bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptive agents may be smarter than you think: unbiasedness in adaptive expectations
Authors: Palestrini A. , Gatti D. Delli , Gallegati M. , Greenwald B.
Published: April 2024

Experimental evidence shows that human subjects frequently rely on adaptive heuristics to form expectations but their forecasting performance in the lab is not as inadequate as assumed in macroeconomic theory. In this paper, we use an agent-based model (ABM) to show that the average forecasting error is indeed close to zero even in a complex environment if we assume that agents augment the canonical adaptive algorithm with a Belief Correction term which takes into account the previous trend of the variable of interest. We investigate the reasons for this result using a streamlined nonlinear macro-dynamic model that captures the essence of the ABM.
A combined EMDR/CBT-based approach for the successful management of cyclical vomiting syndrome: a case study
Authors: Ashcroft Kate
Published: April 2024

Cyclical vomiting syndrome (CVS) is an extremely debilitating condition that can have an adverse impact on physical health and can significantly disrupt social and occupational functioning. It is a poorly understood illness in terms of aetiology, and most research has focused on the pharmacological management of the condition. This article describes a case study of a combined cognitive behavioural therapy (CBT) and eye movement desensitisation and reprocessing (EMDR)-based intervention with an adult with past trauma who had a 20-year history of CVS accompanied by high cannabis use. Therapy led to improvements in physical health and social functioning, reduced use of cannabis, and a significant reduction in the frequency and severity of vomiting episodes and associated hospital admission. Implications for future research and management of the illness are discussed.

Key learning aims

(1)

To understand how the presence of co-morbid untreated trauma in individuals with CVS may result in unhelpful coping strategies that can worsen the course of the illness.

(2)

To explore how the addition of psychological therapy to routine care of gastrointestinal disorders such as CVS can improve treatment outcome.

(3)

To consider how offering an individualised and flexible approach to appointments may benefit individuals who find it more difficult to engage in psychological therapy.
Evolution Modeling and Protection Scheme for Tidal Flats Under Natural Change and Human Pressure, Central Jiangsu Coast
Authors: Zhu Shibing , Gao Shu , Li Mingliang , Wang Ya Ping
Published: April 2024

Amidst escalating global changes and heightened human activities, tidal flats worldwide are facing a transition from accretion to erosion. In order to quantify the growth pattern of tidal flats and its response to changes in multiple external driving factors, here we established a geometric model, in combination with field surveys, to study the historical behavior (1127–1990) and future trends (2100) of a typical tidal flat system on the Jiangsu coast, China. The results indicate that sediment supply and relative sea level change determine the accretion‐erosion status and the eventual morphological pattern of the tidal flat. If these two factors remain stable and sediment supply can compensate for the increase in sediment accommodation space caused by sea level change, the tidal flat will continue to accrete until its growth limit is reached. Otherwise, tidal flats will face erosion risk, which can be further enhanced by localized land subsidence. Furthermore, changes in the coastal profile show a trend of progressive retreating, with the lower part of intertidal zone being eroded more rapidly than its upper part. This demonstrates that the sediment supply has been reduced to such a level that the present “in‐transition” evolution pattern of central Jiangsu coast will soon be replaced by severe inundation and erosion. Hence, we advocate for a comprehensive, multi‐tiered coastal protection strategy focusing on wave suppression, enhancement of sediment retention, and increased storm resistance. This strategy underscores fundamental underlying mechanisms of the accretion‐erosion transition, which is crucial for the future safeguarding of coastal wetlands globally.
Disagreements in Geodetically Inferred Strain Rates in the Western US With Stress Orientations and Geologic Moment Rates
Authors: Johnson Kaj M.
Published: April 2024

I employ an elasticity‐based method to invert a geodetically derived surface velocity field in the western US using for present‐day surface strain rate fields with uncertainties. The method uses distributed body forces in a thin elastic sheet and allows for discontinuities in velocity across creeping faults using the solution for dislocations in a thin elastic plate. I compare the strain rate fields with previously published stress orientations and moment rates from geological slip rate data and previous geodetic studies. Geologic and geodetic moment rates are calculated using slip rate and off‐fault strain rates from the 2023 US National Seismic Hazard Model (NSHM) deformation models. I find that computed total geodetic moment rates are higher than NSHM summed moment rates on faults for all regions of the western US except the highest deforming rate regions including the Western Transverse Ranges and the northern and southern San Andreas Fault (SAF) system in California. Computed geodetic moment rates are comparable to the moment rates derived from the geodetically based NSHM deformation models in all regions. I find systematic differences in orientations of maximum horizontal shortening rate and maximum horizontal compressive stress in the Pacific Northwest region and along much of the SAF system. In the Pacific Northwest, the maximum horizontal stress orientations are rotated counterclockwise 40–90° relative to the maximum horizontal strain rate directions. Along the SAF system, the maximum horizontal stresses are rotated systematically 25–40° clockwise (closer to fault normal) relative to the strain rates.
Incorporation of Sub‐Resolution Porosity Into Two‐Phase Flow Models With a Multiscale Pore Network for Complex Microporous Rocks
Authors: Foroughi Sajjad , Bijeljic Branko , Gao Ying , Blunt Martin J.
Published: April 2024

Porous materials, such as carbonate rocks, frequently have pore sizes which span many orders of magnitude. This is a challenge for models that rely on an image of the pore space, since much of the pore space may be unresolved. In this work, sub‐resolution porosity in X‐ray images is characterized using differential imaging which quantifies the difference between a dry scan and 30 wt% potassium iodide brine saturated images. Once characterized, we develop a robust workflow to incorporate the sub‐resolution pore space into a network model using Darcy‐type elements called microlinks. Each grain voxel with sub‐resolution porosity is assigned to the two nearest resolved pores using an automatic dilation algorithm. By including these microlinks with empirical models in flow modeling, we simulate single‐phase and multiphase flow. By fine‐tuning the microlink empirical models, we match permeability, formation factor (the ratio of the resistivity of a rock filled with brine to the resistivity of that brine), and drainage capillary pressure to experimental results. We then show that our model can successfully predict steady‐state relative permeability measurements on a water‐wet Estaillades carbonate sample within the uncertainty of the experiments and modeling. Our approach of incorporating sub‐resolution porosity in two‐phase flow modeling using image‐based multiscale pore network techniques can capture complex pore structures and accurately predict flow behavior in porous materials with a wide range of pore size.
High frequency deep brain stimulation of the dorsal raphe nucleus prevents methamphetamine priming-induced reinstatement of drug seeking in rats
Authors: Zhang Libo , Meng Shiqiu , Huang Enze , Di Tianqi , Ding Zengbo , Huang Shihao , Chen Wenjun , Zhang Jiayi , Zhao Shenghong , Yuwen Ting , Chen Yang , Xue Yanxue , Wang Feng , Shi Jie , Shi Yu
Published: April 2024

Drug addiction represents a multifaceted and recurrent brain disorder that possesses the capability to create persistent and ineradicable pathological memory. Deep brain stimulation (DBS) has shown a therapeutic potential for neuropsychological disorders, while the precise stimulation targets and therapeutic parameters for addiction remain deficient. Among the crucial brain regions implicated in drug addiction, the dorsal raphe nucleus (DRN) has been found to exert an essential role in the manifestation of addiction memory. Thus, we investigated the effects of DRN DBS in the treatment of addiction and whether it might produce side effects by a series of behavioral assessments, including methamphetamine priming-induced reinstatement of drug seeking behaviors, food-induced conditioned place preference (CPP), open field test and elevated plus-maze test, and examined brain activity and connectivity after DBS of DRN. We found that high-frequency DBS of the DRN significantly lowered the CPP scores and the number of active-nosepokes in the methamphetamine-primed CPP test and the self-administration model. Moreover, both high-frequency and sham DBS group rats were able to establish significant food-induced place preference, and no significant difference was observed in the open field test and in the elevated plus-maze test between the two groups. Immunofluorescence staining and functional magnetic resonance imaging revealed that high-frequency DBS of the DRN could alter the activity and functional connectivity of brain regions related to addiction. These results indicate that high-frequency DBS of the DRN effectively inhibits methamphetamine priming-induced relapse and seeking behaviors in rats and provides a new target for the treatment of drug addiction.
Scutellarin activates IDH1 to exert antitumor effects in hepatocellular carcinoma progression
Authors: Cui Zhao , Li Caifeng , Liu Wei , Sun Mo , Deng Shiwen , Cao Junxian , Yang Hongjun , Chen Peng
Published: April 2024

Isochlorate dehydrogenase 1 (IDH1) is an important metabolic enzyme for the production of α-ketoglutarate (α-KG), which has antitumor effects and is considered to have potential antitumor effects. The activation of IDH1 as a pathway for the development of anticancer drugs has not been attempted. We demonstrated that IDH1 can limit glycolysis in hepatocellular carcinoma (HCC) cells to activate the tumor immune microenvironment. In addition, through proteomic microarray analysis, we identified a natural small molecule, scutellarin (Scu), which activates IDH1 and inhibits the growth of HCC cells. By selectively modifying Cys297, Scu promotes IDH1 active dimer formation and increases α-KG production, leading to ubiquitination and degradation of HIF1a. The loss of HIF1a further leads to the inhibition of glycolysis in HCC cells. The activation of IDH1 by Scu can significantly increase the level of α-KG in tumor tissue, downregulate the HIF1a signaling pathway, and activate the tumor immune microenvironment in vivo. This study demonstrated the inhibitory effect of IDH1–α-KG–HIF1a on the growth of HCC cells and evaluated the inhibitory effect of Scu, the first IDH1 small molecule agonist, which provides a reference for cancer immunotherapy involving activated IDH1.
Glacial isostatic adjustment reduces past and future Arctic subsea permafrost
Authors: Creel Roger C. , Miesner Frederieke , Wilkenskjeld Stiig , Austermann Jacqueline , Overduin Pier Paul
Published: April 2024

Sea-level rise submerges terrestrial permafrost in the Arctic, turning it into subsea permafrost. Subsea permafrost underlies ~ 1.8 million km2 of Arctic continental shelf, with thicknesses in places exceeding 700 m. Sea-level variations over glacial-interglacial cycles control subsea permafrost distribution and thickness, yet no permafrost model has accounted for glacial isostatic adjustment (GIA), which deviates local sea level from the global mean due to changes in ice and ocean loading. Here we incorporate GIA into a pan-Arctic model of subsea permafrost over the last 400,000 years. Including GIA significantly reduces present-day subsea permafrost thickness, chiefly because of hydro-isostatic effects as well as deformation related to Northern Hemisphere ice sheets. Additionally, we extend the simulation 1000 years into the future for emissions scenarios outlined in the Intergovernmental Panel on Climate Change’s sixth assessment report. We find that subsea permafrost is preserved under a low emissions scenario but mostly disappears under a high emissions scenario.
Dynamic inter-domain transformations mediate the allosteric regulation of human 5, 10-methylenetetrahydrofolate reductase
Authors: Blomgren Linnea K. M. , Huber Melanie , Mackinnon Sabrina R. , Bürer Céline , Baslé Arnaud , Yue Wyatt W. , Froese D. Sean , McCorvie Thomas J.
Published: April 2024

5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor s-adenosyl-l-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved catalytic domain (CD) a unique regulatory domain (RD) that confers feedback inhibition by SAM. Here we determine the cryo-electron microscopy structures of human MTHFR bound to SAM and its demethylated product s-adenosyl-l-homocysteine (SAH). In the active state, with the RD bound to a single SAH, the CD is flexible and exposes its active site for catalysis. However, in the inhibited state the RD pocket is remodelled, exposing a second SAM-binding site that was previously occluded. Dual-SAM bound MTHFR demonstrates a substantially rearranged inter-domain linker that reorients the CD, inserts a loop into the active site, positions Tyr404 to bind the cofactor FAD, and blocks substrate access. Our data therefore explain the long-distance regulatory mechanism of MTHFR inhibition, underpinned by the transition between dual-SAM and single-SAH binding in response to cellular methylation status.
Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures
Authors: Leung Pok Man , Grinter Rhys , Tudor-Matthew Eve , Lingford James P. , Jimenez Luis , Lee Han-Chung , Milton Michael , Hanchapola Iresha , Tanuwidjaya Erwin , Kropp Ashleigh , Peach Hanna A. , Carere Carlo R. , Stott Matthew B. , Schittenhelm Ralf B. , Greening Chris
Published: April 2024

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon,Acidianus brierleyi(Thermoproteota), constitutively consumes H2and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome ofA. brierleyiencodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon,Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
An experimental framework to assess biomolecular condensates in bacteria
Authors: Hoang Y , Azaldegui Christopher A. , Dow Rachel E. , Ghalmi Maria , Biteen Julie S. , Vecchiarelli Anthony G.
Published: April 2024

High-resolution imaging of biomolecular condensates in living cells is essential for correlating their properties to those observed through in vitro assays. However, such experiments are limited in bacteria due to resolution limitations. Here we present an experimental framework that probes the formation, reversibility, and dynamics of condensate-forming proteins in Escherichia coli as a means to determine the nature of biomolecular condensates in bacteria. We demonstrate that condensates form after passing a threshold concentration, maintain a soluble fraction, dissolve upon shifts in temperature and concentration, and exhibit dynamics consistent with internal rearrangement and exchange between condensed and soluble fractions. We also discover that an established marker for insoluble protein aggregates, IbpA, has different colocalization patterns with bacterial condensates and aggregates, demonstrating its potential applicability as a reporter to differentiate the two in vivo. Overall, this framework provides a generalizable, accessible, and rigorous set of experiments to probe the nature of biomolecular condensates on the sub-micron scale in bacterial cells.
An ensemble penalized regression method for multi-ancestry polygenic risk prediction
Authors: Zhang Jingning , Zhan Jianan , Jin Jin , Ma Cheng , Zhao Ruzhang , O’Connell Jared , Jiang Yunxuan ,   23andMe Research Team, Koelsch Bertram L. , Zhang Haoyu , Chatterjee Nilanjan
Published: April 2024

Great efforts are being made to develop advanced polygenic risk scores (PRS) to improve the prediction of complex traits and diseases. However, most existing PRS are primarily trained on European ancestry populations, limiting their transferability to non-European populations. In this article, we propose a novel method for generating multi-ancestry Polygenic Risk scOres based on enSemble of PEnalized Regression models (PROSPER). PROSPER integrates genome-wide association studies (GWAS) summary statistics from diverse populations to develop ancestry-specific PRS with improved predictive power for minority populations. The method uses a combination of $${{{{{{\mathscr{L}}}}}}}_{1}$$

L

1

(lasso) and $${{{{{{\mathscr{L}}}}}}}_{2}$$

L

2

(ridge) penalty functions, a parsimonious specification of the penalty parameters across populations, and an ensemble step to combine PRS generated across different penalty parameters. We evaluate the performance of PROSPER and other existing methods on large-scale simulated and real datasets, including those from 23andMe Inc., the Global Lipids Genetics Consortium, and All of Us. Results show that PROSPER can substantially improve multi-ancestry polygenic prediction compared to alternative methods across a wide variety of genetic architectures. In real data analyses, for example, PROSPER increased out-of-sample prediction R2 for continuous traits by an average of 70% compared to a state-of-the-art Bayesian method (PRS-CSx) in the African ancestry population. Further, PROSPER is computationally highly scalable for the analysis of large SNP contents and many diverse populations.
Sm-like protein Rof inhibits transcription termination factor ρ by binding site obstruction and conformational insulation
Authors: Said Nelly , Finazzo Mark , Hilal Tarek , Wang Bing , Selinger Tim Luca , Gjorgjevikj Daniela , Artsimovitch Irina , Wahl Markus C.
Published: April 2024

Transcription termination factor ρ is a hexameric, RNA-dependent NTPase that can adopt active closed-ring and inactive open-ring conformations. The Sm-like protein Rof, a homolog of the RNA chaperone Hfq, inhibits ρ-dependent termination in vivo but recapitulation of this activity in vitro has proven difficult and the precise mode of Rof action is presently unknown. Here, our cryo-EM structures of ρ-Rof and ρ-RNA complexes show that Rof undergoes pronounced conformational changes to bind ρ at the protomer interfaces, undercutting ρ conformational dynamics associated with ring closure and occluding extended primary RNA-binding sites that are also part of interfaces between ρ and RNA polymerase. Consistently, Rof impedes ρ ring closure, ρ-RNA interactions and ρ association with transcription elongation complexes. Structure-guided mutagenesis coupled with functional assays confirms that the observed ρ-Rof interface is required for Rof-mediated inhibition of cell growth and ρ-termination in vitro. Bioinformatic analyses reveal that Rof is restricted to Pseudomonadota and that the ρ-Rof interface is conserved. Genomic contexts of rof differ between Enterobacteriaceae and Vibrionaceae, suggesting distinct modes of Rof regulation. We hypothesize that Rof and other cellular anti-terminators silence ρ under diverse, but yet to be identified, stress conditions when unrestrained transcription termination by ρ may be detrimental.
Hybridizing carbonate and ether at molecular scales for high-energy and high-safety lithium metal batteries
Authors: Chen Jiawei , Zhang Daoming , Zhu Lei , Liu Mingzhu , Zheng Tianle , Xu Jie , Li Jun , Wang Fei , Wang Yonggang , Dong Xiaoli , Xia Yongyao
Published: April 2024

Commonly-used ether and carbonate electrolytes show distinct advantages in active lithium-metal anode and high-voltage cathode, respectively. While these complementary characteristics hold promise for energy-dense lithium metal batteries, such synergy cannot be realized solely through physical blending. Herein, a linear functionalized solvent, bis(2-methoxyethyl) carbonate (BMC), is conceived by intramolecularly hybridizing ethers and carbonates. The integration of the electron-donating ether group with the electron-withdrawing carbonate group can rationalizes the charge distribution, imparting BMC with notable oxidative/reductive stability and relatively weak solvation ability. Furthermore, BMC also offers advantages including the ability to slightly dissolve LiNO3, excellent thermostability and nonflammability. Consequently, the optimized BMC-based electrolyte, even with typical concentrations in the single solvent, demonstrates high-voltage tolerance (4.4 V) and impressive Li plating/stripping Coulombic efficiency (99.4%). Moreover, it fulfills practical lithium metal batteries with satisfactory cycling performance and exceptional tolerance towards thermal/mechanical abuse, showcasing its suitability for safe high-energy lithium metal batteries.
KdpD is a tandem serine histidine kinase that controls K+ pump KdpFABC transcriptionally and post-translationally
Authors: Silberberg Jakob M. , Ketter Sophie , Böhm Paul J. N. , Jordan Kristin , Wittenberg Marcel , Grass Julia , Hänelt Inga
Published: April 2024

Two-component systems, consisting of a histidine kinase and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a histidine kinase of the KdpDE two-component system, which controls production of the potassium pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high potassium levels, using not its C-terminal histidine kinase domain but an N-terminal atypical serine kinase domain. Sequence analysis of KdpDs from different species highlights that some KdpDs are much shorter than others. We show that, while Escherichia coli KdpD’s atypical serine kinase domain responds directly to potassium levels, a shorter version from Deinococcus geothermalis is controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial potassium homeostasis.
Alkyne-tagged SERS nanoprobe for understanding Cu+ and Cu2+ conversion in cuproptosis processes
Authors: Zhang Sihan , Mei Yuxiao , Liu Jiaqi , Liu Zhichao , Tian Yang
Published: April 2024

Simultaneously quantifying mitochondrial Cu+ and Cu2+ levels is crucial for evaluating the molecular mechanisms of copper accumulation-involved pathological processes. Here, a series of molecules containing various diacetylene derivatives as Raman reporters are designed and synthesized, and the alkyne-tagged SERS probe is created for determination Cu+ and Cu2+ with high selectivity and sensitivity. The developed SERS probe generates well-separated distinguishable Raman fingerprint peaks with built-in corrections in the cellular silent region, resulting in accurate quantification of Cu+ and Cu2+. The present probe demonstrates high tempo-spatial resolution for real-time imaging and simultaneously quantifying mitochondrial Cu+ and Cu2+ with long-term stability benefiting from the probe assembly with designed Au-C≡C groups. Using this powerful tool, it is found that mitochondrial Cu+ and Cu2+ increase during ischemia are associated with breakdown of proteins containing copper as well as conversion of Cu+ and Cu2+. Meanwhile, we observe that parts of Cu+ and Cu2+ are transported out of neurons by ATPase. More importantly, cuproptosis in neurons is found including the oxidative stress process caused by the conversion of Cu+ to Cu2+, which dominates at the early stage (<9 h), and subsequent proteotoxic stress. Both oxidative and proteotoxic stresses contribute to neuronal death.
X-ray-activated polymerization expanding the frontiers of deep-tissue hydrogel formation
Authors: Zhang Hailei , Tang Boyan , Zhang Bo , Huang Kai , Li Shanshan , Zhang Yuangong , Zhang Haisong , Bai Libin , Wu Yonggang , Cheng Yongqiang , Yang Yanmin , Han Gang
Published: April 2024

Photo-crosslinking polymerization stands as a fundamental pillar in the domains of chemistry, biology, and medicine. Yet, prevailing strategies heavily rely on ultraviolet/visible (UV/Vis) light to elicit in situ crosslinking. The inherent perils associated with UV radiation, namely the potential for DNA damage, coupled with the limited depth of tissue penetration exhibited by UV/Vis light, severely restrict the scope of photo-crosslinking within living organisms. Although near-infrared light has been explored as an external excitation source, enabling partial mitigation of these constraints, its penetration depth remains insufficient, particularly within bone tissues. In this study, we introduce an approach employing X-ray activation for deep-tissue hydrogel formation, surpassing all previous boundaries. Our approach harnesses a low-dose X-ray-activated persistent luminescent phosphor, triggering on demand in situ photo-crosslinking reactions and enabling the formation of hydrogels in male rats. A breakthrough of our method lies in its capability to penetrate deep even within thick bovine bone, demonstrating unmatched potential for bone penetration. By extending the reach of hydrogel formation within such formidable depths, our study represents an advancement in the field. This application of X-ray-activated polymerization enables precise and safe deep-tissue photo-crosslinking hydrogel formation, with profound implications for a multitude of disciplines.
Remote loop evolution reveals a complex biological function for chitinase enzymes beyond the active site
Authors: Kozome Dan , Sljoka Adnan , Laurino Paola
Published: April 2024

Loops are small secondary structural elements that play a crucial role in the emergence of new enzyme functions. However, the evolutionary molecular mechanisms how proteins acquire these loop elements and obtain new function is poorly understood. To address this question, we study glycoside hydrolase family 19 (GH19) chitinase—an essential enzyme family for pathogen degradation in plants. By revealing the evolutionary history and loops appearance of GH19 chitinase, we discover that one loop which is remote from the catalytic site, is necessary to acquire the new antifungal activity. We demonstrate that this remote loop directly accesses the fungal cell wall, and surprisingly, it needs to adopt a defined structure supported by long-range intramolecular interactions to perform its function. Our findings prove that nature applies this strategy at the molecular level to achieve a complex biological function while maintaining the original activity in the catalytic pocket, suggesting an alternative way to design new enzyme function.
Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments
Authors: Yu Meishun , Zhang Menghui , Zeng Runying , Cheng Ruolin , Zhang Rui , Hou Yanping , Kuang Fangfang , Feng Xuejin , Dong Xiyang , Li Yinfang , Shao Zongze , Jin Min
Published: April 2024

Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.
Topology selectivity of a conformationally flexible precursor through selenium doping
Authors: Cai Liangliang , Gao Tianhao , Wee Andrew T. S.
Published: April 2024

Conformational arrangements within nanostructures play a crucial role in shaping the overall configuration and determining the properties, for example in covalent/metal organic frameworks. In on-surface synthesis, conformational diversity often leads to uncontrollable or disordered structures. Therefore, the exploration of controlling and directing the conformational arrangements is significant in achieving desired nanoarchitectures. Herein, a conformationally flexible precursor 2,4,6-tris(3-bromophenyl)−1,3,5-triazine is employed, and a random phase consisting of C3h and Cs conformers is firstly obtained after deposition of the precursor on Cu(111) at room temperature to 365 K. At low coverage (0.01 ML) selenium doping, we achieve the selectivity of the C3h conformer and improve the nanopore structural homogeneity. The ordered two-dimensional metal organic nanostructure can be fulfilled by selenium doping from room temperature to 365 K. The formation of the conformationally flexible precursor on Cu(111) is explored through the combination of high-resolution scanning tunneling microscopy and non-contact atomic force microscopy. The regulation of energy diagrams in the absence or presence of the Se atom is revealed by density functional theory calculations. These results can enrich the on-surface synthesis toolbox of conformationally flexible precursors, for the design of complex nanoarchitectures, and for future development of engineered nanomaterials.
Nerve growth factor receptor limits inflammation to promote remodeling and repair of osteoarthritic joints
Authors: Zhao Lan , Lai Yumei , Jiao Hongli , Huang Jian
Published: April 2024

Osteoarthritis (OA) is a painful, incurable disease affecting over 500 million people. Recent clinical trials of the nerve growth factor (NGF) inhibitors in OA patients have suggested adverse effects of NGF inhibition on joint structure. Here we report that nerve growth factor receptor (NGFR) is upregulated in skeletal cells during OA and plays an essential role in the remodeling and repair of osteoarthritic joints. Specifically, NGFR is expressed in osteochondral cells but not in skeletal progenitor cells and induced by TNFα to attenuate NF-κB activation, maintaining proper BMP-SMAD1 signaling and suppressing RANKL expression in mice. NGFR deficiency hyper-activates NF-κB in murine osteoarthritic joints, which impairs bone formation and enhances bone resorption as exemplified by a reduction in subchondral bone and osteophytes. In human OA cartilage, NGFR is also negatively associated with NF-κB activation. Together, this study suggests a role of NGFR in limiting inflammation for repair of diseased skeletal tissues.
Frugivores enhance potential carbon recovery in fragmented landscapes
Authors: Bello Carolina , Crowther Thomas W. , Ramos Danielle Leal , Morán-López Teresa , Pizo Marco A. , Dent Daisy H.
Published: April 2024

Forest restoration is fundamental to overcoming biodiversity crises and climate change. In tropical forests, animals can improve forest recovery as they disperse >70% of tree species. However, representing animals in restoration and climate change policies remains challenging because a quantitative assessment of their contribution to forest and carbon recovery is lacking. Here we used individual-based models to assess frugivore-mediated seed rain in open areas along a fragmentation gradient. Movements of large birds were limited in landscapes with <40% forest cover, although small birds continued to disperse seeds. Large birds disperse seeds of late-successional species with higher carbon storage potential. Their restricted movement therefore reduced potential biomass in future forests by 38%. Maintaining forest cover >40% is essential to optimizing animals’ contribution to restoration success. Active restoration (for example, planting trees) is required in more fragmented landscapes to achieve carbon and biodiversity targets.
Plant disease recognition using residual convolutional enlightened Swin transformer networks
Authors: Kalpana Ponugoti , Anandan R. , Hussien Abdelazim G. , Migdady Hazem , Abualigah Laith
Published: April 2024

Agriculture plays a pivotal role in the economic development of a nation, but, growth of agriculture is affected badly by the many factors one such is plant diseases. Early stage prediction of these disease is crucial role for global health and even for game changers the farmer’s life. Recently, adoption of modern technologies, such as the Internet of Things (IoT) and deep learning concepts has given the brighter light of inventing the intelligent machines to predict the plant diseases before it is deep-rooted in the farmlands. But, precise prediction of plant diseases is a complex job due to the presence of noise, changes in the intensities, similar resemblance between healthy and diseased plants and finally dimension of plant leaves. To tackle this problem, high-accurate and intelligently tuned deep learning algorithms are mandatorily needed. In this research article, novel ensemble of Swin transformers and residual convolutional networks are proposed. Swin transformers (ST) are hierarchical structures with linearly scalable computing complexity that offer performance and flexibility at various scales. In order to extract the best deep key-point features, the Swin transformers and residual networks has been combined, followed by Feed forward networks for better prediction. Extended experimentation is conducted using Plant Village Kaggle datasets, and performance metrics, including accuracy, precision, recall, specificity, and F1-rating, are evaluated and analysed. Existing structure along with FCN-8s, CED-Net, SegNet, DeepLabv3, Dense nets, and Central nets are used to demonstrate the superiority of the suggested version. The experimental results show that in terms of accuracy, precision, recall, and F1-rating, the introduced version shown better performances than the other state-of-art hybrid learning models.
Protein feature engineering framework for AMPylation site prediction
Authors: Prabhu Hardik , Bhosale Hrushikesh , Sane Aamod , Dhadwal Renu , Ramakrishnan Vigneshwar , Valadi Jayaraman
Published: April 2024

AMPylation is a biologically significant yet understudied post-translational modification where an adenosine monophosphate (AMP) group is added to Tyrosine and Threonine residues primarily. While recent work has illuminated the prevalence and functional impacts of AMPylation, experimental identification of AMPylation sites remains challenging. Computational prediction techniques provide a faster alternative approach. The predictive performance of machine learning models is highly dependent on the features used to represent the raw amino acid sequences. In this work, we introduce a novel feature extraction pipeline to encode the key properties relevant to AMPylation site prediction. We utilize a recently published dataset of curated AMPylation sites to develop our feature generation framework. We demonstrate the utility of our extracted features by training various machine learning classifiers, on various numerical representations of the raw sequences extracted with the help of our framework. Tenfold cross-validation is used to evaluate the model’s capability to distinguish between AMPylated and non-AMPylated sites. The top-performing set of features extracted achieved MCC score of 0.58, Accuracy of 0.8, AUC-ROC of 0.85 and F1 score of 0.73. Further, we elucidate the behaviour of the model on the set of features consisting of monogram and bigram counts for various representations using SHapley Additive exPlanations.
Lab on a bead with oscillatory centrifugal microfluidics for fast and complete mixing enables fast and accurate biomedical assays
Authors: Williams David E. , Li Wei , Chandrasekhar Mithileshwari , Corazza Carsten Ma On Wong , Deijs Gerrit Sjoerd , Djoko Lionel , Govind Bhavesh , Jose Ellen , Kwon Yong Je , Lowe Tiffany , Panchal Anil , Reshef Gabrielle , Vargas Matheus J. T. , Simpson M. Cather
Published: April 2024

Rapid mixing and precise timing are key for accurate biomedical assay measurement, particularly when the result is determined as the rate of a reaction: for example rapid immunoassay in which the amount of captured target is kinetically determined; determination of the concentration of an enzyme or enzyme substrate; or as the final stage in any procedure that involves a capture reagent when an enzyme reaction is used as the indicator. Rapid mixing and precise timing are however difficult to achieve in point-of-care devices designed for small sample volumes and fast time to result. By using centrifugal microfluidics and transposing the reaction surface from a chamber to a single mm-scale bead we demonstrate an elegant and easily manufacturable solution. Reagents (which may be, for example, an enzyme, enzyme substrate, antibody or antigen) are immobilised on the surface of a single small bead (typically 1–2 mm in diameter) contained in a cylindrical reaction chamber subjected to periodically changing rotational accelerations which promote both mixing and uniform mass-transfer to the bead surface. The gradient of Euler force across the chamber resulting from rotational acceleration of the disc, dΩdisc/dt, drives circulation of fluid in the chamber. Oscillation of Euler force by oscillation of rotational acceleration with period,T, less than that of the hydrodynamic relaxation time of the fluid, folds the fluid streamlines. Movement of the bead in response to the fluid and the changing rotational acceleration provides a dynamically changing chamber shape, further folding and expanding the fluid. Bead rotation and translation driven by fluid flow and disc motion give uniformity of reaction over the surface. Critical parameters for mixing and reaction uniformity are the ratio of chamber radius to bead radius,rchamber/rbead, and the productTrchamber(dΩdisc/dt), of oscillation period and Euler force gradient across the fluid.We illustrate application of the concept using the reaction of horse radish peroxidase (HRP) immobilised on the bead surface with its substrate tetramethylbenzidine (TMB) in solution. Acceleration from rest to break a hydrophobic valve provided precise timing for TMB contact with the bead. Solution uniformity from reaction on the surface of the bead in volumes 20–50 uL was obtained in times of 2.5 s or less. Accurate measurement of the amount of surface-bound HRP by model fitting to the measured kinetics of colour development at 10 s intervals is demonstrated.
Using sentinel-2 satellite images and machine learning algorithms to predict tropical pasture forage mass, crude protein, and fiber content
Authors: Fernandes Marcia Helena Machado da Rocha , FernandesJunior Jalme de Souza , Adams Jordan Melissa , Lee Mingyung , Reis Ricardo Andrade , Tedeschi Luis Orlindo
Published: April 2024

Grasslands cover approximately 24% of the Earth’s surface and are the main feed source for cattle and other ruminants. Sustainable and efficient grazing systems require regular monitoring of the quantity and nutritive value of pastures. This study demonstrates the potential of estimating pasture leaf forage mass (FM), crude protein (CP) and fiber content of tropical pastures using Sentinel-2 satellite images and machine learning algorithms. Field datasets and satellite images were assessed from an experimental area of Marandu palisade grass (Urochloa brizantha sny. Brachiaria brizantha) pastures, with or without nitrogen fertilization, and managed under continuous stocking during the pasture growing season from 2016 to 2020. Models based on support vector regression (SVR) and random forest (RF) machine-learning algorithms were developed using meteorological data, spectral reflectance, and vegetation indices (VI) as input features. In general, SVR slightly outperformed the RF models. The best predictive models to estimate FM were those with VI combined with meteorological data. For CP and fiber content, the best predictions were achieved using a combination of spectral bands and meteorological data, resulting in R2 of 0.66 and 0.57, and RMSPE of 0.03 and 0.04 g/g dry matter. Our results have promising potential to improve precision feeding technologies and decision support tools for efficient grazing management.
The potential of carbon markets to accelerate green infrastructure based water quality trading
Authors: Limb Braden J. , Quinn Jason C. , Johnson Alex , Sowby Robert B. , Thomas Evan
Published: April 2024

Green infrastructure solutions can improve in-stream water quality in lieu of building electricity-consuming gray infrastructure. Permitted under the United States Clean Water Act, these programs allow regulated utilities to trade point-source water quality obligations with non-point source mitigation efforts in the watershed. Carbon financing can provide an incentive for water quality trading. Here we combine data on impaired waters, treatment technologies, and life cycle greenhouse gas emissions in the Contiguous United States, and compare traditional treatment technologies to alternative green infrastructure. We find green infrastructure could save $15.6 billion dollars, 21.2 terawatt-hours of electricity, and 29.8 million tonnes of carbon dioxide equivalent emissions per year while sequestering over 4.2 million tonnes CO2e per year over a 40 year time horizon. Green infrastructure solutions may have the potential to generate $679 million annually in carbon credit revenue (at $20 per credit), which represents a unique opportunity to help accelerate water quality trading.
Non-antibiotic pharmaceuticals are toxic against Escherichia coli with no evolution of cross-resistance to antibiotics
Authors: Hall Rebecca J. , Snaith Ann E. , Element Sarah J. , Moran Robert A. , Smith Hannah , Cummins Elizabeth A. , Bottery Michael J. , Chowdhury Kaniz F. , Sareen Dipti , Ahmad Iqbal , Blair Jessica M. A. , Carter Laura J. , McNally Alan
Published: April 2024

Antimicrobial resistance can arise in the natural environment via prolonged exposure to the effluent released by manufacturing facilities. In addition to antibiotics, pharmaceutical plants also produce non-antibiotic pharmaceuticals, both the active ingredients and other components of the formulations. The effect of these on the surrounding microbial communities is less clear. We aimed to assess whether non-antibiotic pharmaceuticals and other compounds produced by pharmaceutical plants have inherent toxicity, and whether long-term exposure might result in significant genetic changes or select for cross-resistance to antibiotics. To this end, we screened four non-antibiotic pharmaceuticals (acetaminophen, ibuprofen, propranolol, metformin) and titanium dioxide for toxicity against Escherichia coli K-12 MG1655 and conducted a 30 day selection experiment to assess the effect of long-term exposure. All compounds reduced the maximum optical density reached by E. coli at a range of concentrations including one of environmental relevance, with transcriptome analysis identifying upregulated genes related to stress response and multidrug efflux in response ibuprofen treatment. The compounds did not select for significant genetic changes following a 30 day exposure, and no evidence of selection for cross-resistance to antibiotics was observed for population evolved in the presence of ibuprofen in spite of the differential gene expression after exposure to this compound. This work suggests that these compounds, at environmental concentrations, do not select for cross-resistance to antibiotics in E. coli.
A first-principles study of bilayer 1T'-WTe2/CrI3: a candidate topological spin filter
Authors: Staros Daniel , Rubenstein Brenda , Ganesh Panchapakesan
Published: April 2024

The ability to manipulate electronic spin channels in 2D materials is crucial for realizing next-generation spintronics. Spin filters are spintronic components that polarize spins using external electromagnetic fields or intrinsic material properties like magnetism. Recently, topological protection from backscattering has emerged as an enticing feature that can be leveraged to enhance the robustness of 2D spin filters. In this work, we propose and then characterize one of the first 2D topological spin filters: bilayer CrI3/1T’-WTe2. To do so, we use a combination of density functional theory, maximally localized Wannier functions, and quantum transport calculations to demonstrate that a terraced bilayer satisfies the principal criteria for being a topological spin filter: namely, that it is gapless, exhibits spin-polarized charge transfer from WTe2 to CrI3 that renders the bilayer metallic, and has a topological boundary which retains the edge conductance of monolayer 1T’-WTe2. In particular, we observe that small negative ferromagnetic moments are induced on the W atoms in the bilayer, and the atomic magnetic moments on the Cr are approximately 3.2 μB/Cr compared to 2.9 μB/Cr in freestanding monolayer CrI3. Subtracting the charge and spin densities of the constituent monolayers from those of the bilayer further reveals spin-orbit coupling-enhanced spin-polarized charge transfer from WTe2 to CrI3. We demonstrate that the bilayer is topologically trivial by showing that its Chern number is zero. Lastly, we show that interfacial scattering at the boundary between the terraced materials does not remove WTe2’s edge conductance. Altogether, this evidence indicates that BL 1T’-WTe2/CrI3 is gapless, magnetic, and topologically trivial, meaning that a terraced WTe2/CrI3 bilayer heterostructure in which only a portion of a WTe2 monolayer is topped with CrI3 is a promising candidate for a 2D topological spin filter. Our results further suggest that 1D chiral edge states may be realized by stacking strongly ferromagnetic monolayers, like CrI3, atop 2D nonmagnetic Weyl semimetals like 1T’-WTe2.
Preparation of an OHCP nanofiber photocatalyst for cross-dehydrogenation coupling reactions
Authors: Zhao Xingshun , Mi Yunshuai , Cai Tingwei , Chen Wanming , Dong Xia , He Jinxin , Zhao Qiangqiang
Published: April 2024

Phloxine B (PHB) exhibited high catalytic efficiency in cross-dehydrogenation coupling (CDC) reactions.
A wafer scale thin film of ultra-small Sc2O3 nanocrystals on a 2D COF with high rigidity
Authors: Guan Xin , Xu Xiaohui , Yu Zhongliang , Xiong Junjie , Chang Yanhong , Liu Bowen , Wang Bin
Published: April 2024

A method combining surfactant-assisted synthesis and laminar assembly polymerization is employed to fabricate a 2D Sc2O3/COF composite film at ambient temperature and pressure, achieving lateral infinitude, uniformity, and high mechanical strength.
Electroanalysis overview: additive manufactured biosensors using fused filament fabrication
Authors: Crapnell Robert D. , Banks Craig E.
Published: April 2024

Additive manufacturing (3D-printing), in particular fused filament fabrication, presents a paradigm shift in the way electrochemical based biosensing platforms are produced, giving rise to a new generation of personalized and on-demand biosensors.