bluuebunny/crossref_metadata_2025 huggingface dataset:
Introducing The View from the Sea. The Practice of Early Modern Transoceanic Commercial Navigation
Authors: Iannuzzi Giulia
Published: May 2024

Research into maritime history using digital tools is a growing field, with projects that in recent years have focused on the role of sea spaces in the dynamics of globalisation on an economic and juridical level as well as on a cultural level, with respect to the circulation of knowledge. In this introduction to our special issue, we offer some historiographical observations on the codification of knowledge in seafaring practice, emphasising how the use of digital tools to process and represent primary sources may encourage historians to formulate new questions about the relationship between European culture and the sea during the early modern age. In order to present the articles in this issue and the original contribution they make to the field, we also focus on the historical and cultural significance and methodological challenges posed by primary sources such as logbooks. We illustrate how the analysis of logbooks in a digital environment such as Global Sea Routes (GSR), a project conceived and coordinated by Guido Abbattista, can foster a better understanding of the role of routine navigations in early commercial globalisation.
Trade-offs in fishing strategy decisions and conservation implications for small-scale fisheries
Authors: Wade Eric , Biedenweg Kelly
Published: May 2024

People are psychologically predisposed to minimize their losses, even in the face of substantial gains. This predisposition, referred to as ‘loss aversion’, is especially present when people face uncertain outcomes. In small-scale fisheries, where fishers’ decisions are influenced by monetary and non-monetary assets, exploring how loss aversion intersects with conservation efforts may offer insights into how fishers balance short-term and long-term priorities. This study assessed the variables that contribute to loss aversion of small-scale fishers when making trade-offs between two valued assets: information-sharing and catch success. We used a structured questionnaire and a hypothetical simple lottery choice task of 78 fishers across 20 fishing beaches in Jamaica. We found that fishers were marginally more loss averse when both information-sharing opportunities and catch success were threatened than when only catch success was threatened. Communication frequency and size of fishing crew contributed significantly to fishers’ loss aversion in most choice sets, regardless of whether materially or non-materially valued assets were threatened. By exploring the drivers underpinning fishers’ choices, we provide insights into how the consideration of these variables can support the development of fisheries conservation measures that better align with the decision priorities of fishers.
A Regionally Refined and Mass‐Consistent Atmospheric and Hydrological De‐Aliasing Product for GRACE, GRACE‐FO and Future Gravity Missions
Authors: Springer Anne , Mielke Christian A. , Liu Ziyu , Dixit Shashi , Friederichs Petra , Kusche Jürgen
Published: May 2024

De‐aliasing products are used in the estimation process of satellite‐based gravity field computation to reduce errors from high‐frequency mass variations that alias into monthly gravity fields. The latest official product is AOD1B RL07 and describes non‐tidal atmosphere and oceanic mass variations at 3‐hourly resolution. However, the model‐based de‐aliasing products are inevitably incomplete and prone to temporally and spatially correlated errors that substantially contribute to errors in the estimated gravity fields. Here, we investigate possible enhancement of current de‐aliasing products by nesting a regional high‐resolution atmospheric reanalysis over Europe into a global reanalysis. As further novelty we include almost mass consistent terrestrial water storage variability from a regional hydrological model nested into a global model as additional component of the de‐aliasing product. While we find in agreement with earlier studies only minor contributions from increasing the temporal resolution beyond 3‐hourly data, our investigations suggest that contributions from continental hydrology and from regional non‐hydrostatic atmospheric modeling to sub‐monthly mass variations could be relevant already for gravity fields estimated from current gravity missions. Moreover, in the context of extreme events, we find regionally contributions from additional moisture fields, such as cloud liquid water, in the order of a few mm over Europe. We suggest this needs to be taken into account when preparing data analysis schemes for future space gravimetric missions.
AGU Publications Updates Authorship Policy to Foster Greater Equity and Transparency in Global Research Collaborations
Authors: Xenopoulos Marguerite A. , Bond‐Lamberty Ben , Desai Ankur R. , Huntzinger Deborah , Buchanan Paula R. , East Amy E. , Singh Arvind , Wooden Paige , Jewett Kevin , Ricci Mia
Published: May 2024

AGU Publications encourages research collaborations between regions, countries, and communities. When well‐resourced researchers complete research or field work in low‐resourced settings while excluding local communities or researchers from the process, this can be referred to as parachute science or helicopter research. To help address concerns of parachute science and to promote greater equity and transparency in global research collaborations, AGU Publications has updated its authorship policy across its scholarly journals. The implementation of this policy follows a successful 18‐month pilot at JGR: Biogeosciences. For research completed in low‐resourced regions, authors are encouraged to include a disclosure statement pertaining to the ethical and scientific considerations of their research collaborations.
Peaks, sources, and immediate health impacts of PM2.5 and PM1 exposure in Indonesia and Taiwan with microsensors
Authors: Lung Shih-Chun Candice , Tsou Ming-Chien Mark , Cheng Chih-Hui Chloe , Setyawati Wiwiek
Published: May 2024

Background

Microsensors have been used for the high-resolution particulate matter (PM) monitoring.

Objectives

This study applies PM and health microsensors with the objective of assessing the peak exposure, sources, and immediate health impacts of PM2.5 and PM1 in two Asian countries.

Methods

Exposure assessment and health evaluation were carried out for 50 subjects in 2018 and 2019 in Bandung, Indonesia and for 55 subjects in 2019 and 2020 in Kaohsiung, Taiwan. Calibrated AS-LUNG sets and medical-certified RootiRx® sensors were used to assess PM and heart-rate variability (HRV), respectively.

Results

Overall, the 5-min mean exposure of PM2.5 and PM1 was 30.4 ± 20.0 and 27.0 ± 15.7 µg/m3 in Indonesia and 14.9 ± 11.2 and 13.9 ± 9.8 µg/m3 in Taiwan, respectively. The maximum 5-min peak PM2.5 and PM1 exposures were 473.6 and 154.0 µg/m3 in Indonesia and 467.4 and 217.7 µg/m3 in Taiwan, respectively. Community factories and mosquito coil burning are the two most important exposure sources, resulting in, on average, 4.73 and 5.82 µg/m3 higher PM2.5 exposure increments for Indonesian subjects and 10.1 and 9.82 µg/m3 higher PM2.5 exposure for Taiwanese subjects compared to non-exposure periods, respectively. Moreover, agricultural waste burning and incense burning were another two important exposure sources, but only in Taiwan. Furthermore, 5-min PM2.5 and PM1 exposure had statistically significantly immediate impacts on the HRV indices and heart rates of all subjects in Taiwan and the scooter subjects in Indonesia with generalized additive mixed models. The HRV change for a 10 µg/m3 increase in PM2.5 and PM1 ranged from −0.9% to −2.5% except for ratio of low-high frequency, with greater impacts associated with PM1 than PM2.5 in both countries.

Impact statement

This work highlights the ability of microsensors to capture high peaks of PM2.5 and PM1, to identify exposure sources through the integration of activity records, and to assess immediate changes in heart rate variability for a panel of approximately 50 subjects in Indonesia and Taiwan. This study stands out as one of the few to demonstrate the immediate health impacts of peak PM, complementing to the short-term (days or weeks) or long-term effects (months or longer) assessed in most epidemiological studies. The technology/methodology employed offer great potential for researchers in the resource-limited countries with high PM2.5 and PM1 levels.
Altered cortical synaptic lipid signaling leads to intermediate phenotypes of mental disorders
Authors: Tüscher Oliver , Muthuraman Muthuraman , Horstmann Johann-Philipp , Horta Guilherme , Radyushkin Konstantin , Baumgart Jan , Sigurdsson Torfi , Endle Heiko , Ji Haichao , Kuhnhäuser Prisca , Götz Jan , Kepser Lara-Jane , Lotze Martin , Grabe Hans J. , Völzke Henry , Leehr Elisabeth J. , Meinert Susanne , Opel Nils , Richers Sebastian , Stroh Albrecht , Daun Silvia , Tittgemeyer Marc , Uphaus Timo , Steffen Falk , Zipp Frauke , Groß Joachim , Groppa Sergiu , Dannlowski Udo , Nitsch Robert , Vogt Johannes
Published: May 2024

Excitation/inhibition (E/I) balance plays important roles in mental disorders. Bioactive phospholipids like lysophosphatidic acid (LPA) are synthesized by the enzyme autotaxin (ATX) at cortical synapses and modulate glutamatergic transmission, and eventually alter E/I balance of cortical networks. Here, we analyzed functional consequences of altered E/I balance in 25 human subjects induced by genetic disruption of the synaptic lipid signaling modifier PRG-1, which were compared to 25 age and sex matched control subjects. Furthermore, we tested therapeutic options targeting ATX in a related mouse line. Using EEG combined with TMS in an instructed fear paradigm, neuropsychological analysis and an fMRI based episodic memory task, we found intermediate phenotypes of mental disorders in human carriers of a loss-of-function single nucleotide polymorphism of PRG-1 (PRG-1R345T/WT). Prg-1R346T/WT animals phenocopied human carriers showing increased anxiety, a depressive phenotype and lower stress resilience. Network analysis revealed that coherence and phase-amplitude coupling were altered by PRG-1 deficiency in memory related circuits in humans and mice alike. Brain oscillation phenotypes were restored by inhibtion of ATX in Prg-1 deficient mice indicating an interventional potential for mental disorders.
Acute effects of different types of cannabis on young adult and adolescent resting-state brain networks
Authors: Ertl Natalie , Freeman Tom P. , Mokrysz Claire , Ofori Shelan , Borissova Anna , Petrilli Kat , Curran H. Valerie , Lawn Will , Wall Matthew B.
Published: May 2024

Adolescence is a time of rapid neurodevelopment and the endocannabinoid system is particularly prone to change during this time. Cannabis is a commonly used drug with a particularly high prevalence of use among adolescents. The two predominant phytocannabinoids are Delta-9-tetrahydrocannabinol (THC) and cannabidiol (CBD), which affect the endocannabinoid system. It is unknown whether this period of rapid development makes adolescents more or less vulnerable to the effects of cannabis on brain-network connectivity, and whether CBD may attenuate the effects of THC. Using fMRI, we explored the impact of vaporized cannabis (placebo, THC: 8 mg/75 kg, THC + CBD: 8 mg/75 kg THC & 24 mg/75 kg CBD) on resting-state networks in groups of semi-regular cannabis users (usage frequency between 0.5 and 3 days/week), consisting of 22 adolescents (16–17 years) and 24 young adults (26–29 years) matched for cannabis use frequency. Cannabis caused reductions in within-network connectivity in the default mode (F[2,88] = 3.97, P = 0.022, η² = 0.018), executive control (F[2,88] = 18.62, P < 0.001, η² = 0.123), salience (F[2,88] = 12.12, P < 0.001, η² = 0.076), hippocampal (F[2,88] = 14.65, P < 0.001, η² = 0.087), and limbic striatal (F[2,88] = 16.19, P < 0.001, η² = 0.102) networks compared to placebo. Whole-brain analysis showed cannabis significantly disrupted functional connectivity with cortical regions and the executive control, salience, hippocampal, and limbic striatal networks compared to placebo. CBD did not counteract THC’s effects and further reduced connectivity both within networks and the whole brain. While age-related differences were observed, there were no interactions between age group and cannabis treatment in any brain network. Overall, these results challenge the assumption that CBD can make cannabis safer, as CBD did not attenuate THC effects (and in some cases potentiated them); furthermore, they show that cannabis causes similar disruption to resting-state connectivity in the adolescent and adult brain.
Unmet healthcare needs, access to services and experiences with health providers among persons with spinal cord injury in Australia
Authors: Borg Samantha J. , Borg David N. , Arora Mohit , Middleton James W. , Marshall Ruth , Nunn Andrew , Geraghty Timothy
Published: May 2024

Study design

Cross-sectional survey.

Objectives

Appropriate and timely lifelong access to healthcare following a spinal cord injury (SCI) is critical, yet unmet healthcare needs in this population are common. Poor experiences with healthcare providers can be a barrier to health-seeking behaviour, and we hypothesised that there would be an association between unmet healthcare needs and care experiences. This study aimed to: (1) describe healthcare provider utilisation in the past year, unmet care needs and satisfaction with healthcare services; (2) explore the association between experiences with healthcare providers and unmet healthcare needs; and (3) explore the association between healthcare provider utilisation and participant characteristics, including unmet healthcare needs.

Setting

Community.

Methods

Analysis of data for 1579 Australians aged ≥ 18, who were ≥ 1-year post-SCI and living in the community. Bayesian penalised regression was used to model six binary outcomes: unmet healthcare needs; the use of general practitioners (GPs), allied health practitioners, rehabilitation specialists; medical specialists; and hospitalisations in the past 12-months.

Results

Unmet needs were reported by 17% of participants, with service cost the common deterrent. There was evidence of an effect for provider experiences on unmet healthcare needs, but no evidence that unmet healthcare needs was associated with the use of GPs, allied health practitioners, and rehabilitation or medical specialists.

Conclusions

Unmet healthcare needs were reported in the context of high healthcare use and large proportions of secondary conditions in a cohort with long-term SCI. Improved health access for people with SCI include better primary-secondary care collaboration is needed.
Necroptosis induced by ruthenium (II) complexes as mitochondrial disruptors
Authors: Gonçalves Joana , Amaral Joana D. , Capela Rita , Perry Maria de Jesus , Braga Cláudia , Gaspar Maria Manuela , Piedade Fátima M. , Bijlsma Lubertus , Roig Antoni , Pinto Sandra N. , Moreira Rui , Florindo Pedro , Rodrigues Cecília M. P.
Published: May 2024

Inducing necroptosis in cancer cells has emerged as an effective strategy to overcome drug resistance. However, while organic small molecules have been extensively studied for this purpose, metal-based compounds have received relatively little attention as triggers of necroptosis. The development of ruthenium (II) hybrid compounds, particularly those containing triazene (Ru-TRZ), highlights a novel avenue for modulating necroptotic cell death. Here we show that incorporating a methyltriazene moiety, a known alkylating warhead, confers superior mitochondrial-targeting properties and enhances cell death compared to amide-containing counterparts. Ru-hybrid TRZ2 exhibits also antitumor efficacy against in vivo drug-resistant cancer cells. Mechanistically, we demonstrate that Ru-TRZ hybrids induce apoptosis. In addition, by activating downstream RIPK3-driven cell death, TRZ2 proficiently restrains normal mitochondrial function and activity, leading to cancer cell necroptosis. Finally, TRZ2 synergizes anti-proliferative activity and cell death effects induced by conventional drugs. In conclusion, Ru-TRZ2 stands as a promising ruthenium-based chemotherapeutic agent inducing necroptosis in drug resistant cancer cells.
Small body size is associated with increased evolutionary lability of wing skeleton proportions in birds
Authors: Orkney Andrew , Hedrick Brandon P.
Published: May 2024

Birds are represented by 11,000 species and a great variety of body masses. Modular organisation of trait evolution across birds has facilitated simultaneous adaptation of different body regions to divergent ecological requirements. However, the role modularity has played in avian body size evolution, especially small-bodied, rapidly evolving and diverse avian subclades, such as hummingbirds and songbirds, is unknown. Modularity is influenced by the intersection of biomechanical restrictions, adaptation, and developmental controls, making it difficult to uncover the contributions of single factors such as body mass to skeletal organisation. We develop a novel framework to decompose this complexity, assessing factors underlying the modularity of skeletal proportions in fore-limb propelled birds distributed across a range of body masses. We demonstrate that differences in body size across birds triggers a modular reorganisation of flight apparatus proportions consistent with biomechanical expectations. We suggest weakened integration within the wing facilitates radiation in small birds. Our framework is generalisable to other groups and has the capacity to untangle the multi-layered complexity intrinsic to modular evolution.
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater
Authors: Liu Yunxi , Sapoval Nicolae , Gallego-García Pilar , Tomás Laura , Posada David , Treangen Todd J. , Stadler Lauren B.
Published: May 2024

Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.
A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions
Authors: Liu Yuan , Li Dianke , Zhang Xin , Xia Simin , Qu Yingjie , Ling Xinping , Li Yang , Kong Xiangren , Zhang Lingqiang , Cui Chun-Ping , Li Dong
Published: May 2024

Protein ubiquitination regulates a wide range of cellular processes. The degree of protein ubiquitination is determined by the delicate balance between ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase (DUB)-mediated deubiquitination. In comparison to the E3-substrate interactions, the DUB-substrate interactions (DSIs) remain insufficiently investigated. To address this challenge, we introduce a protein sequence-based ab initio method, TransDSI, which transfers proteome-scale evolutionary information to predict unknown DSIs despite inadequate training datasets. An explainable module is integrated to suggest the critical protein regions for DSIs while predicting DSIs. TransDSI outperforms multiple machine learning strategies against both cross-validation and independent test. Two predicted DUBs (USP11 and USP20) for FOXP3 are validated by “wet lab” experiments, along with two predicted substrates (AR and p53) for USP22. TransDSI provides new functional perspective on proteins by identifying regulatory DSIs, and offers clues for potential tumor drug target discovery and precision drug application.
ARPES detection of superconducting gap sign in unconventional superconductors
Authors: Gao Qiang , Bok Jin Mo , Ai Ping , Liu Jing , Yan Hongtao , Luo Xiangyu , Cai Yongqing , Li Cong , Wang Yang , Yin Chaohui , Chen Hao , Gu Genda , Zhang Fengfeng , Yang Feng , Zhang Shenjin , Peng Qinjun , Zhu Zhihai , Liu Guodong , Xu Zuyan , Xiang Tao , Zhao Lin , Choi Han-Yong , Zhou X. J.
Published: May 2024

The superconducting gap symmetry is crucial in understanding the underlying superconductivity mechanism. Angle-resolved photoemission spectroscopy (ARPES) has played a key role in determining the gap symmetry in unconventional superconductors. However, it has been considered so far that ARPES can only measure the magnitude of the superconducting gap but not its phase; the phase has to be detected by other phase-sensitive techniques. Here we propose a method to directly detect the superconducting gap sign by ARPES. This method is successfully validated in a cuprate superconductor Bi2Sr2CaCu2O8+δ with a well-known d-wave gap symmetry. When two bands have a strong interband interaction, the resulted electronic structures in the superconducting state are sensitive to the relative gap sign between the two bands. Our present work provides an approach to detect the gap sign and can be applied to various superconductors, particularly those with multiple orbitals like the iron-based superconductors.
Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms
Authors: Inamo Jun , Suzuki Akari , Ueda Mahoko Takahashi , Yamaguchi Kensuke , Nishida Hiroshi , Suzuki Katsuya , Kaneko Yuko , Takeuchi Tsutomu , Hatano Hiroaki , Ishigaki Kazuyoshi , Ishihama Yasushi , Yamamoto Kazuhiko , Kochi Yuta
Published: May 2024

Alternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer’s disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3’-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.
Memory CD8 T cells are vulnerable to chronic IFN-γ signals but not to CD4 T cell deficiency in MHCII-deficient mice
Authors: Setoguchi Ruka , Sengiku Tomoya , Kono Hiroki , Kawakami Eiryo , Kubo Masato , Yamamoto Tadashi , Hori Shohei
Published: May 2024

The mechanisms by which the number of memory CD8 T cells is stably maintained remains incompletely understood. It has been postulated that maintaining them requires help from CD4 T cells, because adoptively transferred memory CD8 T cells persist poorly in MHC class II (MHCII)-deficient mice. Here we show that chronic interferon-γ signals, not CD4 T cell-deficiency, are responsible for their attrition in MHCII-deficient environments. Excess IFN-γ is produced primarily by endogenous colonic CD8 T cells in MHCII-deficient mice. IFN-γ neutralization restores the number of memory CD8 T cells in MHCII-deficient mice, whereas repeated IFN-γ administration or transduction of a gain-of-function STAT1 mutant reduces their number in wild-type mice. CD127high memory cells proliferate actively in response to IFN-γ signals, but are more susceptible to attrition than CD127low terminally differentiated effector memory cells. Furthermore, single-cell RNA-sequencing of memory CD8 T cells reveals proliferating cells that resemble short-lived, terminal effector cells and documents global downregulation of gene signatures of long-lived memory cells in MHCII-deficient environments. We propose that chronic IFN-γ signals deplete memory CD8 T cells by compromising their long-term survival and by diverting self-renewing CD127high cells toward terminal differentiation.
Control of artificial membrane fusion in physiological ionic solutions beyond the limits of electroformation
Authors: Kim Bong Kyu , Kang Dong-Hyun , Woo Junhyuk , Yoon Wooseung , Ryu Hyunil , Han Kyungreem , Chung Seok , Kim Tae Song
Published: May 2024

Membrane fusion, merging two lipid bilayers, is crucial for fabricating artificial membrane structures. Over the past 40 years, in contrast to precise and controllable membrane fusion in-vivo through specific molecules such as SNAREs, controlling the fusion in-vitro while fabricating artificial membrane structures in physiological ionic solutions without fusion proteins has been a challenge, becoming a significant obstacle to practical applications. We present an approach consisting of an electric field and a few kPa hydraulic pressure as an additional variable to physically control the fusion, enabling tuning of the shape and size of the 3D freestanding lipid bilayers in physiological ionic solutions. Mechanical model analysis reveals that pressure-induced parallel/normal tensions enhance fusion among membranes in the microwell. In-vitro peptide-membrane assay, mimicking vesicular transport via pressure-assisted fusion, and stability of 38 days with in-chip pressure control via pore size-regulated hydrogel highlight the potential for diverse biological applications.
Uniformly elevated future heat stress in China driven by spatially heterogeneous water vapor changes
Authors: Wang Fan , Gao Meng , Liu Cheng , Zhao Ran , McElroy Michael B.
Published: May 2024

The wet bulb temperature (Tw) has gained considerable attention as a crucial indicator of heat-related health risks. Here we report south-to-north spatially heterogeneous trends of Tw in China over 1979-2018. We find that actual water vapor pressure (Ea) changes play a dominant role in determining the different trend of Tw in southern and northern China, which is attributed to the faster warming of high-latitude regions of East Asia as a response to climate change. This warming effect regulates large-scale atmospheric features and leads to extended impacts of the South Asia high (SAH) and the western Pacific subtropical high (WPSH) over southern China and to suppressed moisture transport. Attribution analysis using climate model simulations confirms these findings. We further find that the entire eastern China, that accommodates 94% of the country’s population, is likely to experience widespread and uniform elevated thermal stress the end of this century. Our findings highlight the necessity for development of adaptation measures in eastern China to avoid adverse impacts of heat stress, suggesting similar implications for other regions as well.
Emergence of a short peptide based reductase via activation of the model hydride rich cofactor
Authors: Chatterjee Ayan , Goswami Surashree , Kumar Raushan , Laha Janmejay , Das Dibyendu
Published: May 2024

In extant biology, large and complex enzymes employ low molecular weight cofactors such as dihydronicotinamides as efficient hydride transfer agents and electron carriers for the regulation of critical metabolic processes. In absence of complex contemporary enzymes, these molecular cofactors are generally inefficient to facilitate any reactions on their own. Herein, we report short peptide-based amyloid nanotubes featuring exposed arrays of cationic and hydrophobic residues that can bind small molecular weak hydride transfer agents (NaBH4) to facilitate efficient reduction of ester substrates in water. In addition, the paracrystalline amyloid phases loaded with borohydrides demonstrate recyclability, substrate selectivity and controlled reduction and surpass the capabilities of standard reducing agent such as LiAlH4. The amyloid microphases and their collaboration with small molecular cofactors foreshadow the important roles that short peptide-based assemblies might have played in the emergence of protometabolism and biopolymer evolution in prebiotic earth.
XPD stalled on cross-linked DNA provides insight into damage verification
Authors: Kuper Jochen , Hove Tamsanqa , Maidl Sarah , Neitz Hermann , Sauer Florian , Kempf Maximilian , Schroeder Till , Greiter Elke , Höbartner Claudia , Kisker Caroline
Published: May 2024

The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.
Solar-matched S-scheme ZnO/g-C3N4 for visible light-driven paracetamol degradation
Authors: Hassan Fahad , Backer Sumina Namboorimadathil , Almanassra Ismail W. , Ali Atieh Muataz , Elbahri Mady , Shanableh Abdallah
Published: May 2024

In pursuit of an efficient visible light driven photocatalyst for paracetamol degradation in wastewater, we have fabricated the ZnO/g-C3N4 S-Scheme photocatalysts and explored the optimal percentage to form a composite of graphitic carbon nitride (g-C3N4) with zinc oxide (ZnO) for enhanced performance. Our study aimed to address the urgent need for a catalyst capable of environmentally friendly degradation of paracetamol, a common pharmaceutical pollutant, using visible light conditions. Here, we tailored the band gap of a photocatalyst to match solar radiation as a transformative advancement in environmental catalysis. Notably, the optimized composite, containing 10 wt.% g-C3N4 with ZnO, demonstrated outstanding paracetamol degradation efficiency of 95% within a mere 60-min exposure to visible light. This marked enhancement represented a 2.24-fold increase in the reaction rate compared to lower wt. percentage composites (3 wt.% g-C3N4) and pristine g-C3N4. The exceptional photocatalytic activity of the optimized composite can be attributed to the band gap narrowing that closely matched the maximum solar radiation spectrum. This, coupled with efficient charge transfer mechanisms through S-scheme heterojunction formation and an abundance of active sites due to increased surface area and reduced particle size, contributed to the remarkable performance. Trapping experiments identified hydroxyl radicals as the primary reactive species responsible for paracetamol photoreduction. Furthermore, the synthesized ZnO/g-C3N4 composite exhibited exceptional photostability and reusability, underscoring its practical applicability. Thus, this research marks a significant stride towards the development of an effective and sustainable visible light photocatalyst for the removal of pharmaceutical contaminants from aquatic environments.
Modeling security evaluation framework for IoHT-driven systems using integrated decision-making methodology
Authors: Khan Habib Ullah , Ali Yasir
Published: May 2024

The intensification of the Internet of Health Things devices created security concerns due to the limitations of these devices and the nature of the healthcare data. While dealing with the security challenges, several authentication schemes, protocols, processes, and standards have been adopted. Consequently, making the right decision regarding the installation of a secure authentication solution or procedure becomes tricky and challenging due to the large number of security protocols, complexity, and lack of understanding. The major objective of this study is to propose an IoHT-based assessment framework for evaluating and prioritizing authentication schemes in the healthcare domain. Initially, in the proposed work, the security issues related to authentication are collected from the literature and consulting experts’ groups. In the second step, features of various authentication schemes are collected under the supervision of an Internet of Things security expert using the Delphi approach. The collected features are used to design suitable criteria for assessment and then Graph Theory and Matrix approach applies for the evaluation of authentication alternatives. Finally, the proposed framework is tested and validated to ensure the results are consistent and accurate by using other multi-criteria decision-making methods. The framework produces promising results such as 93%, 94%, and 95% for precision, accuracy, and recall, respectively in comparison to the existing approaches in this area. The proposed framework can be picked as a guideline by healthcare security experts and stakeholders for the evaluation and decision-making related to authentication issues in IoHT systems
Investigates the ability of plant extracts from Lens culinaris to protect zucchini from the Zucchini yellow mosaic virus (ZYMV)
Authors: Ali Rania , Eldidamony Gamal , Askora Ahmed , Galal Abdelmoneim
Published: May 2024

Evaluate the impact of extracts from the Lens culinaris plant on a number of physiological and biochemical parameters in squash leaves infected with ZYMV in this work. Compared to the untreated leaves, ZYMV infected leaves showed a range of symptoms, such as severe mosaic, size reduction, stunting, and deformation. Analysis of physiological data revealed that L. culinaris extract lectin therapies and viral infections had an impact on metabolism. Protein, carbohydrate, and pigment levels were all lowered by viral infection. However, phenolic compounds, total protein, total carbohydrates, total amino acids, proline, total chlorophyll and peroxidases levels are considerably elevated with all extract therapies. The other biochemical parameters also displayed a variety of changes. Moreover shoot length, number of leaves and number of flowers was significantly increased compared to viral control in all treatments. The L. culinaris extract treatment increases the plant’s ZYMV resistance. This is detectable through reduction of the plants treated with lentil lectin pre and post virus inoculation, reduction in disease severity and viral concentration, and percentage of the infected plants has a virus. All findings demonstrate significant metabolic alterations brought by viral infections or L. culinaris extract treatments, and they also suggest that exogenous extract treatments is essential for activating the body’s defences against ZYMV infection.
Temperature-dependent iron motion in extremophile rubredoxins – no need for ‘corresponding states’
Authors: Jenney Francis E. , Wang Hongxin , George Simon J. , Xiong Jin , Guo Yisong , Gee Leland B. , Marizcurrena Juan José , Castro-Sowinski Susana , Staskiewicz Anna , Yoda Yoshitaka , Hu Michael Y. , Tamasaku Kenji , Nagasawa Nobumoto , Li Lei , Matsuura Hiroaki , Doukov Tzanko , Cramer Stephen P.
Published: May 2024

Extremophile organisms are known that can metabolize at temperatures down to − 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins – rubredoxins – from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of ‘corresponding states’ posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although ‘corresponding states’ would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
Fully-automated CT derived body composition analysis reveals sarcopenia in functioning adrenocortical carcinomas
Authors: Santhanam Prasanna , Dinparastisaleh Roshan , Popuri Karteek , Faisal Beg Mirza , Chen Cardenas Stanley M. , Hamrahian Amir
Published: May 2024

Determination of body composition (the relative distribution of fat, muscle, and bone) has been used effectively to assess the risk of progression and overall clinical outcomes in different malignancies. Sarcopenia (loss of muscle mass) is especially associated with poor clinical outcomes in cancer. However, estimation of muscle mass through CT scan has been a cumbersome, manually intensive process requiring accurate contouring through dedicated personnel hours. Recently, fully automated technologies that can determine body composition in minutes have been developed and shown to be highly accurate in determining muscle, bone, and fat mass. We employed a fully automated technology, and analyzed images from a publicly available cancer imaging archive dataset (TCIA) and a tertiary academic center. The results show that adrenocortical carcinomas (ACC) have relatively sarcopenia compared to benign adrenal lesions. In addition, functional ACCs have accelerated sarcopenia compared to non-functional ACCs. Further longitudinal research might shed further light on the relationship between body component distribution and ACC prognosis, which will help us incorporate more nutritional strategies in cancer therapy.
Oral health in youth with visual impairment: A longitudinal survey
Authors: Křížová Petra , Himmlová Lucie , Chramosta Petr , Vařejčko David , Vašáková Jana , Urbanová Wanda
Published: May 2024

This longitudinal survey aims to demonstrate improvement in oral hygiene among a group of youth with visual impairment (VI) achieved by repeated oral hygiene training, compare their progress with healthy peers (CG) and assess their oral health knowledge. In 100 VI (55♀, 45♂; ± 17.8 years) and 45 CG (23♀, 22♂; ± 17.2 years) oral hygiene training and a Quigley-Hein Plaque Index (QHI) rating were repeated six times at three-month intervals. The VI were divided into four subgroups according to the toothbrush hardness/type. A questionnaire was given to both groups. Appropriate statistical analyses were performed at 5% significance level. Both groups showed reduction in QHI, the VI had overall higher QHI values than CG. Use of an electric toothbrush in VI led to lower QHI in the last examination (p < 0.03). 69% of participants recommended dental specialists to improve communications by acquiring more illustrative aids. VI changed toothbrush less often (p < 0.02). A higher incidence of dental plaque was confirmed in VI compared to CG. After education and individual training, gradual plaque reduction has occurred in both groups. Using an electric toothbrush in VI resulted in better QHI outcomes. Repetitive preventive intervention in youth with VI helped them to adopt healthier oral hygiene habits.
Association between atherosclerotic cardiovascular disease score and skin carotenoid levels estimated via refraction spectroscopy in the Japanese population: a cross-sectional study
Authors: Obana Akira , Nakamura Mieko , Miura Ayako , Nozue Miho , Muto Shigeki , Asaoka Ryo
Published: May 2024

Carotenoids play a role in preventing and impeding the progression of atherosclerotic cardiovascular diseases (ASCVDs) through their anti-oxidative effects. This study evaluated associations between ASCVD risk and skin carotenoid (SC) levels, reflecting dietary carotenoid intake. Participants’ ASCVD risk was assessed using the Hisayama ASCVD risk prediction model, and SC levels were measured through a reflection spectroscope (Veggie Meter). The associations between high ASCVD risk and SC levels were analyzed using logistic regression analysis and a restricted cubic spline (RCS) model. A total of 1130 men and women (mean age: 56 years) from participants who underwent a health examination in Seirei Center for Health Promotion and Prevention Medicine in 2019 and 2022 were analyzed. Of these, 4.6% had moderate or high ASCVD risk. Mean SC values were 236, 315, 376, 447, and 606 in quintile Q1 to Q5, respectively. The adjusted odds ratios (95% confidence intervals) of SC quintile for moderate- or high-risk ASCVD was 0.24 (0.12–0.51) in Q5 (495 ≤), 0.42 (0.23–0.77) in Q4, 0.50 (0.29–0.88) in Q3, and 0.68 (0.41–1.12) in Q2 compared to Q1 (< 281). High SC values continuously showed non-linear inverse association with moderate- or high-risk for ASCVD in Japanese adults. Non-invasive SC measurements may be a good indicator for recommending carotenoids to prevent cardiovascular disease.
In vivo phage display identifies novel peptides for cardiac targeting
Authors: Ivanova Alena , Kohl Franziska , González-King Garibotti Hernán , Chalupska Renata , Cvjetkovic Aleksander , Firth Mike , Jennbacken Karin , Martinsson Sofia , Silva Andreia M. , Viken Ida , Wang Qing-Dong , Wiseman John , Dekker Niek
Published: May 2024

Heart failure remains a leading cause of mortality. Therapeutic intervention for heart failure would benefit from targeted delivery to the damaged heart tissue. Here, we applied in vivo peptide phage display coupled with high-throughput Next-Generation Sequencing (NGS) and identified peptides specifically targeting damaged cardiac tissue. We established a bioinformatics pipeline for the identification of cardiac targeting peptides. Hit peptides demonstrated preferential uptake by human induced pluripotent stem cell (iPSC)-derived cardiomyocytes and immortalized mouse HL1 cardiomyocytes, without substantial uptake in human liver HepG2 cells. These novel peptides hold promise for use in targeted drug delivery and regenerative strategies and open new avenues in cardiovascular research and clinical practice.
SARS-CoV-2 detection in pediatric dental clinic wastewater reflects the number of local COVID-19 cases in children under 10 years old
Authors: Kanamori Dai , Sakai Jun , Iijima Takahiro , Oono Yuka , Malla Bikash , Haramoto Eiji , Hayakawa Satoshi , Komine-Aizawa Shihoko , Maesaki Shigefumi , Vorup-Jensen Thomas , Kilgore Paul Evan , Kohase Hikaru , Hoshino Tomonori , Seki Mitsuko
Published: May 2024

This was the first longitudinal study to analyze dental clinic wastewater to estimate asymptomatic SARS-CoV-2 infection trends in children. We monitored wastewater over a 14-month period, spanning three major COVID-19 waves driven by the Alpha, Delta, and Omicron variants. Each Saturday, wastewater was sampled at the Pediatric Dental Clinic of the only dental hospital in Japan’s Saitama Prefecture. The relationship between the weekly number of cases in Saitama Prefecture among residents aged < 10 years (exposure) and wastewater SARS-CoV-2 RNA detection (outcome) was examined. The number of cases was significantly associated with wastewater SARS-CoV-2 RNA positivity (risk ratio, 5.36; 95% confidence interval, 1.72–16.67; Fisher’s exact test, p = 0.0005). A sample from Week 8 of 2022 harbored the Omicron variant. Compared to sporadic individual testing, this approach allows continuous population-level surveillance, which is less affected by healthcare seeking and test availability. Since wastewater from pediatric dental clinics originates from the oral cavities of asymptomatic children, such testing can provide important information regarding asymptomatic COVID-19 in children, complementing clinical pediatric data.
Numerical simulation of the influence of nasal cycle on nasal airflow
Authors: Wei Jing , He Xuan , Yang Qing , Gu Qifei , Zhang Xiaodan , Sui Xue , Zhou Rui , Feng Wei
Published: May 2024

To study the characteristics of nasal airflow in the presence of nasal cycle by computational fluid dynamics. CT scan data of a healthy Chinese individual was used to construct a three-dimensional model of the nasal cavity to be used as simulation domain. A sinusoidal airflow velocity is set at the nasal cavity entrance to reproduce the breathing pattern of a healthy human. There was a significant difference in the cross-sectional area between the two sides of the nasal cavity. Particularly, the decongested side is characterized by a larger cross-section area, and consequently, by a larger volume with respect to the congested side. The airflow velocity, pressure, and nasal resistance were higher on the congested narrow side. The temperature regulation ability on the congested narrow side was stronger than that on the decongested wider side. During the nasal cycle, there are differences in the nasal cavity function between the congested and decongested sides. Therefore, when evaluating the impact of various factors on nasal cavity function, the nasal cycle should be considered.
Expression and potential molecular mechanism of TOP2A in metastasis of non-small cell lung cancer
Authors: Wu Jiatao , Li Wenjuan , Zhang Xueying , Shi Fan , Jia Qianhao , Wang Yufei , Shi Yuqi , Wu Shiwu , Wang Xiaojing
Published: May 2024

DNA topoisomerase II alpha (TOP2A) expression, gene alterations, and enzyme activity have been studied in various malignant tumors. Abnormal elevation of TOP2A expression is considered to be related to the development of non-small cell lung cancer (NSCLC). However, its association with tumor metastasis and its mode of action remains unclear. Bioinformatics, real-time quantitative PCR, immunohistochemistry and immunoblotting were used to detect TOP2A expression in NSCLC tissues and cells. Cell migration and invasion assays as well as cytoskeletal staining were performed to analyze the effects of TOP2A on the motility, migration and invasion ability of NSCLC cells. Cell cycle and apoptosis assays were used to verify the effects of TOP2A on apoptosis as well as cycle distribution in NSCLC. TOP2A expression was considerably upregulated in NSCLC and significantly correlated with tumor metastasis and the occurrence of epithelial–mesenchymal transition (EMT) in NSCLC. Additionally, by interacting with the classical ligand Wnt3a, TOP2A may trigger the canonical Wnt signaling pathway in NSCLC. These observations suggest that TOP2A promotes EMT in NSCLC by activating the Wnt/β-catenin signaling pathway and positively regulates malignant events in NSCLC, in addition to its significant association with tumor metastasis. TOP2A promotes the metastasis of NSCLC by stimulating the canonical Wnt signaling pathway and inducing EMT. This study further elucidates the mechanism of action of TOP2A, suggesting that it might be a potential therapeutic target for anti-metastatic therapy.