bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water Oxygen Consumption Rather Than Sediment Oxygen Consumption Drives the Variation of Hypoxia on the East China Sea Shelf
Authors: Meng Qicheng , Zhang Wenyan , Zhou Feng , Liao Yibo , Yu Peisong , Tang Yanbin , Ma Xiao , Tian Di , Ding Ruibin , Ni Xiaobo , Zeng Dingyong , Schrum Corinna 
Published: January 2022

AbstractSediment oxygen consumption (SOC) is important in modulating the oxygen budget in the East China Sea where seasonal hypoxia occurs. Porewater advection, molecular diffusion and bioturbation supply oxygen for sedimentary organic matter degradation. A pelagic‐benthic coupled model was applied to quantify the SOC. A comparison with observations showed good model performance in reproducing the hydrographic and ecological environments, particularly for the interannual variation in the hypoxic zone. Simulation results show that porewater‐advection‐induced flux is the predominant component of the SOC in sandy areas on the Changjiang bank and outer shelves, while the bioturbation‐induced flux is predominant at mud depocenters. By comparing SOC to the water oxygen consumption (WOC) below the pycnocline, the contribution of SOC is generally below ∼40% in the hypoxic zone. The spatial distribution of SOC in summer is relatively steady from year to year, while the high WOC patches explain more about the interannual variation in the hypoxic zone. WOC rather than SOC drives the variation of hypoxia. Particularly on the Changjiang bank, milder hydrodynamics are favorable for both the higher WOC and bioturbation‐induced benthic oxygen flux but substantially suppress the porewater advective flux, which results in the net lower contribution of SOC to hypoxia. This finding may shed light on other pelagic‐benthic coupling processes in coastal shelf seas where hypoxia occurs on permeable sediments.
Hydro‐Morphological Disturbance and Suitability for Temporary Agriculture of Riverine Islands in a Tropical Wandering River
Authors: Serrao Livia , Brentari Luca , Balcazar Terrones Luz Elita , Huamaní Yupanqui Hugo Alfredo , Rengifo Trigoso Juan Pablo , Zolezzi Guido 
Published: January 2022

AbstractFluvial islands define fundamental interfaces between the aquatic and terrestrial environment in river corridors, have unique environmental value, and represent a place of interest for human communities worldwide. Temporary agriculture occurs in many riverine islands in tropical regions of the planet, but this has received little attention so far. By integrating remote sensing, field and laboratory investigations, hydrological and hydraulic analysis, we quantified controls on their agricultural suitability in terms of fluvial disturbance, morphological stability, soils characteristics, and selection of flood‐resistant crops. A highly dynamic foothill reach of the wandering Huallaga River (Peruvian Amazon) where temporary agriculture is practiced by local farmers is used as a case study. Islands show rapid turnover rates, with their number and total area tripling in the 1986‐2019 period, in association with recent river corridor widening. Simulated disturbance‐free windows of opportunity can be long enough (up to 230 days, for plantain) to cultivate on the most elevated portions of the largest islands, about 3 m above the thalweg. A gradient of increasing agricultural suitability paralleled that of decreasing fluvial disturbance from the most recently developed island (e.g., organic matter 0.2%–1.2%) to the more stable one (0.1%–2.6%) to the established floodplain (0.5%–3.5%). While the floodplain is more suitable for farming, we quantified how suitable islands are for temporary food production. Our results are generalized through a conceptual model for fluvial islands' agricultural suitability, thus filling an important knowledge gap about the characteristics of those highly sensitive environments within floodplains still moderately affected by human activities.
Cardiomyocyte IL-1R2 protects heart from ischemia/reperfusion injury by attenuating IL-17RA-mediated cardiomyocyte apoptosis
Authors: Lin Jun , Li Qinfeng , Jin Tingting , Wang Jiacheng , Gong Yingchao , Lv Qingbo , Wang Meihui , Chen Jiawen , Shang Min , Zhao Yanbo , Fu Guosheng 
Published: January 2022

AbstractMyocardial ischemia reperfusion (I/R) injury is a complex process with intense inflammatory response and cardiomyocyte apoptosis. As a decoy receptor of IL-1β, Interleukin-1 receptor type 2 (IL-1R2) inhibits IL-1β signaling. However, its role in I/R injury remains unknown. Here we found that the serum levels of IL-1R2 were significantly increased in patients with acute myocardial infarction (AMI) following interventional therapy. Similarly, after myocardial I/R surgery, IL-1R2 expression was significantly increased in heart of wild-type mice. In addition, IL-1R2-deficient mice heart showed enlarged infarct size, increased cardiomyocyte apoptosis together with reduced cardiac systolic function. Following exposure to hypoxia and reoxygenation (H/R), neonatal rat ventricular myocytes (NRVM) significantly increased IL-1R2 expression relying on NF-κB activation. Consistently, IL-1R2-deficient mice increased immune cells infiltrating into heart after surgery, which was relevant with cardiac damage. Additionally, IL-1R2 overexpression in cardiomyocyte protected cardiomyocyte against apoptosis through reducing the IL-17RA expression both in vivo and in vitro. Our results indicate that IL-1R2 protects cardiomyocytes from apoptosis, which provides a therapeutic approach to turn down myocardial I/R injury.
Machine learning-informed and synthetic biology-enabled semi-continuous algal cultivation to unleash renewable fuel productivity
Authors: Long Bin , Fischer Bart , Zeng Yining , Amerigian Zoe , Li Qiang , Bryant Henry , Li Man , Dai Susie Y. , Yuan Joshua S. 
Published: January 2022

AbstractAlgal biofuel is regarded as one of the ultimate solutions for renewable energy, but its commercialization is hindered by growth limitations caused by mutual shading and high harvest costs. We overcome these challenges by advancing machine learning to inform the design of a semi-continuous algal cultivation (SAC) to sustain optimal cell growth and minimize mutual shading. An aggregation-based sedimentation (ABS) strategy is then designed to achieve low-cost biomass harvesting and economical SAC. The ABS is achieved by engineering a fast-growing strain, Synechococcus elongatus UTEX 2973, to produce limonene, which increases cyanobacterial cell surface hydrophobicity and enables efficient cell aggregation and sedimentation. SAC unleashes cyanobacterial growth potential with 0.1 g/L/hour biomass productivity and 0.2 mg/L/hour limonene productivity over a sustained period in photobioreactors. Scaling-up the SAC with an outdoor pond system achieves a biomass yield of 43.3 g/m2/day, bringing the minimum biomass selling price down to approximately $281 per ton.
Control of electronic band profiles through depletion layer engineering in core–shell nanocrystals
Authors: Ghini Michele , Curreli Nicola , Lodi Matteo B. , Petrini Nicolò , Wang Mengjiao , Prato Mirko , Fanti Alessandro , Manna Liberato , Kriegel Ilka 
Published: January 2022

AbstractFermi level pinning in doped metal oxide (MO) nanocrystals (NCs) results in the formation of depletion layers, which affect their optical and electronic properties, and ultimately their application in smart optoelectronics, photocatalysis, or energy storage. For a precise control over functionality, it is important to understand and control their electronic bands at the nanoscale. Here, we show that depletion layer engineering allows designing the energetic band profiles and predicting the optoelectronic properties of MO NCs. This is achieved by shell thickness tuning of core–shell Sn:In2O3–In2O3 NCs, resulting in multiple band bending and multi-modal plasmonic response. We identify the modification of the band profiles after the light-induced accumulation of extra electrons as the main mechanism of photodoping and enhance the charge storage capability up to hundreds of electrons per NC through depletion layer engineering. Our experimental results are supported by theoretical models and are transferable to other core-multishell systems as well.
The neglected role of relative humidity in the interannual variability of urban malaria in Indian cities
Authors: Santos-Vega M. , Martinez P. P. , Vaishnav K. G. , Kohli V. , Desai V. , Bouma M. J. , Pascual M. 
Published: January 2022

AbstractThe rapid pace of urbanization makes it imperative that we better understand the influence of climate forcing on urban malaria transmission. Despite extensive study of temperature effects in vector-borne infections in general, consideration of relative humidity remains limited. With process-based dynamical models informed by almost two decades of monthly surveillance data, we address the role of relative humidity in the interannual variability of epidemic malaria in two semi-arid cities of India. We show a strong and significant effect of humidity during the pre-transmission season on malaria burden in coastal Surat and more arid inland Ahmedabad. Simulations of the climate-driven transmission model with the MLE (Maximum Likelihood Estimates) of the parameters retrospectively capture the observed variability of disease incidence, and also prospectively predict that of ‘out-of-fit’ cases in more recent years, with high accuracy. Our findings indicate that relative humidity is a critical factor in the spread of urban malaria and potentially other vector-borne epidemics, and that climate change and lack of hydrological planning in cities might jeopardize malaria elimination efforts.
Carbohydrate-aromatic interface and molecular architecture of lignocellulose
Authors: Kirui Alex , Zhao Wancheng , Deligey Fabien , Yang Hui , Kang Xue , Mentink-Vigier Frederic , Wang Tuo 
Published: January 2022

AbstractPlant cell walls constitute the majority of lignocellulosic biomass and serve as a renewable resource of biomaterials and biofuel. Extensive interactions between polysaccharides and the aromatic polymer lignin make lignocellulose recalcitrant to enzymatic hydrolysis, but this polymer network remains poorly understood. Here we interrogate the nanoscale assembly of lignocellulosic components in plant stems using solid-state nuclear magnetic resonance and dynamic nuclear polarization approaches. We show that the extent of glycan-aromatic association increases sequentially across grasses, hardwoods, and softwoods. Lignin principally packs with the xylan in a non-flat conformation via non-covalent interactions and partially binds the junction of flat-ribbon xylan and cellulose surface as a secondary site. All molecules are homogeneously mixed in softwoods; this unique feature enables water retention even around the hydrophobic aromatics. These findings unveil the principles of polymer interactions underlying the heterogeneous architecture of lignocellulose, which may guide the rational design of more digestible plants and more efficient biomass-conversion pathways.
Cholinergic signals preserve haematopoietic stem cell quiescence during regenerative haematopoiesis
Authors: Fielding Claire , García-García Andrés , Korn Claudia , Gadomski Stephen , Fang Zijian , Reguera Juan L. , Pérez-Simón José A. , Göttgens Berthold , Méndez-Ferrer Simón 
Published: January 2022

AbstractThe sympathetic nervous system has been evolutionary selected to respond to stress and activates haematopoietic stem cells via noradrenergic signals. However, the pathways preserving haematopoietic stem cell quiescence and maintenance under proliferative stress remain largely unknown. Here we found that cholinergic signals preserve haematopoietic stem cell quiescence in bone-associated (endosteal) bone marrow niches. Bone marrow cholinergic neural signals increase during stress haematopoiesis and are amplified through cholinergic osteoprogenitors. Lack of cholinergic innervation impairs balanced responses to chemotherapy or irradiation and reduces haematopoietic stem cell quiescence and self-renewal. Cholinergic signals activate α7 nicotinic receptor in bone marrow mesenchymal stromal cells leading to increased CXCL12 expression and haematopoietic stem cell quiescence. Consequently, nicotine exposure increases endosteal haematopoietic stem cell quiescence in vivo and impairs hematopoietic regeneration after haematopoietic stem cell transplantation in mice. In humans, smoking history is associated with delayed normalisation of platelet counts after allogeneic haematopoietic stem cell transplantation. These results suggest that cholinergic signals preserve stem cell quiescence under proliferative stress.
Structural basis for safe and efficient energy conversion in a respiratory supercomplex
Authors: Kao Wei-Chun , Ortmann de Percin Northumberland Claire , Cheng Tat Cheung , Ortiz Julio , Durand Alexandre , von Loeffelholz Ottilie , Schilling Oliver , Biniossek Martin L. , Klaholz Bruno P. , Hunte Carola 
Published: January 2022

AbstractProton-translocating respiratory complexes assemble into supercomplexes that are proposed to increase the efficiency of energy conversion and limit the production of harmful reactive oxygen species during aerobic cellular respiration. Cytochrome bc complexes and cytochrome aa3 oxidases are major drivers of the proton motive force that fuels ATP generation via respiration, but how wasteful electron- and proton transfer is controlled to enhance safety and efficiency in the context of supercomplexes is not known. Here, we address this question with the 2.8 Å resolution cryo-EM structure of the cytochrome bcc-aa3 (III2-IV2) supercomplex from the actinobacterium Corynebacterium glutamicum. Menaquinone, substrate mimics, lycopene, an unexpected Qc site, dioxygen, proton transfer routes, and conformational states of key protonable residues are resolved. Our results show how safe and efficient energy conversion is achieved in a respiratory supercomplex through controlled electron and proton transfer. The structure may guide the rational design of drugs against actinobacteria that cause diphtheria and tuberculosis.
Aberrant upregulation of the glycolytic enzyme PFKFB3 in CLN7 neuronal ceroid lipofuscinosis
Authors: Lopez-Fabuel Irene , Garcia-Macia Marina , Buondelmonte Costantina , Burmistrova Olga , Bonora Nicolo , Alonso-Batan Paula , Morant-Ferrando Brenda , Vicente-Gutierrez Carlos , Jimenez-Blasco Daniel , Quintana-Cabrera Ruben , Fernandez Emilio , Llop Jordi , Ramos-Cabrer Pedro , Sharaireh Aseel , Guevara-Ferrer Marta , Fitzpatrick Lorna , Thompton Christopher D. , McKay Tristan R. , Storch Stephan , Medina Diego L. , Mole Sara E. , Fedichev Peter O. , Almeida Angeles , Bolaños Juan P. 
Published: January 2022

AbstractCLN7 neuronal ceroid lipofuscinosis is an inherited lysosomal storage neurodegenerative disease highly prevalent in children.CLN7/MFSD8gene encodes a lysosomal membrane glycoprotein, but the biochemical processes affected by CLN7-loss of function are unexplored thus preventing development of potential treatments. Here, we found, in theCln7∆ex2mouse model of CLN7 disease, that failure in autophagy causes accumulation of structurally and bioenergetically impaired neuronal mitochondria. In vivo genetic approach reveals elevated mitochondrial reactive oxygen species (mROS) inCln7∆ex2neurons that mediates glycolytic enzyme PFKFB3 activation and contributes to CLN7 pathogenesis. Mechanistically, mROS sustains a signaling cascade leading to protein stabilization of PFKFB3, normally unstable in healthy neurons. Administration of the highly selective PFKFB3 inhibitor AZ67 inCln7∆ex2mouse brain in vivo and in CLN7 patients-derived cells rectifies key disease hallmarks. Thus, aberrant upregulation of the glycolytic enzyme PFKFB3 in neurons may contribute to CLN7 pathogenesis and targeting PFKFB3 could alleviate this and other lysosomal storage diseases.
Emerging experience-dependent dynamics in primary somatosensory cortex reflect behavioral adaptation
Authors: Waiblinger Christian , McDonnell Megan E. , Reedy April R. , Borden Peter Y. , Stanley Garrett B. 
Published: January 2022

AbstractBehavioral experience and flexibility are crucial for survival in a constantly changing environment. Despite evolutionary pressures to develop adaptive behavioral strategies in a dynamically changing sensory landscape, the underlying neural correlates have not been well explored. Here, we use genetically encoded voltage imaging to measure signals in primary somatosensory cortex (S1) during sensory learning and behavioral adaptation in the mouse. In response to changing stimulus statistics, mice adopt a strategy that modifies their detection behavior in a context dependent manner as to maintain reward expectation. Surprisingly, neuronal activity in S1 shifts from simply representing stimulus properties to transducing signals necessary for adaptive behavior in an experience dependent manner. Our results suggest that neuronal signals in S1 are part of an adaptive framework that facilitates flexible behavior as individuals gain experience, which could be part of a general scheme that dynamically distributes the neural correlates of behavior during learning.
Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module
Authors: Fortinez Camille Marie , Bloudoff Kristjan , Harrigan Connor , Sharon Itai , Strauss Mike , Schmeing T. Martin 
Published: January 2022

AbstractNonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
Operando monitoring of ion activities in aqueous batteries with plasmonic fiber-optic sensors
Authors: Wang Runlin , Zhang Haozhe , Liu Qiyu , Liu Fu , Han Xile , Liu Xiaoqing , Li Kaiwei , Xiao Gaozhi , Albert Jacques , Lu Xihong , Guo Tuan 
Published: January 2022

AbstractUnderstanding ion transport kinetics and electrolyte-electrode interactions at electrode surfaces of batteries in operation is essential to determine their performance and state of health. However, it remains a challenging task to capture in real time the details of surface-localized and rapid ion transport at the microscale. To address this, a promising approach based on an optical fiber plasmonic sensor capable of being inserted near the electrode surface of a working battery to monitor its electrochemical kinetics without disturbing its operation is demonstrated using aqueous Zn-ion batteries as an example. The miniature and chemically inert sensor detects perturbations of surface plasmon waves propagating on its surface to rapidly screen localized electrochemical events on a sub-μm-scale thickness adjacent to the electrode interface. A stable and reproducible correlation between the real-time ion insertions over charge-discharge cycles and the optical plasmon response has been observed and quantified. This new operando measurement tool will provide crucial additional capabilities to battery monitoring methods and help guide the design of better batteries with improved electro-chemistries.
Atherosclerosis amelioration by allicin in raw garlic through gut microbiota and trimethylamine-N-oxide modulation
Authors: Panyod Suraphan , Wu Wei-Kai , Chen Pei-Chen , Chong Kent-Vui , Yang Yu-Tang , Chuang Hsiao-Li , Chen Chieh-Chang , Chen Rou-An , Liu Po-Yu , Chung Ching-Hu , Huang Huai-Syuan , Lin Angela Yu-Chen , Shen Ting-Chin David , Yang Kai-Chien , Huang Tur-Fu , Hsu Cheng-Chih , Ho Chi-Tang , Kao Hsien-Li , Orekhov Alexander N. , Wu Ming-Shiang , Sheen Lee-Yan 
Published: January 2022

AbstractCardiovascular disease (CVD) is strongly associated with the gut microbiota and its metabolites, including trimethylamine-N-oxide (TMAO), formed from metaorganismal metabolism of ʟ-carnitine. Raw garlic juice, with allicin as its primary compound, exhibits considerable effects on the gut microbiota. This study validated the benefits of raw garlic juice against CVD risk via modulation of the gut microbiota and its metabolites. Allicin supplementation significantly decreased serum TMAO in ʟ-carnitine-fed C57BL/6 J mice, reduced aortic lesions, and altered the fecal microbiota in carnitine-induced, atherosclerosis-prone, apolipoprotein E-deficient (ApoE−/−) mice. In human subjects exhibiting high-TMAO production, raw garlic juice intake for a week reduced TMAO formation, improved gut microbial diversity, and increased the relative abundances of beneficial bacteria. In in vitro and ex vivo studies, raw garlic juice and allicin inhibited γ-butyrobetaine (γBB) and trimethylamine production by the gut microbiota. Thus, raw garlic juice and allicin can potentially prevent cardiovascular disease by decreasing TMAO production via gut microbiota modulation.
Increased trunk fat is associated with altered gene expression in breast tissue of normal weight women
Authors: Cho Byuri Angela , Iyengar Neil M. , Zhou Xi Kathy , Mendieta Hillary , Winston Lisle , Falcone Domenick J. , Landa Jonathan , Morrow Monica , Dannenberg Andrew J. 
Published: January 2022

AbstractIncreased trunk fat is associated with an elevated risk of breast cancer in normal-weight postmenopausal women. The main objective of this study was to determine whether levels of trunk fat are associated with changes in breast gene expression in normal-weight women. Non-tumorous breast tissue was collected from 32 normal BMI women who underwent mastectomy for breast cancer risk reduction or treatment. Body composition was measured by dual-energy x-ray absorptiometry. High levels of trunk fat were associated with a large number of differentially expressed genes and changes in multiple pathways and processes potentially linked to breast cancer pathogenesis. High levels of trunk fat were also associated with an elevated immune score and increased levels of leptin, CCL2, VEGF-C, IL6, and aromatase. Collectively, these results help to explain why high levels of trunk fat are associated with an increased risk of breast cancer in normal BMI women.