settings.
Design of silver-zinc-nickel spinel-ferrite mesoporous silica as a powerful and simply separable adsorbent for some textile dye removal
Authors: Okba Ehab A. , Rabea Moamen F. , El-Sheikh Mohamed Y. , Aboelfetoh Eman F.
Published: July 2024

Silver-zinc-nickel spinel ferrite was prepared by the co-precipitation procedure with the precise composition Ag0.1Zn0.4Ni0.5Fe2O4 for bolstering pollutant removal effectiveness while upholding magnetic properties and then coated with a mesoporous silica layer. The surface characteristics and composition of Ag0.1Zn0.4Ni0.5Fe2O4@mSiO2 were confirmed using EDX, FT-IR, VSM, XRD, TEM, SEM, and BET methods. The surface modification of Ag-Zn-Ni ferrite with a silica layer improves the texture properties, where the specific surface area and average pore size of the spinel ferrite rose to 180 m2/g and 3.15 nm, respectively. The prepared spinel ferrite@mSiO2 has been utilized as an efficient adsorbent for eliminating methyl green (MG) and indigo carmine (IC) as models of cationic and anionic dyes from wastewater, respectively. Studying pH, Pzc, adsorbent dosage, dye concentration, and temperature showed that efficient removal of MG was carried out in alkaline media (pH = 12), while the acid medium (pH = 2) was effective for IC removal. Langmuir isotherm and pseudo-second-order kinetics were found to be good fits for the adsorption data. Both dyes were adsorbed in a spontaneous, endothermic process. A possible mechanism for dye removal has been proposed. The adsorbent was effectively recovered and reused.
Airway specific deregulation of asthma-related serpins impairs tracheal architecture and oxygenation in D. melanogaster
Authors: Ehrhardt Birte , Angstmann Hanna , Höschler Beate , Kovacevic Draginja , Hammer Barbara , Roeder Thomas , Rabe Klaus F. , Wagner Christina , Uliczka Karin , Krauss-Etschmann Susanne
Published: July 2024

Serine proteases are important regulators of airway epithelial homeostasis. Altered serum or cellular levels of two serpins, Scca1 and Spink5, have been described for airway diseases but their function beyond antiproteolytic activity is insufficiently understood. To close this gap, we generated fly lines with overexpression or knockdown for each gene in the airways. Overexpression of both fly homologues of Scca1 and Spink5 induced the growth of additional airway branches, with more variable results for the respective knockdowns. Dysregulation of Scca1 resulted in a general delay in fruit fly development, with increases in larval and pupal mortality following overexpression of this gene. In addition, the morphological changes in the airways were concomitant with lower tolerance to hypoxia. In conclusion, the observed structural changes of the airways evidently had a strong impact on the airway function in our model as they manifested in a lower physical fitness of the animals. We assume that this is due to insufficient tissue oxygenation. Future work will be directed at the identification of key molecular regulators following the airway-specific dysregulation of Scca1 and Spink5 expression.
In-silico analysis of cattle blood transcriptome to identify lncRNAs and their role during bovine tuberculosis
Authors: Garg Priyanka , Vanamamalai Venkata Krishna , Sharma Shailesh
Published: July 2024

Long noncoding RNAs (lncRNAs) are RNA molecules with a length greater than 200 nucleotides that do not code for functional proteins. Although, genes play a vital role in immune response against a disease, it is less known that lncRNAs also contribute through gene regulation. Bovine tuberculosis is a significant zoonotic disease caused by Mycobacterium bovis (M. bovis) in cattle. Here, we report the in-silico analysis of the publicly available transcriptomic data of calves infected with M. bovis. A total of 51,812 lncRNAs were extracted across all the samples. A total of 216 genes and 260 lncRNAs were found to be differentially expressed across all the 4 conditions—infected vs uninfected at 8- and 20-week post-infection (WPI), 8 vs 20-WPI of both infected and uninfected. Gene Ontology and Functional annotation showed that 8 DEGs were annotated with immune system GOs and 2 DEGs with REACTOME immune system pathways. Co-expression analysis of DElncRNAs with DEGs revealed the involvement of lncRNAs with the genes annotated with Immune related GOs and pathways. Overall, our study sheds light on the dynamic transcriptomic changes in response to M. bovis infection, particularly highlighting the involvement of lncRNAs with immune-related genes. The identified immune pathways and gene–lncRNA interactions offer valuable insights for further research in understanding host–pathogen interactions and potential avenues for genetic improvement strategies in cattle.
The low-lethal concentrations of rotenone and pyrethrins suppress the population growth of Rhopalosiphum padi
Authors: Xu Li , Wu Zhenghua , Li Jingkun , Xu Yihao , Zhou Feng , Zhang Fulong , Li Dongzhi , Zhou Lin , Liu Runqiang
Published: July 2024

As an important pest on winter wheat, Rhopalosiphum padi (L.) causes damage to the wheat yield by sucking plant nutrients, transmitting plant viruses and producing mildew. R. padi has been reported to develop resistance to pyrethroids and neonicotinoids. To explore potential alternative approaches for R. padi control, the activity of 10 botanical insecticides was evaluated. Results suggested that the toxicity of rotenone and pyrethrins to R. padi were the highest and near to the commonly used chemical insecticides. When exposed to the low-lethal concentrations (LC10, LC30) of rotenone or pyrethrins for 24 h, the lifespan and fecundity of adults in F0 generation decreased significantly compared to control. The negative effect could also be observed in the F1 generation, including the decreased average offspring, longevity of adult, and prolonged nymph period. The population parameters in F1 generation of R. padi were also inhibited by exposing to the low-lethal concentrations of rotenone or pyrethrins, including the decreased net reproductive rate, intrinsic rate of natural increase, finite rate of population increase, and gross reproduction rate. Co-toxocity factor results showed that mixtures of rotenone and thiamethoxam, pyrethrins and thiamethoxam showed synergistic effect. Our work suggested that rotenone and pyrethrins showed negative effect on the population growth under low-lethal concentrations. They are suitable for R. padi control as foliar spraying without causing population resurgence.
Effects of extracorporeal shockwave therapy versus ultrasonic therapy and deep friction massage in the management of lateral epicondylitis: a randomized clinical trial
Authors: Perveen Wajida , Anwar Sahreen , Hashmi Riaz , Ali Misbah Amanat , Raza Asim , Ilyas Umer , Nuhmani Shibili , Khan Masood , Alghadir Ahmad H.
Published: July 2024

The study's goal was to compare and evaluate the benefits of deep friction massage and ultrasonic therapy (US) vs extracorporeal shockwave therapy (ESWT) for people with lateral epicondylitis. This double-blind, parallel-arm randomized clinical trial was conducted after ethical approval on a sample of 80 subjects with lateral epicondylitis. Participants were enrolled based on predefined eligibility criteria. They were randomly allocated to groups A and B. Group A received ESWT, while Group B received the US combined with deep friction massage. Data was collected using the Numeric Pain Rating Score (NPRS) and Patient-rated tennis elbow evaluation questionnaire (PRTEE) at baseline, at 3rd, and at 7th week of treatment. On the basis of the normality of the data, a non-parametric test was applied to evaluate between-group and within-group differences. P value ≤ 0.05 was considered significant. There was a significant difference between groups (p < 0.001). Comparisons of PRTEE scores at 3rd week and 7th week of intervention were found significant for both groups (p < 0.001). While considering between-group comparisons based on percentile scores of PRTEE at baseline, 3rd and 7th week of intervention, in group A Median (IQR) at the baseline was 24.00 (5.00), at 3rd week, 10.00 (5.00) and 7th week was 1.50 (2.50) and in group B Median (IQR) at the baseline was 25.00 (4.00), at 3rd week 19.50 (4.50) and at 7th week was 11.50 (2.50). The results were significant in both groups (p = 0.000), but between-group analysis revealed that ESWT is more effective in patients with lateral epicondylitis.
Causal relationship between type 2 diabetes and glioblastoma: bidirectional Mendelian randomization analysis
Authors: Chen Wei , Zhang Taoyuan , Zhang Hui
Published: July 2024

As the prevalence of Type 2 Diabetes Mellitus (T2DM) and Glioblastoma (GBM) rises globally, the relationship between T2DM and GBM remains controversial. This study aims to investigate whether genetically predicted T2DM is causally associated with GBM. We performed bidirectional Mendelian randomization (MR) analysis using data from genome-wide studies on T2DM (N = 62,892) and GBM (N = 218,792) in European populations. The results of the inverse-variance weighted (IVW) approach served as the primary outcomes. We applied Cochran’s Q test and MR-Egger regression for heterogeneity assessment. Leave-one-out analysis was used to evaluate whether any single SNP significantly influenced the observed effect. Our findings reveal a significant causal association between T2DM and an increased risk of GBM (OR [95% CI] 1.70 [1.09, 2.65], P = 0.019). Conversely, the reverse association between T2DM and GBM was insignificant (OR [95% CI] 1.00 [0.99, 1.01], P = 0.408) (P > 0.40). Furthermore, the results from Cochran’s Q-test and funnel plots in the MR-Egger method indicated no evidence of pleiotropy between the SNPs and GBM. Additionally, we mapped causal SNPs to genes and identified 10 genes, including MACF1, C1orf185, PTGFRN, NOTCH2, ABCB10, GCKR, THADA, RBMS1, SPHKAP, and PPARG, located on chromosomes 1, 2, and 3. These genes are involved in key biological processes such as the BMP signaling pathway and various metabolic pathways relevant to both conditions. This study provides robust evidence of a significant causal relationship between T2DM and an increased risk of GBM. The identified SNP-mapped genes highlight potential biological mechanisms underlying this association.
Diffusion in biological media: a comprehensive numerical-analytical study via surface analysis and diffusivities calculation
Authors: González Pacheco Juan Ignacio , Maldonado Mariela Beatriz
Published: July 2024

The study of diffusion in biological materials is crucial for fields like food science, engineering, and pharmaceuticals. Research that combines numerical and analytical methods is needed to better understand diffusive phenomena across various dimensions and under variable boundary conditions within food matrices. This study aims to bridge this gap by examining the diffusion of substances through biological materials analytically and numerically, calculating diffusivity and conducting surface analysis. The research proposes a process for sweetening Bing-type cherries (Prunus avium) using sucrose/xylitol solutions and a staining technique utilising erythrosine and red gardenia at varying concentrations (119, 238 and 357 ppm) and temperatures (40, 50 and 60 °C). Given the fruit's epidermis resistance, the effective diffusivities of skin were inferior to those in flesh. Temperature and concentration synergise in enhancing diffusion coefficients and dye penetration within the food matrix (357 ppm and 60 °C). Red gardenia displayed significant temperature-dependent variation (p = 0.001), whereas erythrosine dye remained stable by temperature changes (p > 0.05). Gardenia's effective diffusivities in cherry flesh and skin, at 357 ppm and 60 °C, 3.89E−08 and 6.61E−09 m2/s, respectively, significantly differed from those obtained at lower temperatures and concentrations. The results highlight the temperature-concentration impacts on mass transfer calculations for food colouring processes and preservation methodologies.