bluuebunny/crossref_metadata_2025 huggingface dataset:
Significant Human Modification of the Lower Arkansas River Sediment Budget
Authors: Chen Hehe , Shaw John B. , Sharman Glenn R. , Marshall Jill A.
Published: September 2022

Anthropogenic stressors on large rivers have significantly modified riverine sediment transport. However, the impacts of dredging and sand and gravel (S&G) mining are poorly monitored. We quantify these impacts on the lower Arkansas River, USA, where anthropogenic processes are well documented. The construction of dams caused a 98% reduction in suspended sediment discharge (Qss). Since dam construction, fluvially transported suspended sediment (4.4 ± 0.5 Mtyr−1) and suspended sand discharge (Qsand) (1.1 ± 0.1 Mtyr−1) are of the same order as the dredging rate (1.2 ± 0.1 Mtyr−1) and S&G mining rate (1.7 ± 0.1 Mtyr−1). While the modern sediment deficit on the Arkansas River is smaller than in rivers documented in developing countries, dredging and mining significantly alter the sediment balance in this large river, indicating that extraction management is needed worldwide, especially in developing economies, to improve ecosystem sustainability in large rivers.
Smaller Sensitivity of Precipitation to Surface Temperature Under Massive Atmospheres
Authors: Xiong Junyan , Yang Jun , Liu Jiachen
Published: September 2022

Precipitation and its response to forcing is an important aspect of planetary climate system. In this study, we examine the strength of precipitation in the experiments with different atmospheric masses and their response to surface warming, using three global atmospheric general circulation models and one regional cloud‐resolving model. We find that precipitation is weaker when atmospheric mass is larger for a given surface temperature. Furthermore, the increasing rate of precipitation with increasing surface temperature under a larger atmospheric mass is smaller than that under a smaller atmospheric mass. These behaviors can be understood based on atmospheric or surface energy balance. Atmospheric mass influences Rayleigh scattering, multiple scattering in the atmosphere, pressure broadening, lapse rate, and thereby precipitation strength. These results have important implications on the climate and habitability of early Earth, early Mars, and exoplanets with oceans.
The Influence of Agulhas Leakage on Primary Production and Nitrogen Cycling in the Southeastern Atlantic Ocean
Authors: Wallschuss Sina , Mdutyana Mhlangabezi , Parrott Ruan G. , Forrer Heather J. , Roman Raymond , Walker David R. , Ansorge Isabelle J. , Fawcett Sarah E.
Published: September 2022

The well‐established importance of Agulhas Current “leakage” for Indian‐Atlantic Ocean exchange of heat and salt raises the question of the relevance of Agulhas eddies for carbon and nitrogen cycling. We measured net primary production (NPP), nitrate and ammonium uptake, and nitrification along a transect of the Cape Basin (CB) in winter 2017, including across an anticyclonic Agulhas eddy sampled at high‐resolution. Euphotic zone‐integrated rates of NPP and nitrogen uptake were more than three‐fold lower at the eddy center than at its edges, with intermediate rates measured outside the eddy. Additionally, proportionally more nitrate was consumed at the eddy edges than at its center. Mixed‐layer integrated nitrification rates were highest at the eddy‐center, with lower rates at the edges and in the surrounding basin. Accounting for phytoplankton consumption of newly nitrified nitrate in the eddy decreased the carbon export potential inferred from nitrate uptake (i.e., the f‐ratio) by 66% ± 37% (vs. a 14% ± 22% decrease across the rest of the transect). At most stations, NPP and total measured nitrogen uptake were decoupled relative to stoichiometric expectations, with roughly a third of NPP possibly supported by regenerated dissolved organic nitrogen (DON). Accounting for DON uptake decreased the average f‐ratio from 0.28 ± 0.26 to 0.22 ± 0.21, with the highest f‐ratio estimated for an eddy‐edge station (0.64) and the lowest for its center (0.00). While the low productivity metrics measured in the eddy‐center could imply that Agulhas leakage decreases carbon export potential in the CB, enhanced nutrient supply and consumption at eddy edges may (partly) offset this reduction.
Importance of Parameterizing Lake Surface and Internal Thermal Processes in WRF for Simulating Freeze Onset of an Alpine Deep Lake
Authors: Ma Xiaogang , Yang Kun , La Zhu , Lu Hui , Jiang Yaozhi , Zhou Xu , Yao Xiangnan , Li Xin
Published: September 2022

The alpine lakes widely distributed over the Tibetan Plateau (TP) are not only highly sensitive to climate but also regulate the regional climate. However, the lack of TP alpine lake observations limits the understanding of the lake‐atmosphere interactions. Here, we show the relative importance of parameterizing lake surface and internal thermal processes in describing the lake energy budget and lake‐atmosphere interactions. Based on the in situ observations at Lake Nam Co, a large and deep lake in the TP, we employed the coupled Weather Research and Forecasting with lake (WRF‐Lake) model to clarify their relative roles. Results show that the original model produces cold biases and too early timing of lake freeze onset. The adjustments of parameterizations of lake internal (temperature of maximum water density, extinction coefficient) and lake surface (roughness length) processes significantly improve the ability of the WRF‐Lake in simulating the lake thermal features and the freeze onset timing. The different parameterizations of lake internal thermal processes affect the onset timing of lake freeze mainly by altering the release of turbulent heat fluxes in summer, but the adjustments of lake surface roughness lengths change the turbulent heat fluxes during the unfrozen season from summer through early winter. Accordingly, the simulated lake freeze onset is much more sensitive to the surface roughness length schemes than to the internal thermal processes schemes. As the lake‐atmosphere interactions are very sensitive to the lake freeze onset, our results are critical for understanding and simulating the impact of TP lakes on the regional climate.
Inhibition of FKBP51 induces stress resilience and alters hippocampal neurogenesis
Authors: Codagnone Martin G. , Kara Nirit , Ratsika Anna , Levone Brunno Rocha , van de Wouw Marcel , Tan Laura A. , Cunningham Jacobi I. , Sanchez Connie , Cryan John F. , O’Leary Olivia F.
Published: September 2022

Stress-related psychiatric disorders such as depression are among the leading causes of morbidity and mortality. Considering that many individuals fail to respond to currently available antidepressant drugs, there is a need for antidepressants with novel mechanisms. Polymorphisms in the gene encoding FK506-binding protein 51 (FKBP51), a co-chaperone of the glucocorticoid receptor, have been linked to susceptibility to stress-related psychiatric disorders. Whether this protein can be targeted for their treatment remains largely unexplored. The aim of this work was to investigate whether inhibition of FKBP51 with SAFit2, a novel selective inhibitor, promotes hippocampal neuron outgrowth and neurogenesis in vitro and stress resilience in vivo in a mouse model of chronic psychosocial stress. Primary hippocampal neuronal cultures or hippocampal neural progenitor cells (NPCs) were treated with SAFit2 and neuronal differentiation and cell proliferation were analyzed. Male C57BL/6 mice were administered SAFit2 while concurrently undergoing a chronic stress paradigm comprising of intermittent social defeat and overcrowding, and anxiety and depressive -related behaviors were evaluated. SAFit2 increased neurite outgrowth and number of branch points to a greater extent than brain derived neurotrophic factor (BDNF) in primary hippocampal neuronal cultures. SAFit2 increased hippocampal NPC neurogenesis and increased neurite complexity and length of these differentiated neurons. In vivo, chronic SAFit2 administration prevented stress-induced social avoidance, decreased anxiety in the novelty-induced hypophagia test, and prevented stress-induced anxiety in the open field but did not alter adult hippocampal neurogenesis in stressed animals. These data warrant further exploration of inhibition of FKBP51 as a strategy to treat stress-related disorders.
Introducing a depression-like syndrome for translational neuropsychiatry: a plea for taxonomical validity and improved comparability between humans and mice
Authors: von Mücke-Heim Iven-Alex , Urbina-Treviño Lidia , Bordes Joeri , Ries Clemens , Schmidt Mathias V. , Deussing Jan M.
Published: September 2022

Depressive disorders are the most burdensome psychiatric disorders worldwide. Although huge efforts have been made to advance treatment, outcomes remain unsatisfactory. Many factors contribute to this gridlock including suboptimal animal models. Especially limited study comparability and replicability due to imprecise terminology concerning depressive-like states are major problems. To overcome these issues, new approaches are needed. Here, we introduce a taxonomical concept for modelling depression in laboratory mice, which we call depression-like syndrome (DLS). It hinges on growing evidence suggesting that mice possess advanced socioemotional abilities and can display non-random symptom patterns indicative of an evolutionary conserved disorder-like phenotype. The DLS approach uses a combined heuristic method based on clinical depression criteria and the Research Domain Criteria to provide a biobehavioural reference syndrome for preclinical rodent models of depression. The DLS criteria are based on available, species-specific evidence and are as follows: (I) minimum duration of phenotype, (II) significant sociofunctional impairment, (III) core biological features, (IV) necessary depressive-like symptoms. To assess DLS presence and severity, we have designed an algorithm to ensure statistical and biological relevance of findings. The algorithm uses a minimum combined threshold for statistical significance and effect size (p value ≤ 0.05 plus moderate effect size) for each DLS criterion. Taken together, the DLS is a novel, biologically founded, and species-specific minimum threshold approach. Its long-term objective is to gradually develop into an inter-model validation standard and microframework to improve phenotyping methodology in translational research.
Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana
Authors: Bartolek Zinka , van Creveld Shiri Graff , Coesel Sacha , Cain Kelsy R , Schatz Megan , Morales Rhonda , Virginia Armbrust E
Published: September 2022

Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effects of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive morphology of enlarged cells with increased chloroplast content and enlarged nuclei, similar to what was previously observed when the diatom was co-cultured with live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.
FBXW7 inactivation induces cellular senescence via accumulation of p53
Authors: Gong Longyuan , Cui Danrui , Liu Dian , Shen Xiao , Pan Hui , Xiong Xiufang , Zhao Yongchao
Published: September 2022

F-box and WD repeat domain containing 7 (FBXW7) acts as a substrate receptor of SKP1-CUL1-F-box (SCF) E3 ubiquitin ligase and plays crucial roles in the regulation of several cellular processes, including cell growth, division, and differentiation, by targeting diverse key regulators for degradation. However, its role in regulating cellular senescence remains elusive. Here, we found that FBXW7 inactivation by siRNA-based knockdown or CRISPR/Cas9-based knockout induced significant cellular senescence in p53 wild-type cells, but not in p53 mutant or null cells, along with activation of both the p53/p21 and p16INK4a/Rb pathways. Simultaneous p53 inactivation abrogated senescence and cell growth arrest induced by FBXW7 deficiency as well as the alteration of both the p53/p21 and p16INK4a/Rb pathways. Moreover, Fbxw7 deletion accelerated replicative senescence of primary mouse embryonic fibroblasts in a p53-dependent manner. In addition, FBXW7 deletion induced the senescence-associated secretory phenotype to trigger secondary senescence. Importantly, in a radiation-induced senescence mouse model, simultaneous deletion of p53 rescued accelerated senescence and aging caused by Fbxw7 loss. Thus, our study uncovered a novel role for FBXW7 in the regulation of senescence by eliminating p53.
Rapid shifting of a deep magmatic source at Fagradalsfjall volcano, Iceland
Authors: Halldórsson Sæmundur A. , Marshall Edward W. , Caracciolo Alberto , Matthews Simon , Bali Enikő , Rasmussen Maja B. , Ranta Eemu , Robin Jóhann Gunnarsson , Guðfinnsson Guðmundur H. , Sigmarsson Olgeir , Maclennan John , Jackson Matthew G. , Whitehouse Martin J. , Jeon Heejin , van der Meer Quinten H. A. , Mibei Geoffrey K. , Kalliokoski Maarit H. , Repczynska Maria M. , Rúnarsdóttir Rebekka Hlín , Sigurðsson Gylfi , Pfeffer Melissa Anne , Scott Samuel W. , Kjartansdóttir Ríkey , Kleine Barbara I. , Oppenheimer Clive , Aiuppa Alessandro , Ilyinskaya Evgenia , Bitetto Marcello , Giudice Gaetano , Stefánsson Andri
Published: September 2022

Recent Icelandic rifting events have illuminated the roles of centralized crustal magma reservoirs and lateral magma transport1–4, important characteristics of mid-ocean ridge magmatism1,5. A consequence of such shallow crustal processing of magmas4,5 is the overprinting of signatures that trace the origin, evolution and transport of melts in the uppermost mantle and lowermost crust6,7. Here we present unique insights into processes occurring in this zone from integrated petrologic and geochemical studies of the 2021 Fagradalsfjall eruption on the Reykjanes Peninsula in Iceland. Geochemical analyses of basalts erupted during the first 50 days of the eruption, combined with associated gas emissions, reveal direct sourcing from a near-Moho magma storage zone. Geochemical proxies, which signify different mantle compositions and melting conditions, changed at a rate unparalleled for individual basaltic eruptions globally. Initially, the erupted lava was dominated by melts sourced from the shallowest mantle but over the following three weeks became increasingly dominated by magmas generated at a greater depth. This exceptionally rapid trend in erupted compositions provides an unprecedented temporal record of magma mixing that filters the mantle signal, consistent with processing in near-Moho melt lenses containing 107–108 m3 of basaltic magma. Exposing previously inaccessible parts of this key magma processing zone to near-real-time investigations provides new insights into the timescales and operational mode of basaltic magma systems.
Factors related to cognitive function in type-2 diabetes and neuropathic pain patients, the role of mood and sleep disorders in this relationship
Authors: Palomo-Osuna Jenifer , Dueñas María , Naranjo Cristina , De Sola Helena , Salazar Alejandro , Failde Inmaculada
Published: September 2022

To compare cognitive function in patients with diabetes mellitus type-2 (T2DM) both with and without diabetic neuropathic pain (DNP). To analyse the relationship between mood and sleep disorders, quality of life and cognitive function in patients with DNP. Cross-sectional study conducted in patients with T2DM and neuropathy. The presence of DNP, cognitive function, mood status, sleep quality, health-related quality of life, pain intensity and phenotype of pain were measured. Descriptive, bivariate and multivariate analyses were performed. A total of 149 patients (71 with DNP) were included. Patients with and without DNP presented similar scores on the TYM (41.46; SD = 6.70 vs. 41.97; SD = 5.50) and those with DNP had a slightly higher frequency of cognitive impairment (TYM score ≤ 41: 40.8% vs. 43.6%). The patients without DNP performed better in the verbal fluency dimension (mean = 3.53; SD = 0.98 vs. mean = 3.82; SD = 0.66). Being older (B = − 0.258) and under treatment with insulin (B = − 2.919) were related with greater cognitive impairment. Obesity (OR = 17.277) and a longer duration of diabetes (OR = 1.317) were also related to greater risk of cognitive impairment. Impaired cognitive function in patients with DNP is more related to T2DM factors than pain factors. The presence of depression and a worse quality of life were related to a greater risk of cognitive impairment. Identifying and controlling these factors should be an essential intervention for maintaining the cognitive function in patients with T2DM and DNP.
Network-based integration of multi-omics data for clinical outcome prediction in neuroblastoma
Authors: Wang Conghao , Lue Wu , Kaalia Rama , Kumar Parvin , Rajapakse Jagath C.
Published: September 2022

Multi-omics data are increasingly being gathered for investigations of complex diseases such as cancer. However, high dimensionality, small sample size, and heterogeneity of different omics types pose huge challenges to integrated analysis. In this paper, we evaluate two network-based approaches for integration of multi-omics data in an application of clinical outcome prediction of neuroblastoma. We derive Patient Similarity Networks (PSN) as the first step for individual omics data by computing distances among patients from omics features. The fusion of different omics can be investigated in two ways: the network-level fusion is achieved using Similarity Network Fusion algorithm for fusing the PSNs derived for individual omics types; and the feature-level fusion is achieved by fusing the network features obtained from individual PSNs. We demonstrate our methods on two high-risk neuroblastoma datasets from SEQC project and TARGET project. We propose Deep Neural Network and Machine Learning methods with Recursive Feature Elimination as the predictor of survival status of neuroblastoma patients. Our results indicate that network-level fusion outperformed feature-level fusion for integration of different omics data whereas feature-level fusion is more suitable incorporating different feature types derived from same omics type. We conclude that the network-based methods are capable of handling heterogeneity and high dimensionality well in the integration of multi-omics.
Background climate modulates the impact of land cover on urban surface temperature
Authors: Naserikia Marzie , Hart Melissa A. , Nazarian Negin , Bechtel Benjamin
Published: September 2022

Cities with different background climates experience different thermal environments. Many studies have investigated land cover effects on surface urban heat in individual cities. However, a quantitative understanding of how background climates modify the thermal impact of urban land covers remains elusive. Here, we characterise land cover and their impacts on land surface temperature (LST) for 54 highly populated cities using Landsat-8 imagery. Results show that urban surface characteristics and their thermal response are distinctly different across various climate regimes, with the largest difference for cities in arid climates. Cold cities show the largest seasonal variability, with the least seasonality in tropical and arid cities. In tropical, temperate, and cold climates, normalised difference built-up index (NDBI) is the strongest contributor to LST variability during warm months followed by normalised difference vegetation index (NDVI), while normalised difference bareness index (NDBaI) is the most important factor in arid climates. These findings provide a climate-sensitive basis for future land cover planning oriented at mitigating local surface warming.
Integrating mineralogy, geochemistry and aeromagnetic data for detecting Fe–Ti ore deposits bearing layered mafic intrusion, Akab El-Negum, Eastern Desert, Egypt
Authors: Kharbish Sherif , Eldosouky Ahmed M. , Amer Omar
Published: September 2022

This study delineated the Fe–Ti oxide deposit concurrencies on the layered mafic intrusion in Gabal Akab El-Negum (GAN), South Eastern Desert, Egypt, using aeromagnetic mapping and chemical analysis of the hosted mafic rocks and mineralogical studies. Aeromagnetic data was improved using the enhanced horizontal gradient amplitudeto detect the primary structures (edges/contacts/faults) that control the distribution of Fe–Ti ore deposit. GAN layered gabbros are differentiated into troctolite, olivine–, pyroxene–, and hornblende–gabbros. These mafic rocks primarily comprise plagioclase, olivine, pyroxene, and hornblende with Fe–Ti ores (magnetite and ilmenite). The significant variation in Mg# of clinopyroxene between 0.70 and 0.82 indicates the importance of fractional crystallization in developing layered mafic intrusion. Clinopyroxene and plagioclase thermometry yielded low temperatures similar to the fractionated primary basaltic magma. The pairs of magnetite–ilmenite minerals in gabbros provide equilibrium temperatures of 539.44–815.56, and highfO2, reflecting various cooling and subsolidus reequilibration phases of minerals. The enrichment of GAN gabbros in light rare–earth elements relative to heavy rare–earth elements indicates the interaction between the Fe–Ti rich mantle and the fractionated tholeiitic magmas in the back-arc setting, generating Fe–Ti oxide ores.
Epidemiology, genetic diversity, and association of canine circovirus infection in dogs with respiratory disease
Authors: Dankaona Wichan , Mongkholdej Emmita , Satthathum Chakkarin , Piewbang Chutchai , Techangamsuwan Somporn
Published: September 2022

Although canine circovirus (CanineCV)-associated with gastroenteritis has been well documented, the virus is also detectable in the respiratory discharge of dogs with respiratory disease. In this study, an epidemiological approach was used to explore the association between the presence of CanineCV and respiratory symptoms in dogs. Respiratory swabs were collected from 76 healthy dogs and 114 dogs with respiratory illness and tested for CanineCV using conventional PCR (cPCR). Furthermore, lung tissues collected from 15 necropsied dogs showing pneumonia were tested using the real-time PCR (qPCR) and in situ hybridization (ISH) technique. A total of 8.95% (17/190) of dogs were CanineCV positive, with a significant association (p = 0.013) in dogs with respiratory signs. Four necropsied dogs were qPCR positive with the CanineCV-DNA labeling localized in tracheobronchial lymphoid cells (3/4), pulmonary parenchyma, capillary endothelia, and mononuclear cells harboring in alveoli (2/4). Full-length genome sequences of seven CanineCV strains were analyzed, indicating that the detected CanineCV genome clustered in the CanineCV-4 genotype. Genetic recombination was also evident in the replicase (Rep) gene. Although the role of CanineCV primarily affecting lung lesions could not be determined from this study, the presence of CanineCV DNA in pulmonary-associated cells indicated the potential association of the virus with canine respiratory disease; thus, linking causality must be examined in further studies.
Effects of alfacalcidol on cardiovascular outcomes according to alkaline phosphatase levels in the J-DAVID trial
Authors: Oka Tatsufumi , Sakaguchi Yusuke , Isaka Yoshitaka , Ishii Haruka , Kabata Daijiro , Shintani Ayumi , Nakatani Shinya , Morioka Tomoaki , Mori Katsuhito , Inaba Masaaki , Emoto Masanori , Shoji Tetsuo
Published: September 2022

In the Japan Dialysis Active Vitamin D (J-DAVID) trial, oral alfacalcidol numerically, but not significantly, increased the risk of cardiovascular events among patients undergoing hemodialysis. Because the cardiovascular effect of alfacalcidol could be modulated by bone turnover status, this post-hoc analysis of the J-DAVID examined how alkaline phosphatase (ALP), a more precise marker of bone turnover than parathyroid hormone (PTH), modifies the impact of alfacalcidol. The J-DAVID was a 48-month, open-label, randomized controlled trial comparing oral alfacalcidol with no vitamin D receptor activators use in terms of cardiovascular events among 976 hemodialysis patients without secondary hyperparathyroidism. This post-hoc analysis included 959 patients with available data on baseline ALP. The median [25–75th percentile] baseline ALP level was 234 [183–296] U/L. In a Cox proportional hazards model, ALP did not significantly modify the effect of alfacalcidol on the rate of cardiovascular events or all-cause death (P for effect modification = 0.54 and 0.74, respectively). The effect of alfacalcidol on time-series changes in calcium, phosphate, and intact PTH were similar across ALP subgroups. In conclusion, oral alfacalcidol did not significantly affect cardiovascular outcomes irrespective of bone turnover status.
The p-ERG spatial acuity in the biomedical pig under physiological conditions
Authors: Ventrella Domenico , Maya-Vetencourt José Fernando , Elmi Alberto , Barone Francesca , Aniballi Camilla , Muscatello Luisa Vera , Mete Maurizio , Pertile Grazia , Benfenati Fabio , Bacci Maria Laura
Published: September 2022

Pigs are becoming an important pre-clinical animal species for translational ophthalmology, due to similarities with humans in anatomical and physiological patterns. Different models of eye disorders have been proposed, and they are good candidates to assess biocompatibility/functionality of retinal prostheses. Electroretinography is a common tool allowing to gain information on retinal function, with several types of electroretinogram (ERG) been implemented including full field (ff-ERG), multifocal (mf-ERG) and pattern (p-ERG). p-ERG represents a valuable tool to monitor Retinal Ganglion Cells (RGCs) activity and can be used to calculate p-ERG spatial acuity. Unfortunately, scarce methodological data are available regarding recording/interpretation of p-ERG and retinal acuity in biomedical pigs yet enhancing knowledge regarding pig vision physiology will allow for more refined and responsible use of such species. Aim of this study was to record p-ERG in juvenile pigs to functionally assess visual acuity. Six female hybrid pigs underwent two p-ERG recording sessions at 16 and 19 weeks of age. Photopic ff-ERG were also recorded; optical coherence tomography (OCT) and histology were used to confirm retinal integrity. ff-ERG signals were repeatable within/across sessions. All p-ERG traces consistently displayed characterizing peaks, and the progressive decrease of amplitude in response to the increment of spatial frequency revealed the reliability of the method. Mean p-ERG spatial acuities were 5.7 ± 0.14 (16 weeks) and 6.2 ± 0.15 cpd (19 weeks). Overall, the p-ERG recordings described in the present work seem reliable and repeatable, and may represent an important tool when it comes to vision assessment in pigs.
Selection in a growing colony biases results of mutation accumulation experiments
Authors: Mahilkar Anjali , Raj Namratha , Kemkar Sharvari , Saini Supreet
Published: September 2022

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 108). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.
Selection pressure on the rhizosphere microbiome can alter nitrogen use efficiency and seed yield in Brassica rapa
Authors: Garcia Joshua , Gannett Maria , Wei LiPing , Cheng Liang , Hu Shengyuan , Sparks Jed , Giovannoni James , Kao-Kniffin Jenny
Published: September 2022

Microbial experimental systems provide a platform to observe how networks of groups emerge to impact plant development. We applied selection pressure for microbiome enhancement ofBrassica rapabiomass to examine adaptive bacterial group dynamics under soil nitrogen limitation. In the 9th and final generation of the experiment, selection pressure enhancedB. rapaseed yield and nitrogen use efficiency compared to our control treatment, with no effect between the random selection and control treatments. Aboveground biomass increased for both the high biomass selection and random selection plants. Soil bacterial diversity declined under highB. rapabiomass selection, suggesting a possible ecological filtering mechanism to remove bacterial taxa. Distinct sub-groups of interactions emerged among bacterial phyla such asProteobacteriaandBacteroidetesin response to selection. Extended Local Similarity Analysis and NetShift indicated greater connectivity of the bacterial community, with more edges, shorter path lengths, and altered modularity through the course of selection for enhanced plant biomass. In contrast, bacterial communities under random selection and no selection showed less complex interaction profiles of bacterial taxa. These results suggest that group-level bacterial interactions could be modified to collectively shift microbiome functions impacting the growth of the host plant under soil nitrogen limitation.
Oral microbial extracellular DNA initiates periodontitis through gingival degradation by fibroblast-derived cathepsin K in mice
Authors: Kondo Takeru , Okawa Hiroko , Hokugo Akishige , Shokeen Bhumika , Sundberg Oskar , Zheng Yiying , McKenna Charles E. , Lux Renate , Nishimura Ichiro
Published: September 2022

Periodontitis is a highly prevalent disease leading to uncontrolled osteoclastic jawbone resorption and ultimately edentulism; however, the disease onset mechanism has not been fully elucidated. Here we propose a mechanism for initial pathology based on results obtained using a recently developed Osteoadsorptive Fluogenic Sentinel (OFS) probe that emits a fluorescent signal triggered by cathepsin K (Ctsk) activity. In a ligature-induced mouse model of periodontitis, a strong OFS signal is observed before the establishment of chronic inflammation and bone resorption. Single cell RNA sequencing shows gingival fibroblasts to be the primary cellular source of early Ctsk. The in vivo OFS signal is activated when Toll-Like Receptor 9 (TLR9) ligand or oral biofilm extracellular DNA (eDNA) is topically applied to the mouse palatal gingiva. This previously unrecognized interaction between oral microbial eDNA and Ctsk of gingival fibroblasts provides a pathological mechanism for disease initiation and a strategic basis for early diagnosis and treatment of periodontitis.
A SERS and fluorescence dual-channel microfluidic droplet platform for exploring telomerase activity at the single-cell level
Authors: Qi Guohua , Du Xing , Yi Xuan , Wang Minmin , Zhu Hongyan , Sun Dan
Published: September 2022

Overview of the workflow of the fluorescence and SERS dual-channel microfluidic droplet system for encapsulating a single cell and detecting telomerase.
Fully automated station for testing, characterizing and modifying screen-printed electrodes
Authors: Zitka Jan , Sileny Jan , Kudr Jiri , Koudelkova Zuzana , Ilieva Lada , Richtera Lukas , Syrovy Tomas , Adam Vojtech , Zitka Ondrej
Published: September 2022

A novel unique device for automated screen printed electrodes testing and processing is described. It simplifies electrochemical optimization studies, and/or processing steps during SPE sensor/biosensor development.
A diversity oriented clicking strategy: the stereoselective synthesis of highly-functionalised olefins from 2-substituted-alkynyl-1-sulfonyl fluorides
Authors: Smedley Christopher J.
Published: September 2022

A novel series of addition reactions for the synthesis of two highly-functionalised sulfonyl fluoride containing olefins from 2-substituted-alkynyl-1-sulfonyl fluorides using a diversity oriented clicking strategy.
Oligomeric phosphate clusters in macrocyclic channels
Authors: Pramanik Subhamay , Thordarson Pall , Day Victor W. , Bowman-James Kristin
Published: September 2022

Thirty-six-membered ring macrocycles form sandwich-like channels for oligomeric chains of hexaphosphate clusters.
Strain effects in the electron orbital coupling and electric structure of graphene
Authors: Quan Silong , Zhang Yuhua , Chen Wenzhou
Published: September 2022

Uniaxial strain can give rise to the symmetry breaking of graphene and open the band gap. The mechanism of band gap opening in graphene is that the uniaxial strain weakens the coupling of different electron orbitals.
Thermoelectric properties of Ag-doped CuI: a temperature dependent optical phonon study
Authors: Kumar Santosh , Battabyal Manjusha , K. Sethupathi , Satapathy Dillip K.
Published: September 2022

Temperature-dependent evolution of optical phonon modes in Ag-doped CuI and its correlation with thermoelectric properties.
The principal component analysis of the ring deformation in the nonadiabatic surface hopping dynamics
Authors: Zhu Yifei , Peng Jiawei , Kang Xu , Xu Chao , Lan Zhenggang
Published: September 2022

We proposed a “hierarchical” protocol based on the unsupervised machine learning algorithms (principal component analysis and clustering approaches) to automatically analyze the ring deformation in the nonadiabatic molecular dynamics.
Bayesian optimization with known experimental and design constraints for chemistry applications
Authors: Hickman Riley J. , Aldeghi Matteo , Häse Florian , Aspuru-Guzik Alán
Published: September 2022

A Bayesian optimization algorithm that satisfies known constraints has been developed. The usefulness of considering experimental and design constraints are shown in two simulated chemistry applications.
Ambient characterisation of PurpleAir particulate matter monitors for measurements to be considered as indicative
Authors: Caseiro Alexandre , Schmitz Seán , Villena Guillermo , Jagatha Janani Venkatraman , von Schneidemesser Erika
Published: September 2022

Using low-cost systems to obtain indicative measurements when no calibration is possible.
The rapid self-reconstruction of Fe-modified Ni hydroxysulfide for efficient and stable large-current-density water/seawater oxidation
Authors: Huang Chuqiang , Zhou Qiancheng , Duan Dingshuo , Yu Luo , Zhang Wei , Wang Zhouzhou , Liu Jin , Peng Bowen , An Pengfei , Zhang Jing , Li Liping , Yu Jiaguo , Yu Ying
Published: September 2022

S leaching induces rapid self-reconstruction and the ready formation of Ni4+ in an Fe–NiSOH electrode, supporting high-efficiency and stable alkaline large-current-density water/seawater oxidation.
Demonstration of 10+ hour energy storage with ϕ1′′ laboratory size solid oxide iron–air batteries
Authors: Tang Qiming , Zhang Yongliang , Xu Nansheng , Lei Xueling , Huang Kevin
Published: September 2022

Long duration electricity storage (LDES) with 10+ hour cycle duration is an economically competitive strategy to accelerate the penetration of renewable energy into the utility market.
Solid-state cooling: thermoelectrics
Authors: Qin Yongxin , Qin Bingchao , Wang Dongyang , Chang Cheng , Zhao Li-Dong
Published: September 2022

This review systematically elucidates the thermoelectric cooling technology, and proposes a strategy for boosting the power factor by improving carrier mobility through utilizing the material-planification concept.
Electrolyte-free electrochemical C–H trifluoromethylation of 2-pyridones under batch and flow conditions
Authors: Leclercq Elise , Moncomble Aurélien , Debavelaere Céline , Beaucamp Mathieu , Penhoat Maël , Chausset-Boissarie Laëtitia
Published: September 2022

An environmentally friendly electrochemical process for the direct trifluoromethylation of 2-pyridones with a broad substrate scope has been developed.
Sensitive online speciation analysis of arsenic in biological samples by ambient mass spectrometry
Authors: Wu Debo , Li Dian , Dong Lulu , Li Guolin , Wang Li , Tang Ziyang , Rahman Md. Matiur , Yang Shuiping
Published: September 2022

Various arsenic species in biological samples were directly molecularly analyzed by ambient EESI-HG-MPT-MS with enhanced sensitivity.
An efficient method for high-precision potassium isotope analysis in carbonate materials
Authors: Wang Xi-Kai , Liu Xiao-Ming , Chen Heng
Published: September 2022

The developed dual-column chromatographic method can purify K in 100–150 mg carbonate materials with satisfactory recovery (∼100%) and negligible blank (∼30 ng) for high-precision K isotope analysis using MC-ICP-MS.
Cellulose composites containing active constituents of coffee and tea: a prospective novel wound dressing
Authors: Firmanda Afrinal , Fahma Farah , Syamsu Khaswar , Cabral Jaydee , Pletzer Daniel , Gustiananda Marsia
Published: September 2022

Cellulose-based wound dressings are increasingly in demand due to their biocompatibility and extracellular matrix (ECM) mimicking properties.
Attractive curves: the role of deformations in adhesion and friction on graphene
Authors: Antonov P. V. , Restuccia P. , Righi M. C. , Frenken J. W. M.
Published: September 2022

The increase of chemical reactivity in curved graphene explains the reduction in friction for monolayer graphene over oxidized/unoxidized copper substrates.
Controlling the rotation modes of hematite nanospindles using dynamic magnetic fields
Authors: Honecker Dirk , Bender Philipp , Falke Yannic , Dresen Dominique , Kundt Matthias , Schmidt Annette M. , Tschöpe Andreas , Sztucki Michael , Burghammer Manfred , Disch Sabrina
Published: September 2022

Time-resolved SAXS reveals how hematite nanospindles undergo a transition from a coherent precession into a synchronized spinning mode when actuated by rotating magnetic fields with increasing frequency.
Confined growth of Ag nanoflakes induced by LSPR-driven carrier transfer in periodic nanopatterned arrays
Authors: Xu Wei , Zhao Xiaoyu , Zhang Fengyi , Liu Jia , Zhang Kun , Guo Xiaojie , Wen Jiahong , Zhang Jian , Liu Xiaolian , Wang Yaxin , Yang Shikuan , Zhang Yongjun
Published: September 2022

The fabrication of Ag nanoflakes induced by the surface plasma LSPR-driven carriers on the periodic nanopatterned arrays.
Human placental lipid content and lipid metabolic enzyme abundance in obesity and across gestation
Authors: Bidne Katie L. , Uhlson Charis , Palmer Claire , Zemski-Berry Karin , Powell Theresa L.
Published: September 2022

Changes in placental lipid metabolism influence the delivery of lipids critical for fetal development and fetal requirements for lipids change across gestation. We hypothesized that placental lipid content and metabolic enzyme protein levels increase across gestation and are elevated in obesity. Placentas (4–40 weeks’ gestation) were collected from control (body mass index, BMI = 18.5–24.9, n=37) and obese (BMI > 30, n=19) pregnant women. Trophoblast villous tissue was homogenized and subjected to liquid chromatography tandem mass spectrometry (LC–MS/MS) for phospholipid and triacylglycerol (TAG) analysis and western blot for protein quantification. The placental content of TAG species and nine of 35 identified phosphatidylcholines (PC) were significantly higher (P<0.05) in first trimester (28–79%, 10-47%, respectively). Furthermore, two TAG and three PC differed by maternal BMI and were significantly increased (P<0.05) in the obese group in first trimester (72–87%, 88–119%, respectively). Placental protein abundance of glycerol-2-phosphate (GPAT3) and 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 (AGPAT2), involved in de novo synthesis of PC and TAG, were higher (P<0.05) in the first trimester (66 and 74%, respectively). The protein abundance of the PC-remodeling enzyme PLA2G4c was also higher (63%) in first trimester (P<0.05). In conclusion, the placental content of many phospholipid and TAG species and the protein level of associated synthesis enzymes are higher in first-trimester human placenta. The high PC content may be related to the rapid membrane expansion in early pregnancy and the low placental oxygen tension may promote the accumulation of tissue TAGs in first trimester. Maternal obesity had only limited impact on placental lipid content and metabolic enzyme protein abundance.
Analysis of interactive manufacturing systems: Towards a performance‐based assessment methodology
Authors: Mulet alberola Jose Antonio , Fassi Irene
Published: September 2022

Current manufacturing systems are forced to meet the most dynamic market demands under sustainable factors. However, not only technical transformations will address the challenge but, to fully cover social needs, the analysis of the human role in highly interactive systems is still decisive, following a socially sustainable approach. To fully extract the most from both agents under a performance point of view, the main added value of agents in the work environment needs to be carefully analysed, captured, and boosted. The context shapes a specific operation or task, which consequently drives the final outcome according to individual necessities. Furthermore, a methodology that potentially helps a proper assessment of these performance‐based interactions is still missing. The contribution focusses on the definition of a novel human‐centric methodology under a holistic point of view to analyse performance‐based interactions and to define appropriate indices and metrics that helps assessing the human‐system interactions in the manufacturing domain. The methodology is applied in a case study to guide practitioners with its use.
A novel time‐domain numerical methodology for the electromagnetic analysis of an H‐plane tee power divider
Authors: Arab Homa , Arabsalmanabadi Bita , Dufour Steven
Published: September 2022

A time‐domain numerical methodology for the transient analysis of multisection waveguide power dividers is proposed. Waveguide power dividers are essential components of microwave systems for high‐power applications. A numerical strategy based on the 3D discontinuous Galerkin time‐domain finite element method is used to estimate the electromagnetic propagation inside a power divider with three ports. The proposed approach leads to simulations that are fast, robust, and accurate, this being the result of a parallel local discretisation of the full‐wave time‐domain Maxwell's equations on unstructured tetrahedral meshes. The stability of the overall numerical scheme is obtained using an upwind numerical flux, an implicit second‐order accurate time integration scheme, and Whitney's edge elements. Good agreements are obtained when the computed results are compared with other HFSS simulation results, and with measurement results found in the literature.
Comparison of machine learning algorithms used to classify the asteroids observed by all-sky surveys
Authors: Klimczak H. , Oszkiewicz D. , Carry B. , Penttilä A. , Kotlowski W. , Kryszczyńska A. , Wilawer E.
Published: September 2022

Context. Multifilter photometry from large sky surveys is commonly used to assign asteroid taxonomic types and study various problems in planetary science. To maximize the science output of those surveys, it is important to use methods that best link the spectro-photometric measurements to asteroid taxonomy.

Aims. We aim to determine which machine learning methods are the most suitable for the taxonomic classification for various sky surveys.

Methods. We utilized five machine learning supervised classifiers: logistic regression, naive Bayes, support vector machines (SVMs), gradient boosting, and MultiLayer Perceptrons (MLPs). Those methods were found to reproduce the Bus-DeMeo taxonomy at various rates depending on the set of filters used by each survey. We report several evaluation metrics for a comprehensive comparison (prediction accuracy, balanced accuracy, F1 score, and the Matthews correlation coefficient) for 11 surveys and space missions.

Results. Among the methods analyzed, multilayer perception and gradient boosting achieved the highest accuracy and naive Bayes achieved the lowest accuracy in taxonomic prediction across all surveys. We found that selecting the right machine learning algorithm can improve the success rate by a factor of >2. The best balanced accuracy (~85% for a taxonomic type prediction) was found for the Visible and Infrared Survey telescope for Astronomy (VISTA) and the ESA Euclid mission surveys where broadband filters best map the 1 µm and 2 µm olivine and pyroxene absorption bands.

Conclusions. To achieve the highest accuracy in the taxonomic type prediction based on multifilter photometric measurements, we recommend the use of gradient boosting and MLP optimized for each survey. This can improve the overall success rate even when compared with naive Bayes. A merger of different datasets can further boost the prediction accuracy. For the combination of the Legacy Survey of Space and Time and VISTA survey, we achieved 90% for the taxonomic type prediction.