bluuebunny/crossref_metadata_2025 huggingface dataset:
Making manifestos for urban history: creative collaboration in a conference workshop
Authors: Faire Lucy , McHugh Denise , Williams Chris A.
Published: April 2024

This survey reflects on a creative workshop which the authors ran for the ‘The State of Urban History: Past, Present, Future’ conference (July 2023). ‘Making manifestos for urban history’ was an experiment to encourage small group work and co-operative outputs in a conference setting, allowing for an atypical ‘many-to-many’ model of participation. During the session, five groups each produced a manifesto poster addressing issues that they thought were important for the future of urban history. The survey sets out the form the workshop followed, considers those who were involved and comments on how successful the workshop was in fostering conference community and active learning. Feedback recorded at the end of the session indicated that it was indeed successful in both these areas. Overall, the workshop demonstrated that when urban historians work together across generations and continents, they produce work of real value, which is resilient and sustainable.
Making the global turn matter: strategies and pathways
Authors: Lees Lynn Hollen
Published: April 2024

The survey examines the past, present and future of the urban history field in Britain, mixing memories and reflections. I trace the global turn of that field and the challenges it brings. One argument concerns the impact of a global scale on the methods and the explanatory frameworks used. A second concern is the role of economic history and economic frameworks of analysis in the writing of urban history, and I advocate their continued relevance.
Digital Transformations of Public Administration in the Context of the COVID-19 Pandemic: EU Countries Case Study
Authors: Savchenko Nataliia , Fedirko Oleksandr , Muravytska Hanna , Fedirko Nataliia , Nemyrovska Oksana
Published: April 2024

The digital transformation of public administration and public services has become an urgent need for many governments around the world. This article aims to explore the homogeneity and pace of digital transformation of public administration through the impact of the COVID-19 pandemic and to identify problems and forecasts of research processes at the EU level. The method of cluster analysis was used to study the similarity of the digital transformation of public administration in the EU. The pace of digitalization of public administration in the context of the COVID-19 pandemic was studied through trend analysis. The results show that the EU countries, according to the level of public administration digitalization, are grouped into five clusters, between which there are significant digital gaps. The COVID-19 pandemic has widened the gaps, potentially impacting the EU’s strategy for digitalizing society and establishing e-government. Public e-services usage in 2020 to 2021 is higher than predicted by trend analysis for 2009 to 2019. This suggests an acceleration of digitalization in the EU during the COVID-19 pandemic. The proposed technique can be used to predict the level of digitization of any country or group of countries.
Substance or Noise?
Authors: Meisters Julia , Hoffmann Adrian , Musch Jochen
Published: April 2024

Abstract: Indirect questioning techniques aim to provide more valid prevalence estimates for sensitive attributes than conventional direct questions. Despite being an important prerequisite for high estimation validity, indirect questioning techniques’ retest stability has rarely been addressed. For temporally stable attributes, high stability of both prevalence estimates and individual responses is expected; however, insufficient understanding of the instructions and random response behavior may compromise retest stability. The present study is the first to assess the retest stability of the Extended Crosswise Model (ECWM), a recent indirect questioning technique, and to compare it to the retest stability of a conventional direct question (DQ). With a retest interval of approximately 10 days, we asked N = 2,317 mothers twice whether they had smoked during a previous pregnancy. In both ECWM and DQ conditions, prevalence estimates were virtually identical over time, and most respondents answered consistently (ECWM: 89%, DQ: 95%). In the ECWM condition, inconsistent response behavior was slightly more prevalent and negatively associated with respondents’ education. However, as these effects were small, the retest stability of both ECWM and DQ in surveys on sensitive attributes was evaluated as high.
Spontaneous Formation of an Internal Shear Band in Ice Flowing Over Topographically Variable Bedrock
Authors: Liu Emma Weijia , Räss Ludovic , Herman Frédéric , Podladchikov Yury , Suckale Jenny
Published: April 2024

Ice surface speed increases dramatically from upstream to downstream in many ice streams and glaciers. This speed‐up is thought to be associated with a transition from internal distributed deformation to highly localized deformation or sliding at the ice‐bedrock interface. The physical processes governing this transition remain unclear. Here, we argue that highly localized deformation does not necessarily initiate at the ice‐bedrock interface, but could also take the form of an internal shear band inside the ice flow that connects topographic highs. The power‐law exponent n in the ice rheology amplifies the feedback between shear heating and shear localization, leading to the spontaneous formation of an internal shear band that can create flow separation within the ice. We model the thermomechanical ice flow over a sinusoidal basal topography by building on the high‐resolution Stokes solver FastICE v1.0. We compile a regime diagram summarizing cases in which a sinusoidal topography with a given amplitude and wavelength leads to shear band formation for a given rheology. We compare our model results to borehole measurements from Greenland and find evidence to support the existence of an internal shear band. Our study highlights the importance of re‐evaluating the degree to which internal deformation contributes to total deformation in the ice column and to the flow‐to‐sliding transition.
The Incomplete Record of Autogenic Processes Sets Limits on Signal Detectability
Authors: Griffin C. , Duller R. A. , Straub K. M.
Published: April 2024

Spectral analysis is a central tool regularly used by the scientific community to identify the presence of periodic processes within a time series of information, as spectral peaks at an imposed periodicity can be differentiated from internal (autogenic) variance. In scientific disciplines, such as seismology, the time series of information is of high temporal resolution. Hence, although temporal gaps are present, they do not impact the overall noise structure, meaning that the full spectrum of autogenic variance can be reconstructed. However, power spectra generated from stratigraphic information are affected by temporal incompleteness due to varying episodes of erosion and geomorphic stasis, which generate gaps over a range of scales. This removes information related to the natural and autogenic variability present within sediment‐transport systems, which makes it challenging to accurately reconstruct the structure and strength of paleo‐surface processes, which defines the detectability of past environmental signals. We explore how incompleteness impacts the temporal structure of autogenic noise within power spectra, and how this influences the detectability of spectral spikes related to environmental signals. We utilize a sediment flux time series from a physical rice pile and progressively degrade these data to mimic varying degrees of stratigraphic incompleteness. We find that incompleteness strongly influences the timescales and spectral structure of autogenic noise evident, and can render signals over all periodicities undetectable within a highly incomplete time series. This offers the ability to confidently justify the interpretation of subtle environmental signals from field measurements and understand the records that may best preserve paleoenvironmental variability.
Adeno-associated virus as a delivery vector for gene therapy of human diseases
Authors: Wang Jiang-Hui , Gessler Dominic J. , Zhan Wei , Gallagher Thomas L. , Gao Guangping
Published: April 2024

Adeno-associated virus (AAV) has emerged as a pivotal delivery tool in clinical gene therapy owing to its minimal pathogenicity and ability to establish long-term gene expression in different tissues. Recombinant AAV (rAAV) has been engineered for enhanced specificity and developed as a tool for treating various diseases. However, as rAAV is being more widely used as a therapy, the increased demand has created challenges for the existing manufacturing methods. Seven rAAV-based gene therapy products have received regulatory approval, but there continue to be concerns about safely using high-dose viral therapies in humans, including immune responses and adverse effects such as genotoxicity, hepatotoxicity, thrombotic microangiopathy, and neurotoxicity. In this review, we explore AAV biology with an emphasis on current vector engineering strategies and manufacturing technologies. We discuss how rAAVs are being employed in ongoing clinical trials for ocular, neurological, metabolic, hematological, neuromuscular, and cardiovascular diseases as well as cancers. We outline immune responses triggered by rAAV, address associated side effects, and discuss strategies to mitigate these reactions. We hope that discussing recent advancements and current challenges in the field will be a helpful guide for researchers and clinicians navigating the ever-evolving landscape of rAAV-based gene therapy.
Mex-3 RNA binding family member A (MEX3A)/circMPP6 complex promotes colorectal cancer progression by inhibiting autophagy
Authors: Chen Ri-Xin , Xu Shui-Dan , Deng Min-Hua , Hao Shi-Hui , Chen Jie-Wei , Ma Xiao-Dan , Zhuang Wei-Tao , Cao Jing-Hua , Lv Yong-Rui , Lin Jin-Long , Li Si-Yu , Qiao Gui-Bin , Xie Dan , Wang Feng-Wei
Published: April 2024

RNA-binding proteins (RBPs)-RNA networks have contributed to cancer development. Circular RNAs (circRNAs) are considered as protein recruiters; nevertheless, the patterns of circRNA-protein interactions in colorectal cancer (CRC) are still lacking. Processing bodies (PBs) formed through liquid-liquid phase separation (LLPS) are membrane-less organelles (MLOs) consisting of RBPs and RNA. Previous evidence suggests a connection between PBs dynamics and cancer progression. Despite the increasingly acknowledged crucial role of RBPs and RNA in the accumulation and maintenance of MLOs, there remains a lack of specific research on the interactions between PBs-related RBPs and circRNAs in CRC. Herein, we identify that MEX-3 RNA binding family member A (MEX3A), frequently upregulated in CRC tissues, predicts poorer patient survival. Elevated MEX3A accelerates malignance and inhibits autophagy of CRC cells. Importantly, MEX3A undergoes intrinsically disordered regions (IDRs)-dependent LLPS in the cytoplasm. Specifically, circMPP6 acts as a scaffold to facilitate the interaction between MEX3A and PBs proteins. The MEX3A/circMPP6 complex modulates PBs dynamic and promotes UPF-mediated phosphodiesterase 5A (PDE5A) mRNA degradation, consequently leading to the aggressive properties of CRC cells. Clinically, CRC patients exhibiting high MEX3A expression and low PDE5A expression have the poorest overall survival. Our findings reveal a collaboration between MEX3A and circMPP6 in the regulation of mRNA decay through triggering the PBs aggregation, which provides prognostic markers and/or therapeutic targets for CRC.
XELOX (capecitabine plus oxaliplatin) plus bevacizumab (anti-VEGF-A antibody) with or without adoptive cell immunotherapy in the treatment of patients with previously untreated metastatic colorectal cancer: a multicenter, open-label, randomized, controlled, phase 3 trial
Authors: Pan Qiu-Zhong , Zhao Jing-Jing , Liu Liang , Zhang Dong-Sheng , Wang Li-Ping , Hu Wen-Wei , Weng De-Sheng , Xu Xiang , Li Yi-Zhuo , Tang Yan , Zhang Wei-Hong , Li Jie-Yao , Zheng Xiao , Wang Qi-Jing , Li Yong-Qiang , Xiang Tong , Zhou Li , Yang Shuang-Ning , Wu Chen , Huang Rong-Xing , He Jia , Du Wei-Jiao , Chen Lu-Jun , Wu Yue-Na , Xu Bin , Shen Qiong , Zhang Yi , Jiang Jing-Ting , Ren Xiu-Bao , Xia Jian-Chuan
Published: April 2024

Fluoropyrimidine-based combination chemotherapy plus targeted therapy is the standard initial treatment for unresectable metastatic colorectal cancer (mCRC), but the prognosis remains poor. This phase 3 trial (ClinicalTrials.gov: NCT03950154) assessed the efficacy and adverse events (AEs) of the combination of PD-1 blockade-activated DC-CIK (PD1-T) cells with XELOX plus bevacizumab as a first-line therapy in patients with mCRC. A total of 202 participants were enrolled and randomly assigned in a 1:1 ratio to receive either first-line XELOX plus bevacizumab (the control group, n = 102) or the same regimen plus autologous PD1-T cell immunotherapy (the immunotherapy group, n = 100) every 21 days for up to 6 cycles, followed by maintenance treatment with capecitabine and bevacizumab. The main endpoint of the trial was progression-free survival (PFS). The median follow-up was 19.5 months. Median PFS was 14.8 months (95% CI, 11.6–18.0) for the immunotherapy group compared with 9.9 months (8.0–11.8) for the control group (hazard ratio [HR], 0.60 [95% CI, 0.40–0.88]; p = 0.009). Median overall survival (OS) was not reached for the immunotherapy group and 25.6 months (95% CI, 18.3–32.8) for the control group (HR, 0.57 [95% CI, 0.33–0.98]; p = 0.043). Grade 3 or higher AEs occurred in 20.0% of patients in the immunotherapy group and 23.5% in the control groups, with no toxicity-associated deaths reported. The addition of PD1-T cells to first-line XELOX plus bevacizumab demonstrates significant clinical improvement of PFS and OS with well tolerability in patients with previously untreated mCRC.
Overcoming barriers to single-cell RNA sequencing adoption in low- and middle-income countries
Authors: Boakye Serebour Tracy , Cribbs Adam P. , Baldwin Mathew J. , Masimirembwa Collen , Chikwambi Zedias , Kerasidou Angeliki , Snelling Sarah J. B.
Published: April 2024

The advent of single-cell resolution sequencing and spatial transcriptomics has enabled the delivery of cellular and molecular atlases of tissues and organs, providing new insights into tissue health and disease. However, if the full potential of these technologies is to be equitably realised, ancestrally inclusivity is paramount. Such a goal requires greater inclusion of both researchers and donors in low- and middle-income countries (LMICs). In this perspective, we describe the current landscape of ancestral inclusivity in genomic and single-cell transcriptomic studies. We discuss the collaborative efforts needed to scale the barriers to establishing, expanding, and adopting single-cell sequencing research in LMICs and to enable globally impactful outcomes of these technologies.
Machine-learning potentials for nanoscale simulations of tensile deformation and fracture in ceramics
Authors: Lin Shuyao , Casillas-Trujillo Luis , Tasnádi Ferenc , Hultman Lars , Mayrhofer Paul H. , Sangiovanni Davide G. , Koutná Nikola
Published: April 2024

Machine-learning interatomic potentials (MLIPs) offer a powerful avenue for simulations beyond length and timescales of ab initio methods. Their development for investigation of mechanical properties and fracture, however, is far from trivial since extended defects—governing plasticity and crack nucleation in most materials—are too large to be included in the training set. Using TiB2 as a model ceramic material, we propose a training strategy for MLIPs suitable to simulate mechanical response of monocrystals until failure. Our MLIP accurately reproduces ab initio stresses and fracture mechanisms during room-temperature uniaxial tensile deformation of TiB2 at the atomic scale ( ≈ 103 atoms). More realistic tensile tests (low strain rate, Poisson’s contraction) at the nanoscale ( ≈ 104–106 atoms) require MLIP up-fitting, i.e., learning from additional ab initio configurations. Consequently, we elucidate trends in theoretical strength, toughness, and crack initiation patterns under different loading directions. As our MLIP is specifically trained to modelling tensile deformation, we discuss its limitations for description of different loading conditions and lattice structures with various Ti/B stoichiometries. Finally, we show that our MLIP training procedure is applicable to diverse ceramic systems. This is demonstrated by developing MLIPs which are subsequently validated by simulations of uniaxial strain and fracture in TaB2, WB2, ReB2, TiN, and Ti2AlB2.
Organic carbon source controlled microbial olivine dissolution in small-scale flow-through bioreactors, for CO2 removal
Authors: Corbett Thomas D. W. , Westholm Marcus , Rosling Anna , Calogiuri Tullia , Poetra Reinaldy , Niron Harun , Hagens Mathilde , Vidal Alix , Van Groenigen Jan Willem , Hartmann Jens , Janssens Ivan A. , Rieder Lukas , Struyf Eric , Van Tendeloo Michiel , Vlaeminck Siegfried E. , Vicca Sara , Neubeck Anna
Published: April 2024

The development of carbon dioxide removal methods, coupled with decreased CO2 emissions, is fundamental to achieving the targets outlined in the Paris Agreement limiting global warming to 1.5 °C. Here we are investigating the importance of the organic carbon feedstock to support silicate mineral weathering in small-scale flow through bioreactors and subsequent CO2 sequestration. Here, we combine two bacteria and two fungi, widely reported for their weathering potential, in simple flow through bioreactors (columns) consisting of forsterite and widely available, cheap organic carbon sources (wheat straw, bio-waste digestate of pig manure and biowaste, and manure compost), over six weeks. Compared to their corresponding abiotic controls, the inoculated straw and digestate columns release more total alkalinity (~2 times more) and produce greater dissolved and solid inorganic carbon (29% for straw and 13% for digestate), suggesting an increase in CO2 sequestration because of bio-enhanced silicate weathering. Microbial biomass is higher in the straw columns compared to the digestate and manure compost columns, with a phospholipid fatty acid derived total microbial biomass 10 x greater than the other biotic columns. Scanning Electron Microscopy imaging shows the most extensive colonisation and biofilm formation on the mineral surfaces in the straw columns. The biotic straw and digestate columns sequester 50 and 14 mg C more than their abiotic controls respectively, while there is no difference in the manure columns. The selection of organic carbon sources to support microbial communities in the flow through bioreactors controlls the silicate weathering rates and CO2 sequestration.
Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections
Authors: Mahout Maxime , Carlson Ross P. , Simon Laurent , Peres Sabine
Published: April 2024

Minimal Cut Sets (MCSs) identify sets of reactions which, when removed from a metabolic network, disable certain cellular functions. The traditional search for MCSs within genome-scale metabolic models (GSMMs) targets cellular growth, identifies reaction sets resulting in a lethal phenotype if disrupted, and retrieves a list of corresponding gene, mRNA, or enzyme targets. Using the dual link between MCSs and Elementary Flux Modes (EFMs), our logic programming-based tool aspefm was able to compute MCSs of any size from GSMMs in acceptable run times. The tool demonstrated better performance when computing large-sized MCSs than the mixed-integer linear programming methods. We applied the new MCSs methodology to a medically-relevant consortium model of two cross-feeding bacteria, Staphylococcus aureus and Pseudomonas aeruginosa. aspefm constraints were used to bias the computation of MCSs toward exchanged metabolites that could complement lethal phenotypes in individual species. We found that interspecies metabolite exchanges could play an essential role in rescuing single-species growth, for instance inosine could complement lethal reaction knock-outs in the purine synthesis, glycolysis, and pentose phosphate pathways of both bacteria. Finally, MCSs were used to derive a list of promising enzyme targets for consortium-level therapeutic applications that cannot be circumvented via interspecies metabolite exchange.
Automatic design of gene regulatory mechanisms for spatial pattern formation
Authors: Mousavi Reza , Lobo Daniel
Published: April 2024

Abstract

Gene regulatory mechanisms (GRMs) control the formation of spatial and temporal expression patterns that can serve as regulatory signals for the development of complex shapes. Synthetic developmental biology aims to engineer such genetic circuits for understanding and producing desired multicellular spatial patterns. However, designing synthetic GRMs for complex, multi-dimensional spatial patterns is a current challenge due to the nonlinear interactions and feedback loops in genetic circuits. Here we present a methodology to automatically design GRMs that can produce any given two-dimensional spatial pattern. The proposed approach uses two orthogonal morphogen gradients acting as positional information signals in a multicellular tissue area or culture, which constitutes a continuous field of engineered cells implementing the same designed GRM. To efficiently design both the circuit network and the interaction mechanisms—including the number of genes necessary for the formation of the target spatial pattern—we developed an automated algorithm based on high-performance evolutionary computation. The tolerance of the algorithm can be configured to design GRMs that are either simple to produce approximate patterns or complex to produce precise patterns. We demonstrate the approach by automatically designing GRMs that can produce a diverse set of synthetic spatial expression patterns by interpreting just two orthogonal morphogen gradients. The proposed framework offers a versatile approach to systematically design and discover complex genetic circuits producing spatial patterns.
A directed enolization strategy enables by-product-free construction of contiguous stereocentres en route to complex amino acids
Authors: Hong Fenglin , Aldhous Timothy P. , Kemmitt Paul D. , Bower John F.
Published: April 2024

Homochiral α-amino acids are widely used in pharmaceutical design as key subunits in chiral catalyst synthesis or as building blocks in synthetic biology. Many synthetic methods have been developed to access rare or unnatural variants by controlling the installation of the α-stereocentre. By contrast, and despite their importance, α-amino acids possessing β-stereocentres are much harder to synthesize. Here we demonstrate an iridium-catalysed protocol that allows the direct upconversion of simple alkenes and glycine derivatives to give β-substituted α-amino acids with exceptional levels of regio- and stereocontrol. Our method exploits the native directing ability of a glycine-derived N–H unit to facilitate Ir-catalysed enolization of the adjacent carbonyl. The resulting stereodefined enolate cross-couples with a styrene or α-olefin to install two contiguous stereocentres. The process offers very high levels of regio- and stereocontrol and occurs with complete atom economy. In broader terms, our reaction design offers a unique directing-group-controlled strategy for the direct stereocontrolled α-alkylation of carbonyl compounds, and provides a powerful approach for the synthesis of challenging contiguous stereocentres.
The covariance environment defines cellular niches for spatial inference
Authors: Haviv Doron , Remšík Ján , Gatie Mohamed , Snopkowski Catherine , Takizawa Meril , Pereira Nathan , Bashkin John , Jovanovich Stevan , Nawy Tal , Chaligne Ronan , Boire Adrienne , Hadjantonakis Anna-Katerina , Pe’er Dana
Published: April 2024

A key challenge of analyzing data from high-resolution spatial profiling technologies is to suitably represent the features of cellular neighborhoods or niches. Here we introduce the covariance environment (COVET), a representation that leverages the gene–gene covariate structure across cells in the niche to capture the multivariate nature of cellular interactions within it. We define a principled optimal transport-based distance metric between COVET niches that scales to millions of cells. Using COVET to encode spatial context, we developed environmental variational inference (ENVI), a conditional variational autoencoder that jointly embeds spatial and single-cell RNA sequencing data into a latent space. ENVI includes two decoders: one to impute gene expression across the spatial modality and a second to project spatial information onto single-cell data. ENVI can confer spatial context to genomics data from single dissociated cells and outperforms alternatives for imputing gene expression on diverse spatial datasets.
Self-pigmenting textiles grown from cellulose-producing bacteria with engineered tyrosinase expression
Authors: Walker Kenneth T. , Li Ivy S. , Keane Jennifer , Goosens Vivianne J. , Song Wenzhe , Lee Koon-Yang , Ellis Tom
Published: April 2024

Environmental concerns are driving interest in postpetroleum synthetic textiles produced from microbial and fungal sources. Bacterial cellulose (BC) is a promising sustainable leather alternative, on account of its material properties, low infrastructure needs and biodegradability. However, for alternative textiles like BC to be fully sustainable, alternative ways to dye textiles need to be developed alongside alternative production methods. To address this, we genetically engineer Komagataeibacter rhaeticus to create a bacterial strain that grows self-pigmenting BC. Melanin biosynthesis in the bacteria from recombinant tyrosinase expression achieves dark black coloration robust to material use. Melanated BC production can be scaled up for the construction of prototype fashion products, and we illustrate the potential of combining engineered self-pigmentation with tools from synthetic biology, through the optogenetic patterning of gene expression in cellulose-producing bacteria. With this study, we demonstrate that combining genetic engineering with current and future methods of textile biofabrication has the potential to create a new class of textiles.
Greenhouse gas emissions, carbon stocks and wheat productivity following biochar, compost and vermicompost amendments: comparison of non-saline and salt-affected soils
Authors: Farooqi Zia Ur Rahman , Qadir Ayesha Abdul , Khalid Sehrish , Murtaza Ghulam , Ashraf Muhammad Nadeem , Shafeeq-ur-Rahman  , Javed Wasim , Waqas Muhammad Ahmed , Xu Minggang
Published: April 2024

Understanding the impact of greenhouse gas (GHG) emissions and carbon stock is crucial for effective climate change assessment and agroecosystem management. However, little is known about the effects of organic amendments on GHG emissions and dynamic changes in carbon stocks in salt-affected soils. We conducted a pot experiment with four treatments including control (only fertilizers addition), biochar, vermicompost, and compost on non-saline and salt-affected soils, with the application on a carbon equivalent basis under wheat crop production. Our results revealed that the addition of vermicompost significantly increased soil organic carbon content by 18% in non-saline soil and 52% in salt-affected soil compared to the control leading to improvements in crop productivity i.e., plant dry biomass production by 57% in non-saline soil with vermicompost, while 56% with the same treatment in salt-affected soil. The grain yield was also noted 44 and 50% more with vermicompost treatment in non-saline and salt-affected soil, respectively. Chlorophyll contents were observed maximum with vermicompost in non-saline (24%), and salt-affected soils (22%) with same treatments. Photosynthetic rate (47% and 53%), stomatal conductance (60% and 12%), and relative water contents (38% and 27%) were also noted maximum with the same treatment in non-saline and salt-affected soils, respectively. However, the highest carbon dioxide emissions were observed in vermicompost- and compost-treated soils, leading to an increase in emissions of 46% in non-saline soil and 74% in salt-affected soil compared to the control. The compost treatment resulted in the highest nitrous oxide emissions, with an increase of 57% in non-saline soil and 62% in salt-affected soil compared to the control. In saline and non-saline soils treated with vermicompost, the global warming potential was recorded as 267% and 81% more than the control, respectively. All treatments, except biochar in non-saline soil, showed increased net GHG emissions due to organic amendment application. However, biochar reduced net emissions by 12% in non-saline soil. The application of organic amendments increased soil organic carbon content and crop yield in both non-saline and salt-affected soils. In conclusion, biochar is most effective among all tested organic amendments at increasing soil organic carbon content in both non-saline and salt-affected soils, which could have potential benefits for soil health and crop production.
The impact of a chemical reaction on the heat and mass transfer mechanisms in a dissipative and radiative nanofluid flow over a nonlinear stretching sheet
Authors: Abbas W. , Megahed Ahmed M. , Fares Eman
Published: April 2024

This paper presents a numerical investigation of the flow of a non-Newtonian tangent hyperbolic nanofluid over a nonlinearly stretched surface, taking into account factors such as thermal radiation, prescribed surface temperature, and a chemical reaction mechanism. Furthermore, the analysis includes the consideration of both viscous dissipation and the influence of a magnetic field within a Darcy porous medium. A mathematical framework for addressing the issue, rooted in the principles of conserving momentum, energy, and mass. The MATHEMATICA tools were employed to apply the shooting technique in order to solve the modeled equations describing the temperature, velocity, and concentration fields of the proposed physical system. Graphs are used to illustrate how certain key parameters affect the profiles of concentration, velocity, and temperature. Data tables are utilized to display information pertaining to the local Nusselt number, local Sherwood number, and local skin friction coefficient. The present results have been confirmed through a comparison with previously published findings. This research holds significant importance as it focuses on the extensive utilization of tangent hyperbolic nanofluids in cooling electronic components that produce substantial heat during their operation. The observed pattern indicates that as the local Weisbsenberg number, magnetic number, local porous parameter, and power law index increase, there is a reduction in the boundary layer thickness. Conversely, in the instances of concentration and temperature distributions, an escalation in these parameters leads to an expansion of the boundary layer thickness.
Clinically significant changes in genes and variants associated with epilepsy over time: implications for re-analysis
Authors: Robertson Alan J. , Tran Khoa A. , Bennett Carmen , Sullivan Clair , Stark Zornitza , Vadlamudi Lata , Waddell Nicola
Published: April 2024

Despite the significant advances in understanding the genetic architecture of epilepsy, many patients do not receive a molecular diagnosis after genomic testing. Re-analysing existing genomic data has emerged as a potent method to increase diagnostic yields—providing the benefits of genomic-enabled medicine to more individuals afflicted with a range of different conditions. The primary drivers for these new diagnoses are the discovery of novel gene-disease and variants-disease relationships; however, most decisions to trigger re-analysis are based on the passage of time rather than the accumulation of new knowledge. To explore how our understanding of a specific condition changes and how this impacts re-analysis of genomic data from epilepsy patients, we developed Vigelint. This approach combines the information from PanelApp and ClinVar to characterise how the clinically relevant genes and causative variants available to laboratories change over time, and this approach to five clinical-grade epilepsy panels. Applying the Vigelint pipeline to these panels revealed highly variable patterns in new, clinically relevant knowledge becoming publicly available. This variability indicates that a more dynamic approach to re-analysis may benefit the diagnosis and treatment of epilepsy patients. Moreover, this work suggests that Vigelint can provide empirical data to guide more nuanced, condition-specific approaches to re-analysis.
Spectral band selection and ANIMR-GAN for high-performance multispectral coal gangue classification
Authors: Wang Qingya , Hua Huaitian , Tao Liangliang , Liang Yage , Deng Xiaozheng , Yu Fen
Published: April 2024

Low-energy and efficient coal gangue sorting is crucial for environmental protection. Multispectral imaging (MSI) has emerged as a promising technology in this domain. This work addresses the challenge of low resolution and poor recognition performance in underground MSI equipment. We propose an attention-based multi-level residual network (ANIMR) within a super-resolution reconstruction model (ANIMR-GAN) inspired by CycleGAN. This model incorporates improvements to the discriminator and loss function. We trained the model on 600 coal and gangue MSI samples and validated it on an independent set of 120 samples. The ANIMR-GAN, combined with a random forest classifier, achieved a maximum accuracy of 97.78% and an average accuracy of 93.72%. Furthermore, the study identifies the 959.37 nm band as optimal for coal and gangue classification. Compared to existing super-resolution methods, ANIMR-GAN offers advantages, paving the way for intelligent and efficient coal gangue sorting, ultimately promoting advancements in sustainable mineral processing.
Light squeezing enhancement by coupling nonlinear optical cavities
Authors: Jabri H. , Eleuch H.
Published: April 2024

In this paper, we explore the squeezing effect generated by two coupled optical cavities. Each cavity contains a second-order nonlinear material and coherently pumped by a laser. Our results show that light intensity is strongly improved due to the presence of the nonlinearities and mainly depends on the detunings between external laser frequencies and cavity modes. More interestingly, the proposed scheme could enhance light squeezing for moderate coupling between cavities : the squeezing generated by one cavity is enhanced by the other one. For resonant interaction, highest squeezing effect is obtained near resonance. When fields are non resonant, squeezing increases near resonance of the considered cavity, but decreases for large detunings relative to the second cavity. Further, when the dissipation rate of the second cavity is smaller than the first, the squeezing could be improved, attaining nearly the perfect squeezing. While the temperature elevation has a negative impact overall on the nonclassical light, squeezing shows an appreciable resistance against thermal baths for appropriate parameter sets.
Innovative numerical modeling for predicting soil relaxation in the design of twin circular culverts
Authors: Shiau Jim , Nguyen Tan , Sams Mathew , Bhattacharya Paramita
Published: April 2024

This study presents a finite difference model for analyzing ground stability and settlement of twin circular culverts in undrained clay. The model is verified through simulations of soil movement and relaxation around a tunnel-boring machine's shield. Stability numbers and ground settlement are evaluated across various culvert geometries and soil ratios and compared to rigorous solutions and previous models. The settlement data obtained is used to determine inflection point parameters for practical culvert design, considering dimensionless ratios. The findings highlight the importance of precise design methodologies that consider soil properties and geometry. The finite difference model proves to be a valuable tool in culvert design, providing accurate analysis of stability and settlement characteristics. The presented design figures and regression equations serve as practical tools for engineers in designing stable twin circular culverts in undrained clay. The study emphasizes the need to carefully consider soil properties and geometry for successful culvert design. In conclusion, the finite difference model offers insights into ground stability and settlement of twin circular culverts. The presented design figures and regression equations support engineers in making informed design decisions, ensuring the stability and long-term performance of culverts in undrained clay conditions.
Phylogeny and biogeography of the wingless orthopteran family Rhaphidophoridae
Authors: Kim Do-Yoon , Kim Sangil , Song Hojun , Shin Seunggwan
Published: April 2024

Cave crickets (Rhaphidophoridae) are insects of an ancient and wingless lineage within Orthoptera that are distributed worldwide except in Antarctica, and each subfamily has a high level of endemicity. Here, we show the comprehensive phylogeny of cave crickets using multi-gene datasets from mitochondrial and nuclear loci, including all extant subfamilies for the first time. We reveal phylogenetic relationships between subfamilies, including the sister relationship between Anoplophilinae and Gammarotettiginae, based on which we suggest new synapomorphies. Through biogeographic analyses based on divergence time estimations and ancestral range reconstruction, we propose novel hypotheses regarding the biogeographic history of cave crickets. We suggest that Gammarotettiginae in California originated from the Asian lineage when Asia and the Americas were connected by the Bering land bridge, and the opening of the western interior seaway affected the division of Ceuthophilinae from Tropidischiinae in North America. We estimate that Rhaphidophoridae originated at 138 Mya throughout Pangea. We further hypothesize that the loss of wings in Rhaphidophoridae could be the result of their adaptation to low temperatures in the Mesozoic era.
Deletion of podocyte Rho-associated, coiled-coil-containing protein kinase 2 protects mice from focal segmental glomerulosclerosis
Authors: Matoba Keiichiro , Nagai Yosuke , Sekiguchi Kensuke , Ohashi Shinji , Mitsuyoshi Etsuko , Shimoda Masayuki , Tachibana Toshiaki , Kawanami Daiji , Yokota Tamotsu , Utsunomiya Kazunori , Nishimura Rimei
Published: April 2024

Focal segmental glomerulosclerosis (FSGS) shares podocyte damage as an essential pathological finding. Several mechanisms underlying podocyte injury have been proposed, but many important questions remain. Rho-associated, coiled-coil-containing protein kinase 2 (ROCK2) is a serine/threonine kinase responsible for a wide array of cellular functions. We found that ROCK2 is activated in podocytes of adriamycin (ADR)-induced FSGS mice and cultured podocytes stimulated with ADR. Conditional knockout mice in which the ROCK2 gene was selectively disrupted in podocytes (PR2KO) were resistant to albuminuria, glomerular sclerosis, and podocyte damage induced by ADR injection. In addition, pharmacological intervention for ROCK2 significantly ameliorated podocyte loss and kidney sclerosis in a murine model of FSGS by abrogating profibrotic factors. RNA sequencing of podocytes treated with a ROCK2 inhibitor proved that ROCK2 is a cyclic nucleotide signaling pathway regulator. Our study highlights the potential utility of ROCK2 inhibition as a therapeutic option for FSGS.
Water is a radiation protection agent for ionised pyrrole
Authors: Johny Melby , Schouder Constant A. , Al-Refaie Ahmed , He Lanhai , Wiese Joss , Stapelfeldt Henrik , Trippel Sebastian , Küpper Jochen
Published: April 2024

Radiation-induced damage of biological matter is an ubiquitous problem in nature.
Quantitative reaction monitoring using parahydrogen-enhanced benchtop NMR spectroscopy
Authors: Robinson Alastair D. , Hill-Casey Fraser , Duckett Simon B. , Halse Meghan E.
Published: April 2024

The parahydrogen-induced polarisation (PHIP) NMR signal enhancement technique is used to study H2 addition to Vaska’s complex (trans-[IrCl(CO)(PPh3)2]) and a mixture of Vaska’s complex derivatives with benchtop (1 T) NMR detection.
Automated salting-out assisted single-phase liquid–liquid extraction of Cr(vi) from river water samples prior to its atomic absorption spectrometric determination
Authors: Cunha Francisco Antonio S. , Fernandes Julys Pablo A. , Lyra Wellington S. , Pessoa Amalia Geiza G. , Santos Josué C. C. , Araújo Mario C. U. , Almeida Luciano F.
Published: April 2024

A new automated method was developed combining the features of the salting-out effect, single-phase liquid–liquid extraction (SPLLE), and flow-batch analysis to determine Cr(vi) in river water samples by ETAAS.
Vacancy engineering modulates spin polarization to enhance the charge dynamics of CuIn5S8 for photocatalytic sterilization
Authors: Wu Wenbin , Wang Jing , Liang Xiaojie , Luo Laixi , Yang Yaohong , Zhou Fan , Deng Shuduan , Song Yumin , Yang Le , Kang Kunyong
Published: April 2024

Photocatalytic sterilization technology is a strategy that is environmentally friendly for killing drug-resistant bacteria using solar energy.
Maximizing polypropylene recovery from waste carpet feedstock: a solvent-driven pathway towards circular economy
Authors: Salazar Heider , Baragau Ioan-Alexandru , Lu Zhen , Román-Ramírez Luis A. , Kellici Suela
Published: April 2024

A novel approach for the efficient recovery of polypropylene from waste carpet feedstock utilising a solvent based method.
Spectroelectrochemical determination of thiolate self-assembled monolayer adsorptive stability in aqueous and non-aqueous electrolytes
Authors: Siddiqui Abdur-Rahman , N'Diaye Jeanne , Santiago-Carboney Armando , Martin Kristin , Bhargava Rohit , Rodríguez-López Joaquín
Published: April 2024

The stable potential window (SPW) is the potential range that an electrode modified by a self-assembled monolayer (SAM) can operate without desorbing the SAM. Here we introduce SPWs for aromatic SAMs at Au.
A sequential light-harvesting system with thermosensitive colorimetric emission in both aqueous solution and hydrogel
Authors: Tang Lu , Wu Zhiying , Zhang Qiaona , Hu Qiulin , Dang Xiaoman , Cui Fengyao , Tang Long , Xiao Tangxin
Published: April 2024

An artificial thermoresponsive light-harvesting system with sequential energy transfer has been successfully constructed, which shows thermosensitive colorimetric fluorescence in both aqueous solution and hydrogel.
Phenoxazinyl Zn(ii) diradical complex formed via redox-driven cyclization of a 2-aminophenol-based N3O ligand. Isolation of the modified N3 ligand radical and its Ni(ii) complex
Authors: Mukhopadhyay Narottam , Sengupta Arunava , Lloret Francesc , Mukherjee Rabindranath
Published: April 2024

Intramolecular cyclization of an N3O ligand in air affording a phenoxazinyl Zn(ii) diradical complex and isolation of the modified N3 ligand-radical.
High biomass content, anti-flammable and degradable epoxy thermosets by curing a tyramine-derived epoxy monomer with a furan-derived diamine for non-destructively recyclable carbon fiber composite application
Authors: Niu Hao-Xin , Yang Tian-Mo , Wang Xin , Zhang Ping , Guo Wenwen , Song Lei , Hu Yuan
Published: April 2024

High biomass content, anti-flammable and degradable epoxy thermosets were prepared by curing a tyramine-derived epoxy monomer (TVEP) with a furan-derived diamine (DFDA) for non-destructively recyclable carbon fiber composite application.
Highly efficient electrocatalytic oxidation of furfural to maleic acid over MOF-derived MnCeOx
Authors: Yuan Xue , Huang Xin , Hu Meimin , Liu Jinjia , Guo Wenhao , Hao Yuchen , Li Zhenting , Zhang Kai , Han Buxing
Published: April 2024

Furfural could be selectively electro-oxidized to maleic acid over a MOF-derived MnCeOx catalyst with suitable surface oxygen vacancies.
Highly-stable Silverton-type UIV-containing polyoxomolybdate frameworks for the heterogeneous catalytic synthesis of quinazolinones
Authors: Li Ke , Liu Yufeng , Yang Guoping , Zheng Zhijian , Lin Xiaoling , Zhang Zhibin , Li Shujun , Liu Yunhai , Wei Yongge
Published: April 2024

The first series of Silverton {UMo12O40}-based polyoxomolybdates linked by FeII, CoII, and NiII were synthesized and characterized. They exhibited excellent stabilities and were used as heterogeneous catalysts for the synthesis of quinazolinones.
Lignin-derivable, thermoplastic, non-isocyanate polyurethanes with increased hydrogen-bonding content and toughness vs. petroleum-derived analogues
Authors: Mahajan Jignesh S. , Hinton Zachary R. , Nombera Bueno Eduardo , Epps, III Thomas H. , Korley LaShanda T. J.
Published: April 2024

This work highlights lignin-derivable, thermoplastic, non-isocyanate polyurethanes as potential alternatives to petroleum-derived analogues with increased toughness and processability due to the functionality of lignin-aromatics (methoxy groups).
Evaluation of ketoclomazone and its analogues as inhibitors of 1-deoxy-d-xylulose 5-phosphate synthases and other thiamine diphosphate (ThDP)-dependent enzymes
Authors: Chan Alex H. Y. , Ho Terence C. S. , Fathoni Imam , Hamid Rawia , Hirsch Anna K. H. , Saliba Kevin J. , Leeper Finian J.
Published: April 2024

Most pathogenic bacteria, apicomplexan parasites and plants rely on the methylerythritol phosphate (MEP) pathway to obtain precursors of isoprenoids.
Synthesis of 3,5-disubstituted isoxazoles by domino reductive Nef reaction/cyclization of β-nitroenones
Authors: Khan Muhammad Ehtisham Ibraheem , Cassini Tomas Lighuen , Petrini Marino , Palmieri Alessandro
Published: April 2024

β-Nitroenones were converted into 3,5-disubstituted isoxazoles via a domino reaction promoted by tin(ii) dichloride. The protocol efficiently works under both microwave and flow conditions.
Biochemical and structural impact of two novel missense mutations in cystathionine β-synthase gene associated with homocystinuria
Authors: Al-Sadeq Duaa W. , Conter Carolina , Thanassoulas Angelos , Al-Dewik Nader , Safieh-Garabedian Bared , Martínez-Cruz Luis Alfonso , Nasrallah Gheyath K. , Astegno Alessandra , Nomikos Michail
Published: April 2024

Homocystinuria is a rare disease caused by mutations in the CBS gene that results in a deficiency of cystathionine β-synthase (CBS). CBS is an essential pyridoxal 5′-phosphate (PLP)-dependent enzyme in the transsulfuration pathway, responsible for combining serine with homocysteine to produce cystathionine, whose activity is enhanced by the allosteric regulator S-adenosylmethionine (SAM). CBS also plays a role in generating hydrogen sulfide (H2S), a gaseous signaling molecule with diverse regulatory functions within the vascular, nervous, and immune systems. In this study, we present the clinical and biochemical characterization of two novel CBS missense mutations that do not respond to pyridoxine treatment, namely c.689T > A (L230Q) and 215A > T (K72I), identified in a Chinese patient. We observed that the disease-associated K72I genetic variant had no apparent effects on the spectroscopic and catalytic properties of the full-length enzyme. In contrast, the L230Q variant expressed in Escherichia coli did not fully retain heme and when compared with the wild-type enzyme, it exhibited more significant impairments in both the canonical cystathionine-synthesis and the alternative H2S-producing reactions. This reduced activity is consistent with both in vitro and in silico evidence, which indicates that the L230Q mutation significantly decreases the overall protein's stability, which in turn, may represent the underlying cause of its pathogenicity.