bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tides, Internal and Near‐Inertial Waves in the Yermak Pass at the Entrance of the Atlantic Water to the Arctic Ocean
Authors: Artana Camila , Provost Christine , Ferrari Ramiro , Bricaud Clément , Poli Léa , Park Young‐Hyang 
Published: December 2022

AbstractIn the crucial region of the Yermak Plateau where warm Atlantic water enters the Arctic ocean, we examined high frequency variations in the Yermak Pass Branch over a 34 months‐long mooring data set. The mooring was ice covered only half of the time with ice‐free periods both in summer and winter. We investigated the contribution of residual tidal currents to the low frequency flow of Atlantic Water (AW) and high frequency variations in velocity shears possibly associated with internal waves. High resolution model simulations including tides show that diurnal tide forced an anticyclonic circulation around the Yermak Plateau. This residual circulation helps the northward penetration of the AW into the Arctic. Tides should be taken into account when examining low frequency AW inflow. High frequency variations in velocity shears are mainly concentrated in a broad band around 12 hr in the Yermak Pass. Anticyclonic eddies, observed during ice‐free conditions, modulate the shear signal. Semi‐diurnal internal stationary waves dominate high frequency variations in velocity shears. The stationary waves could result from the interaction of freely propagating semi‐diurnal internal waves generated by diurnal barotropic tides on critical slopes around the plateau. The breaking of the stationary waves with short length scales possibly contribute to mixing of AW at the entrance to the Arctic.
ARHGAP35 is a novel factor disrupted in human developmental eye phenotypes
Authors: Reis Linda M. , Chassaing Nicolas , Bardakjian Tanya , Thompson Samuel , Schneider Adele , Semina Elena V. 
Published: December 2022

AbstractARHGAP35 has known roles in cell migration, invasion and division, neuronal morphogenesis, and gene/mRNA regulation; prior studies indicate a role in cancer in humans and in the developing eyes, neural tissue, and renal structures in mice. We identified damaging variants in ARHGAP35 in five individuals from four families affected with anophthalmia, microphthalmia, coloboma and/or anterior segment dysgenesis disorders, together with variable non-ocular phenotypes in some families including renal, neurological, or cardiac anomalies. Three variants affected the extreme C-terminus of the protein, with two resulting in a frameshift and C-terminal extension and the other a missense change in the Rho-GAP domain; the fourth (nonsense) variant affected the middle of the gene and is the only allele predicted to undergo nonsense-mediated decay. This study implicates ARHGAP35 in human developmental eye phenotypes. C-terminal clustering of the identified alleles indicates a possible common mechanism for ocular disease but requires further studies.
Catalytic nitrogen fixation using visible light energy
Authors: Ashida Yuya , Onozuka Yuto , Arashiba Kazuya , Konomi Asuka , Tanaka Hiromasa , Kuriyama Shogo , Yamazaki Yasuomi , Yoshizawa Kazunari , Nishibayashi Yoshiaki 
Published: December 2022

AbstractThe synthesis of ammonia from atmospheric dinitrogen, nitrogen fixation, is one of the essential reactions for human beings. Because the current industrial nitrogen fixation depends on dihydrogen produced from fossil fuels as raw material, the development of a nitrogen fixation reaction that relies on the energy provided by renewable energy, such as visible light, is an important research goal from the viewpoint of sustainable chemistry. Herein, we establish an iridium- and molybdenum-catalysed process for synthesizing ammonia from dinitrogen under ambient reaction conditions and visible light irradiation. In this reaction system, iridium complexes and molybdenum triiodide complexes bearing N-heterocyclic carbene-based pincer ligands act as cooperative catalysts to activate 9,10-dihydroacridine and dinitrogen, respectively. The reaction of dinitrogen with 9,10-dihydroacridine is not thermodynamically favoured, and it only takes place under visible light irradiation. Therefore, the described reaction system is one that affords visible light energy–driven ammonia formation from dinitrogen catalytically.
Moonlighting chaperone activity of the enzyme PqsE contributes to RhlR-controlled virulence of Pseudomonas aeruginosa
Authors: Borgert Sebastian Roman , Henke Steffi , Witzgall Florian , Schmelz Stefan , zur Lage Susanne , Hotop Sven-Kevin , Stephen Steffi , Lübken Dennis , Krüger Jonas , Gomez Nicolas Oswaldo , van Ham Marco , Jänsch Lothar , Kalesse Markus , Pich Andreas , Brönstrup Mark , Häussler Susanne , Blankenfeldt Wulf 
Published: December 2022

AbstractPseudomonas aeruginosa is a major cause of nosocomial infections and also leads to severe exacerbations in cystic fibrosis or chronic obstructive pulmonary disease. Three intertwined quorum sensing systems control virulence of P. aeruginosa, with the rhl circuit playing the leading role in late and chronic infections. The majority of traits controlled by rhl transcription factor RhlR depend on PqsE, a dispensable thioesterase in Pseudomonas Quinolone Signal (PQS) biosynthesis that interferes with RhlR through an enigmatic mechanism likely involving direct interaction of both proteins. Here we show that PqsE and RhlR form a 2:2 protein complex that, together with RhlR agonist N-butanoyl-L-homoserine lactone (C4-HSL), solubilizes RhlR and thereby renders the otherwise insoluble transcription factor active. We determine crystal structures of the complex and identify residues essential for the interaction. To corroborate the chaperone-like activity of PqsE, we design stability-optimized variants of RhlR that bypass the need for C4-HSL and PqsE in activating PqsE/RhlR-controlled processes of P. aeruginosa. Together, our data provide insight into the unique regulatory role of PqsE and lay groundwork for developing new P. aeruginosa-specific pharmaceuticals.
Small molecule binding to surface-supported single-site transition-metal reaction centres
Authors: DeJong M. , Price A. J. A. , Mårsell E. , Tom G. , Nguyen G. D. , Johnson E. R. , Burke S. A. 
Published: December 2022

AbstractDespite dominating industrial processes, heterogeneous catalysts remain challenging to characterize and control. This is largely attributable to the diversity of potentially active sites at the catalyst-reactant interface and the complex behaviour that can arise from interactions between active sites. Surface-supported, single-site molecular catalysts aim to bring together benefits of both heterogeneous and homogeneous catalysts, offering easy separability while exploiting molecular design of reactivity, though the presence of a surface is likely to influence reaction mechanisms. Here, we use metal-organic coordination to build reactive Fe-terpyridine sites on the Ag(111) surface and study their activity towards CO and C2H4 gaseous reactants using low-temperature ultrahigh-vacuum scanning tunnelling microscopy, scanning tunnelling spectroscopy, and atomic force microscopy supported by density-functional theory models. Using a site-by-site approach at low temperature to visualize the reaction pathway, we find that reactants bond to the Fe-tpy active sites via surface-bound intermediates, and investigate the role of the substrate in understanding and designing single-site catalysts on metallic supports.
Fungal sensing by dectin-1 directs the non-pathogenic polarization of TH17 cells through balanced type I IFN responses in human DCs
Authors: Gringhuis Sonja I. , Kaptein Tanja M. , Remmerswaal Ester B. M. , Drewniak Agata , Wevers Brigitte A. , Theelen Bart , D’Haens Geert R. A. M. , Boekhout Teun , Geijtenbeek Teunis B. H. 
Published: December 2022

AbstractThe non-pathogenic TH17 subset of helper T cells clears fungal infections, whereas pathogenic TH17 cells cause inflammation and tissue damage; however, the mechanisms controlling these distinct responses remain unclear. Here we found that fungi sensing by the C-type lectin dectin-1 in human dendritic cells (DCs) directed the polarization of non-pathogenic TH17 cells. Dectin-1 signaling triggered transient and intermediate expression of interferon (IFN)-β in DCs, which was mediated by the opposed activities of transcription factors IRF1 and IRF5. IFN-β-induced signaling led to integrin αvβ8 expression directly and to the release of the active form of the cytokine transforming growth factor (TGF)-β indirectly. Uncontrolled IFN-β responses as a result of IRF1 deficiency induced high expression of the IFN-stimulated gene BST2 in DCs and restrained TGF-β activation. Active TGF-β was required for polarization of non-pathogenic TH17 cells, whereas pathogenic TH17 cells developed in the absence of active TGF-β. Thus, dectin-1-mediated modulation of type I IFN responses allowed TGF-β activation and non-pathogenic TH17 cell development during fungal infections in humans.
Parenteral BCG vaccine induces lung-resident memory macrophages and trained immunity via the gut–lung axis
Authors: Jeyanathan Mangalakumari , Vaseghi-Shanjani Maryam , Afkhami Sam , Grondin Jensine A. , Kang Alisha , D’Agostino Michael R. , Yao Yushi , Jain Shreya , Zganiacz Anna , Kroezen Zachary , Shanmuganathan Meera , Singh Ramandeep , Dvorkin-Gheva Anna , Britz-McKibbin Philip , Khan Waliul I. , Xing Zhou 
Published: December 2022

AbstractAside from centrally induced trained immunity in the bone marrow (BM) and peripheral blood by parenteral vaccination or infection, evidence indicates that mucosal-resident innate immune memory can develop via a local inflammatory pathway following mucosal exposure. However, whether mucosal-resident innate memory results from integrating distally generated immunological signals following parenteral vaccination/infection is unclear. Here we show that subcutaneous Bacillus Calmette–Guérin (BCG) vaccination can induce memory alveolar macrophages (AMs) and trained immunity in the lung. Although parenteral BCG vaccination trains BM progenitors and circulating monocytes, induction of memory AMs is independent of circulating monocytes. Rather, parenteral BCG vaccination, via mycobacterial dissemination, causes a time-dependent alteration in the intestinal microbiome, barrier function and microbial metabolites, and subsequent changes in circulating and lung metabolites, leading to the induction of memory macrophages and trained immunity in the lung. These data identify an intestinal microbiota-mediated pathway for innate immune memory development at distal mucosal tissues and have implications for the development of next-generation vaccine strategies against respiratory pathogens.
Data-driven identification of post-acute SARS-CoV-2 infection subphenotypes
Authors: Zhang Hao , Zang Chengxi , Xu Zhenxing , Zhang Yongkang , Xu Jie , Bian Jiang , Morozyuk Dmitry , Khullar Dhruv , Zhang Yiye , Nordvig Anna S. , Schenck Edward J. , Shenkman Elizabeth A. , Rothman Russell L. , Block Jason P. , Lyman Kristin , Weiner Mark G. , Carton Thomas W. , Wang Fei , Kaushal Rainu 
Published: December 2022

AbstractThe post-acute sequelae of SARS-CoV-2 infection (PASC) refers to a broad spectrum of symptoms and signs that are persistent, exacerbated or newly incident in the period after acute SARS-CoV-2 infection. Most studies have examined these conditions individually without providing evidence on co-occurring conditions. In this study, we leveraged the electronic health record data of two large cohorts, INSIGHT and OneFlorida+, from the national Patient-Centered Clinical Research Network. We created a development cohort from INSIGHT and a validation cohort from OneFlorida+ including 20,881 and 13,724 patients, respectively, who were SARS-CoV-2 infected, and we investigated their newly incident diagnoses 30–180 days after a documented SARS-CoV-2 infection. Through machine learning analysis of over 137 symptoms and conditions, we identified four reproducible PASC subphenotypes, dominated by cardiac and renal (including 33.75% and 25.43% of the patients in the development and validation cohorts); respiratory, sleep and anxiety (32.75% and 38.48%); musculoskeletal and nervous system (23.37% and 23.35%); and digestive and respiratory system (10.14% and 12.74%) sequelae. These subphenotypes were associated with distinct patient demographics, underlying conditions before SARS-CoV-2 infection and acute infection phase severity. Our study provides insights into the heterogeneity of PASC and may inform stratified decision-making in the management of PASC conditions.
SOMAS: a platform for data-driven material discovery in redox flow battery development
Authors: Gao Peiyuan , Andersen Amity , Sepulveda Jonathan , Panapitiya Gihan U. , Hollas Aaron , Saldanha Emily G. , Murugesan Vijayakumar , Wang Wei 
Published: December 2022

AbstractAqueous organic redox flow batteries offer an environmentally benign, tunable, and safe route to large-scale energy storage. The energy density is one of the key performance parameters of organic redox flow batteries, which critically depends on the solubility of the redox-active molecule in water. Prediction of aqueous solubility remains a challenge in chemistry. Recently, machine learning models have been developed for molecular properties prediction in chemistry and material science. The fidelity of a machine learning model critically depends on the diversity, accuracy, and abundancy of the training datasets. We build a comprehensive open access organic molecular database “Solubility of Organic Molecules in Aqueous Solution” (SOMAS) containing about 12,000 molecules that covers wider chemical and solubility regimes suitable for aqueous organic redox flow battery development efforts. In addition to experimental solubility, we also provide eight distinctive quantum descriptors including optimized geometry derived from high-throughput density functional theory calculations along with six molecular descriptors for each molecule. SOMAS builds a critical foundation for future efforts in artificial intelligence-based solubility prediction models.
Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes
Authors: Higgins Kendall , Moore Bret A. , Berberovic Zorana , Adissu Hibret A. , Eskandarian Mohammad , Flenniken Ann M. , Shao Andy , Imai Denise M. , Clary Dave , Lanoue Louise , Newbigging Susan , Nutter Lauryl M. J. , Adams David J. , Bosch Fatima , Braun Robert E. , Brown Steve D. M. , Dickinson Mary E. , Dobbie Michael , Flicek Paul , Gao Xiang , Galande Sanjeev , Grobler Anne , Heaney Jason D. , Herault Yann , de Angelis Martin Hrabe , Chin Hsian-Jean Genie , Mammano Fabio , Qin Chuan , Shiroishi Toshihiko , Sedlacek Radislav , Seong J.-K. , Xu Ying ,   The IMPC Consortium, Beaudet Arthur L. , Braun Bob , Karp Natasha , Mallon Ann-Marie , Meehan Terrence , Obata Yuichi , Parkinson Helen , Smedley Damian , Tocchini-Valentini Glauco , Wells Sara , Lloyd K. C. Kent , McKerlie Colin , Moshiri Ala 
Published: December 2022

AbstractWe searched a database of single-gene knockout (KO) mice produced by the International Mouse Phenotyping Consortium (IMPC) to identify candidate ciliopathy genes. We first screened for phenotypes in mouse lines with both ocular and renal or reproductive trait abnormalities. The STRING protein interaction tool was used to identify interactions between known cilia gene products and those encoded by the genes in individual knockout mouse strains in order to generate a list of “candidate ciliopathy genes.” From this list, 32 genes encoded proteins predicted to interact with known ciliopathy proteins. Of these, 25 had no previously described roles in ciliary pathobiology. Histological and morphological evidence of phenotypes found in ciliopathies in knockout mouse lines are presented as examples (genesAbi2, Wdr62, Ap4e1, Dync1li1,andPrkab1). Phenotyping data and descriptions generated on IMPC mouse line are useful for mechanistic studies, target discovery, rare disease diagnosis, and preclinical therapeutic development trials. Here we demonstrate the effective use of the IMPC phenotype data to uncover genes with no previous role in ciliary biology, which may be clinically relevant for identification of novel disease genes implicated in ciliopathies.
Oscillating flower colour changes of Causonis japonica (Thunb.) Raf. (Vitaceae) linked to sexual phase changes
Authors: Furukawa Y. , Tsukaya H. , Kawakubo N. 
Published: December 2022

AbstractFlower colour change may represent an ‘honest signal’ for pollinators, denoting flowers with good conditions for rewards and pollination. All previously reported flower colour changes are unidirectional, except for an incomplete case in one Fabaceae species. In this study, we discovered a very rare example of complete oscillating flower colour change associated with sexual phase changes in Causonis japonica (Vitaceae). More specifically, flower discs of C. japonica exhibit an orange colour in the initial male phase then soon fade into pink with desorption of the stamens. Several hours later in the daytime of the same or the following day, with stigma maturation and style elongation, the orange flower disc colour is recovered before fading into pink again. Importantly, we found that the colour change is caused by the accumulation and the degradation of carotenoids. Moreover, nectar secretion was roughly correlated with the abovementioned colour changes. This is the first example of an apparent oscillating colour change mediated by carotenoid content alteration in flowers.
Increase in repulsive guidance molecule-a (RGMa) in lacunar and cortical stroke patients is related to the severity of the insult
Authors: Parray Aijaz , Akhtar Naveed , Pir Ghulam Jeelani , Pananchikkal Sajitha V. , Ayadathil Raheem , Mir Fayaz Ahmad , Francis Reny , Own Ahmed , Shuaib Ashfaq 
Published: December 2022

AbstractRepulsive guidance molecule-a (RGMa) inhibits angiogenesis and increases inflammation. Animal models of cerebral ischemia have shown that an increased expression of RGMa leads to larger infarction and its inhibition attenuates effects of ischemia. We report on the relationship of RGMa to stroke types and severity. This is a prospective study in patients admitted to the stroke service in Qatar. We collected the clinical determinants, including NIHSS at admission, imaging and outcome at discharge and 90-days. RGMa levels were determined by measuring mRNA levels extracted from peripheral blood mononuclear cells (PBMCs) within 24 h of onset and at 5 days. There were 90 patients (lacunar: 64, cortical: 26) and 35 age-matched controls. RGMa mRNA levels were significantly higher in the stroke patients: day 1: 1.007 ± 0.13 versus 2.152 ± 0.19 [p < 0.001] and day-5: 3.939 ± 0.36 [p < 0.0001]) and significantly higher in patients with severe stroke (NIHSS ≥ 8) compared to milder symptoms (NIHSS < 8) at day 1 (NIHSS ≥ 8: 2.563 ± 0.36; NIHSS < 8: 1.947 ± 0.2) and day 5 (NIHSS ≥ 8: 5.25 ± 0.62; NIHSS < 8: 3.259 ± 0.419). Cortical stroke patients had marginally higher RGMa mRNA levels compared to lacunar stroke at day 1 (cortical stroke: 2.621 ± 0.46 vs lacunar stroke: 1.961 ± 0.19) and day 5 (cortical stroke: 4.295 ± 0.76 vs lacunar stroke: 3.774 ± 0.39). In conclusion, there is an increase in the level of RGMa mRNA in patients with acute stroke and seen in patients with lacunar and cortical stroke. The increase in RGMa mRNA levels is related to the severity of the stroke and increases over the initial 5 days. Further studies are required to determine the effects of the increase in RGMa on stroke recovery.
Childhood trauma and other formative life experiences predict environmental engagement
Authors: Raja Urooj S. , Carrico Amanda R. 
Published: December 2022

AbstractEnvironmental problems continue to intensify. Yet, despite scientific consensus on threats such as climate change, broadscale public engagement with the issue is elusive. In this paper, we focus on childhood formative experiences and the extent to which they are correlated with environmental engagement. We consider two forms of environmental engagement: civic engagement, measured in hours per month devoted to an environmental protection cause, and private-sphere green behavior. Past studies about significant life experiences have shown that formative experiences, especially in childhood, correlate with environmentally sensitive attitudes and vocations in later life. However, we know less about the formative life events experienced by contemporary environmentally engaged persons. Looking at a nationally representative sample of American adults (n = 449), we find that childhood trauma predicts both civic engagement and green behavior. We also find that childhood experiences in nature and childhood travel experiences predict green behavior but not civic engagement.
Asynchronous calibration of quantitative computed tomography bone mineral density assessment for opportunistic osteoporosis screening: phantom-based validation and parameter influence evaluation
Authors: Skornitzke Stephan , Vats Neha , Kopytova Taisiya , Tong Elizabeth Wai Yee , Hofbauer Tobias , Weber Tim Frederik , Rehnitz Christoph , von Stackelberg Oyunbileg , Maier-Hein Klaus , Stiller Wolfram , Biederer Jürgen , Kauczor Hans-Ulrich , Heußel Claus-Peter , Wielpütz Mark , Palm Viktoria 
Published: December 2022

AbstractAsynchronous calibration could allow opportunistic screening based on routine CT for early osteoporosis detection. In this phantom study, a bone mineral density (BMD) calibration phantom and multi-energy CT (MECT) phantom were imaged on eight different CT scanners with multiple tube voltages (80–150 kVp) and image reconstruction settings (e.g. soft/hard kernel). Reference values for asynchronous BMD estimation were calculated from the BMD-phantom and validated with six calcium composite inserts of the MECT-phantom with known ground truth. Relative errors/changes in estimated BMD were calculated and investigated for influence of tube voltage, CT scanner and reconstruction setting. Reference values for 282 acquisitions were determined, resulting in an average relative error between calculated BMD and ground truth of − 9.2% ± 14.0% with a strong correlation (R2 = 0.99; p < 0.0001). Tube voltage and CT scanner had a significant effect on calculated BMD (p < 0.0001), with relative differences in BMD of 3.8% ± 28.2% when adapting reference values for tube voltage, − 5.6% ± 9.2% for CT scanner and 0.2% ± 0.2% for reconstruction setting, respectively. Differences in BMD were small when using reference values from a different CT scanner of the same model (0.0% ± 1.4%). Asynchronous phantom-based calibration is feasible for opportunistic BMD assessment based on CT images with reference values adapted for tube voltage and CT scanner model.