bluuebunny/crossref_metadata_2025_split huggingface dataset:
Status of terrestrial mammals in the Yangambi Landscape, Democratic Republic of the Congo
Authors: van Vliet Nathalie , Quintero Simón , Muhindo Jonas , Nyumu Jonas , Omar Cerutti Paolo , Nasi Robert , Rovero Francesco 
Published: June 2023

AbstractIn this study we provide the first comprehensive camera-trap assessment of terrestrial mammals in the Yangambi landscape, comprising the Yangambi Biosphere Reserve and a logging concession in the Democratic Republic of the Congo. The terrestrial mammal community in this area exhibits lower occupancy and species richness compared to other conservation areas in the Congo Basin. The community is dominated by four species: Emin's pouched rat Cricetomys emini (1.3 kg), African brush-tailed porcupine Atherurus africanus (2.8 kg), blue duiker Philantomba monticola (5 kg) and bay duiker Cephalophus dorsalis (12 kg), which are known to be highly resilient. Large ungulates and medium-sized carnivores have particularly low abundances. Our study also confirmed the presence of four species categorized as threatened on the IUCN Red List: the chimpanzee Pan troglodytes, giant ground pangolin Smutsia gigantea, black-bellied pangolin Phataginus tetradactyla and white-bellied pangolin Phataginus tricuspis. Our findings highlight the need to consider wildlife conservation at the landscape level, including the logging concession, where species showed higher occupancy levels compared to the Biosphere Reserve, and highlighting the need for planning infrastructure construction and developing mitigation schemes, reducing forest degradation from logging and developing permanent cash crop agriculture. Landscape-level conservation will only be possible if a collaborative management model steered by local communities is developed with the participation of all constituencies.
Making Andesite Through Shallow Hybridization of Magmas Derived From Variably Enriched Lithospheric Mantle
Authors: Wang Song‐Jie , Brown Michael 
Published: June 2023

AbstractWe integrate textural and in situ compositional information from plagioclase and clinopyroxene (Cpx) phenocrysts together with groundmass compositions in early Cretaceous andesite dykes within the Sulu belt of China to propose a new petrogenetic model for andesite. Plagioclase phenocrysts are mostly andesine; they are depleted in high field strength elements (HFSE). However, Cpx phenocrysts are either reversely zoned (type I) or homogeneous (type II), with the zoned Cpx divided into subtypes IA and IB. All Cpx has high Mg#, low Na2O and generally low Al2O3, with depletions in HFSE and variably high 87Sr/86Sr ratios, suggesting crystallization above the Moho from magmas derived from enriched lithospheric mantle. The cores of type IA/IB and type II Cpx have normal major‐ and trace‐element compositional variations and similar 87Sr/86Sr ratios to each other and to plagioclase, consistent with fractional crystallization from a common magma (magma 1). The rims of type IA and IB Cpx also have normal major‐ and trace‐element compositional variations, but these are not as evolved as the cores, and the rims have lower 87Sr/86Sr ratios, demonstrating crystallization from an isotopically distinct magma (magma 2). Based on modeled major and rare earth element compositions of magmas inferred to have been in equilibrium with different Cpx (±plagioclase) domains, the measured groundmass compositions can be reproduced by variable mixing between the two magmas. Our study demonstrates for the first time that andesite magma can be made through fractionation and shallow hybridization of magmas derived from variably enriched lithospheric mantle.
Skimming Flow and Sand Transport Within and Above Ammophila (Marram) Grass on a Foredune
Authors: Rotnicka Joanna , Dłużewski Maciej , Hesp Patrick A. , Tomczak Joanna O. 
Published: June 2023

AbstractAn investigation of wind flow and sand transport over a low to high density Ammophila dominated foredune on the Łeba barrier, Poland, utilizing multiple anemometers and sand traps is presented. The study provides the first high resolution data on modified saltation and suspended sand transport over a foredune under conditions of both canopy and skimming flow. Topographic acceleration of flow and topographic steering over the foredune were observed during oblique incident above threshold flow conditions. The concentration of sand in aeolian transport decreases with height to a minimum that is reached at different elevations above the ground, depending on Ammophila grass density. Of the three Ammophila (marram) grass densities investigated, nearly half (46%) of the total sand‐transport rate occurred above the lower density Ammophila grass, whereas up to 70% of the total transport occurred above the higher density marram grass. This likely results from both elastic collisions of sand grains with grass leaves over the Ammophila canopy and the different positions of the canopy rebounding surface, which is sensitive to even slight changes in wind speed. In addition, as plant density increases, there is less flow penetration into the canopy, vegetative forcing (similar to topographic forcing) of vertical flow is greater, and sand in both modified saltation and suspension is forced higher above the canopy in skimming flow. The maximum sand transport above the vegetation canopy increased in elevation from 32 to 48 to 53 cm as the vegetation density increased from low to moderate to high, respectively. The study also demonstrates that in skimming flow, relatively more sand is transported at higher elevations above a canopy surface than above a bare sand surface.
Microneedle array facilitates hepatic sinusoid construction in a large-scale liver-acinus-chip microsystem
Authors: Li Shibo , Li Chengpan , Khan Muhammad Imran , Liu Jing , Shi Zhengdi , Gao Dayong , Qiu Bensheng , Ding Weiping 
Published: June 2023

AbstractHepatic sinusoids play a key role in maintaining high activities of liver cells in the hepatic acinus. However, the construction of hepatic sinusoids has always been a challenge for liver chips, especially for large-scale liver microsystems. Herein, we report an approach for the construction of hepatic sinusoids. In this approach, hepatic sinusoids are formed by demolding a self-developed microneedle array from a photocurable cell-loaded matrix in a large-scale liver-acinus-chip microsystem with a designed dual blood supply. Primary sinusoids formed by demolded microneedles and spontaneously self-organized secondary sinusoids can be clearly observed. Benefiting from significantly enhanced interstitial flows by formed hepatic sinusoids, cell viability is witnessed to be considerably high, liver microstructure formation occurs, and hepatocyte metabolism is enhanced. In addition, this study preliminarily demonstrates the effects of the resulting oxygen and glucose gradients on hepatocyte functions and the application of the chip in drug testing. This work paves the way for the biofabrication of fully functionalized large-scale liver bioreactors.
The novel uncompetitive NMDA receptor antagonist esmethadone (REL-1017) has no meaningful abuse potential in recreational drug users
Authors: Shram Megan J. , Henningfield Jack E. , Apseloff Glen , Gorodetzky Charles W. , De Martin Sara , Vocci Frank L. , Sapienza Frank L. , Kosten Thomas R. , Huston Jeff , Buchhalter August , Ashworth Judy , Lanier Ryan , Folli Franco , Mattarei Andrea , Guidetti Clotilde , Comai Stefano , O’Gorman Cedric , Traversa Sergio , Inturrisi Charles E. , Manfredi Paolo L. , Pappagallo Marco 
Published: June 2023

AbstractEsmethadone (REL-1017) is the opioid-inactive dextro-isomer of methadone and a low-affinity, low-potency uncompetitive NMDA receptor antagonist. In a Phase 2, randomized, double-blind, placebo-controlled trial, esmethadone showed rapid, robust, and sustained antidepressant effects. Two studies were conducted to evaluate the abuse potential of esmethadone. Each study utilized a randomized, double-blind, active-, and placebo-controlled crossover design to assess esmethadone compared with oxycodone (Oxycodone Study) or ketamine (Ketamine Study) in healthy recreational drug users. Esmethadone 25 mg (proposed therapeutic daily dose), 75 mg (loading dose), and 150 mg (Maximum Tolerated Dose) were evaluated in each study. Positive controls were oral oxycodone 40 mg and intravenous ketamine 0.5 mg/kg infused over 40 min. The Ketamine study included oral dextromethorphan 300 mg as an exploratory comparator. The primary endpoint was maximum effect (Emax) for Drug Liking, assessed using a bipolar 100-point visual analog scale (VAS). A total of 47 and 51 participants completed the Oxycodone Study and the Ketamine Study, respectively (Completer Population). In both studies, esmethadone doses ranging from therapeutic (25 mg) to 6 times therapeutic (150 mg) had a meaningful and statistically significantly (p < 0.001) lower Drug Liking VAS Emax compared with the positive control. Results were consistent for all secondary endpoints in both studies. In both studies, all doses of esmethadone were statistically equivalent to placebo on Drug Liking VAS Emax (p < 0.05). In the Ketamine Study, Drug Liking VAS Emax scores for esmethadone at all tested doses were significantly lower vs. dextromethorphan (p < 0.05) (exploratory endpoint). These studies indicate no meaningful abuse potential for esmethadone at all tested doses.
The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements
Authors: Korn Sophie Marianne , Dhamotharan Karthikeyan , Jeffries Cy M. , Schlundt Andreas 
Published: June 2023

AbstractThe nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N’s N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5’-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain’s flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.
Single-site decorated copper enables energy- and carbon-efficient CO2 methanation in acidic conditions
Authors: Fan Mengyang , Miao Rui Kai , Ou Pengfei , Xu Yi , Lin Zih-Yi , Lee Tsung-Ju , Hung Sung-Fu , Xie Ke , Huang Jianan Erick , Ni Weiyan , Li Jun , Zhao Yong , Ozden Adnan , O’Brien Colin P. , Chen Yuanjun , Xiao Yurou Celine , Liu Shijie , Wicks Joshua , Wang Xue , Abed Jehad , Shirzadi Erfan , Sargent Edward H. , Sinton David 
Published: June 2023

AbstractRenewable CH4produced from electrocatalytic CO2reduction is viewed as a sustainable and versatile energy carrier, compatible with existing infrastructure. However, conventional alkaline and neutral CO2-to-CH4systems suffer CO2loss to carbonates, and recovering the lost CO2requires input energy exceeding the heating value of the produced CH4. Here we pursue CH4-selective electrocatalysis in acidic conditions via a coordination method, stabilizing free Cu ions by bonding Cu with multidentate donor sites. We find that hexadentate donor sites in ethylenediaminetetraacetic acid enable the chelation of Cu ions, regulating Cu cluster size and forming Cu-N/O single sites that achieve high CH4selectivity in acidic conditions. We report a CH4Faradaic efficiency of 71% (at 100 mA cm−2) with <3% loss in total input CO2that results in an overall energy intensity (254 GJ/tonne CH4), half that of existing electroproduction routes.
Coherent Stokes Raman scattering microscopy (CSRS)
Authors: Heuke Sandro , Rigneault Hervé 
Published: June 2023

AbstractWe report the first implementation of laser scanning coherent Stokes Raman scattering (CSRS) microscopy. To overcome the major challenge in CSRS imaging, we show how to suppress the fluorescence background by narrow bandpass filter and a lock-in based demodulation. Near background free CSRS imaging of polymer beads, human skin, onion cells, avocado flesh and the wing disc of a drosphila larva are presented. Finally, we explain and demonstrate numerically that CSRS solves a major obstacle of other coherent Raman techniques by sending a significant part (up to 100%) of the CSRS photons into the backward direction under tight focusing conditions. We believe that this discovery will pave the way for numerous technological advances, e.g., in epi-detected coherent Raman multi-focus imaging, real-time laser scanning based spectroscopy or efficient endoscopy.
A high-throughput test enables specific detection of hepatocellular carcinoma
Authors: Cheishvili David , Wong Chifat , Karim Mohammad Mahbubul , Kibria Mohammad Golam , Jahan Nusrat , Das Pappu Chandra , Yousuf Md. Abul Khair , Islam Md. Atikul , Das Dulal Chandra , Noor-E-Alam Sheikh Mohammad , Szyf Moshe , Alam Sarwar , Khan Wasif A. , Al Mahtab Mamun 
Published: June 2023

AbstractHigh-throughput tests for early cancer detection can revolutionize public health and reduce cancer morbidity and mortality. Here we show a DNA methylation signature for hepatocellular carcinoma (HCC) detection in liquid biopsies, distinct from normal tissues and blood profiles. We developed a classifier using four CpG sites, validated in TCGA HCC data. A single F12 gene CpG site effectively differentiates HCC samples from other blood samples, normal tissues, and non-HCC tumors in TCGA and GEO data repositories. The markers were validated in a separate plasma sample dataset from HCC patients and controls. We designed a high-throughput assay using next-generation sequencing and multiplexing techniques, analyzing plasma samples from 554 clinical study participants, including HCC patients, non-HCC cancers, chronic hepatitis B, and healthy controls. HCC detection sensitivity was 84.5% at 95% specificity and 0.94 AUC. Implementing this assay for high-risk individuals could significantly decrease HCC morbidity and mortality.
The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells
Authors: Quendera Ana Patrícia , Pinto Sandra Nunes , Pobre Vânia , Antunes Wilson , Bonifácio Vasco D. B. , Arraiano Cecília Maria , Andrade José Marques 
Published: June 2023

AbstractBiofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. Here we show that the RNA-binding protein and ribonuclease polynucleotide phosphorylase (PNPase) is a positive regulator of biofilm formation in the human pathogen Listeria monocytogenes, a major responsible for food contamination in food-processing environments. The PNPase mutant strain produces less biofilm biomass and exhibits an altered biofilm morphology that is more susceptible to antibiotic treatment. Through biochemical assays and microscopical analysis, we demonstrate that PNPase is a previously unrecognized regulator of the composition of the biofilm extracellular matrix, greatly affecting the levels of proteins, extracellular DNA, and sugars. Noteworthy, we have adapted the use of the fluorescent complex ruthenium red-phenanthroline for the detection of polysaccharides in Listeria biofilms. Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. Overall, this work demonstrates that PNPase is an important post-transcriptional regulator for virulence and adaptation to the biofilm lifestyle of Gram-positive bacteria and highlights the expanding role of ribonucleases as critical players in pathogenicity.
Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage
Authors: Leung Howell , Xiong Ling , Ni Yueqiong , Busch Anne , Bauer Michael , Press Adrian T. , Panagiotou Gianni 
Published: June 2023

AbstractCurrently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.
Interchange reconnection as the source of the fast solar wind within coronal holes
Authors: Bale S. D. , Drake J. F. , McManus M. D. , Desai M. I. , Badman S. T. , Larson D. E. , Swisdak M. , Horbury T. S. , Raouafi N. E. , Phan T. , Velli M. , McComas D. J. , Cohen C. M. S. , Mitchell D. , Panasenco O. , Kasper J. C. 
Published: June 2023

AbstractThe fast solar wind that fills the heliosphere originates from deep within regions of open magnetic field on the Sun called ‘coronal holes’. The energy source responsible for accelerating the plasma is widely debated; however, there is evidence that it is ultimately magnetic in nature, with candidate mechanisms including wave heating1,2 and interchange reconnection3–5. The coronal magnetic field near the solar surface is structured on scales associated with ‘supergranulation’ convection cells, whereby descending flows create intense fields. The energy density in these ‘network’ magnetic field bundles is a candidate energy source for the wind. Here we report measurements of fast solar wind streams from the Parker Solar Probe (PSP) spacecraft6 that provide strong evidence for the interchange reconnection mechanism. We show that the supergranulation structure at the coronal base remains imprinted in the near-Sun solar wind, resulting in asymmetric patches of magnetic ‘switchbacks’7,8 and bursty wind streams with power-law-like energetic ion spectra to beyond 100 keV. Computer simulations of interchange reconnection support key features of the observations, including the ion spectra. Important characteristics of interchange reconnection in the low corona are inferred from the data, including that the reconnection is collisionless and that the energy release rate is sufficient to power the fast wind. In this scenario, magnetic reconnection is continuous and the wind is driven by both the resulting plasma pressure and the radial Alfvénic flow bursts.
Structural basis for FGF hormone signalling
Authors: Chen Lingfeng , Fu Lili , Sun Jingchuan , Huang Zhiqiang , Fang Mingzhen , Zinkle Allen , Liu Xin , Lu Junliang , Pan Zixiang , Wang Yang , Liang Guang , Li Xiaokun , Chen Gaozhi , Mohammadi Moosa 
Published: June 2023

Abstractα/βKlotho coreceptors simultaneously engage fibroblast growth factor (FGF) hormones (FGF19, FGF21 and FGF23)1,2 and their cognate cell-surface FGF receptors (FGFR1–4) thereby stabilizing the endocrine FGF–FGFR complex3–6. However, these hormones still require heparan sulfate (HS) proteoglycan as an additional coreceptor to induce FGFR dimerization/activation and hence elicit their essential metabolic activities6. To reveal the molecular mechanism underpinning the coreceptor role of HS, we solved cryo-electron microscopy structures of three distinct 1:2:1:1 FGF23–FGFR–αKlotho–HS quaternary complexes featuring the ‘c’ splice isoforms of FGFR1 (FGFR1c), FGFR3 (FGFR3c) or FGFR4 as the receptor component. These structures, supported by cell-based receptor complementation and heterodimerization experiments, reveal that a single HS chain enables FGF23 and its primary FGFR within a 1:1:1 FGF23–FGFR–αKlotho ternary complex to jointly recruit a lone secondary FGFR molecule leading to asymmetric receptor dimerization and activation. However, αKlotho does not directly participate in recruiting the secondary receptor/dimerization. We also show that the asymmetric mode of receptor dimerization is applicable to paracrine FGFs that signal solely in an HS-dependent fashion. Our structural and biochemical data overturn the current symmetric FGFR dimerization paradigm and provide blueprints for rational discovery of modulators of FGF signalling2 as therapeutics for human metabolic diseases and cancer.
Unveiling the transition from niche to dispersal assembly in ecology
Authors: Loke Lynette H. L. , Chisholm Ryan A. 
Published: June 2023

AbstractA central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a ‘niche detector’ and a tool for assessing when communities are niche versus dispersal assembled.