bluuebunny/crossref_metadata_2025 huggingface dataset:
An analysis approach for building collapse accident using system thinking approach and SEA model
Authors: He Yu-Ting , Atangana Njock Pierre Guy
Published: September 2023

The frequent occurrence of building collapse accidents not only causes significant casualties, but also jeopardizes local economies. This paper adopts a combinatory assessment approach to showcase the lessons learned from a recent building collapse in Changsha, China. The proposed approach blends the system thinking approach and strategic environmental assessment (SEA) model. It delineates the causes of collapse and provide key leverage points for safety management. The results show that the primary causes for the collapse are the poor construction quality, illegal alterations, and lack of regulations enforcement. The management of rural housing construction in Hunan Province achieved a total score of 4 out of 30. It was also determined that the key prevention measures for abating these deleterious phenomena involve ensuring quality assurance/quality control, efficiently assessing safety risk, and timely performing structural health monitoring. This study is bound to enhance the understanding of collapse accidents and foster the achievement of sustainable cities and communities.
Multi-scale reconstruction of turbulent rotating flows with proper orthogonal decomposition and generative adversarial networks
Authors: Li Tianyi , Buzzicotti Michele , Biferale Luca , Bonaccorso Fabio , Chen Shiyi , Wan Minping
Published: September 2023

Data reconstruction of rotating turbulent snapshots is investigated utilizing data-driven tools. This problem is crucial for numerous geophysical applications and fundamental aspects, given the concurrent effects of direct and inverse energy cascades. Additionally, benchmarking of various reconstruction techniques is essential to assess the trade-off between quantitative supremacy, implementation complexity and explicability. In this study, we use linear and nonlinear tools based on the proper orthogonal decomposition (POD) and generative adversarial network (GAN) for reconstructing rotating turbulence snapshots with spatial damages (inpainting). We focus on accurately reproducing both statistical properties and instantaneous velocity fields. Different gap sizes and gap geometries are investigated in order to assess the importance of coherency and multi-scale properties of the missing information. Surprisingly enough, concerning point-wise reconstruction, the nonlinear GAN does not outperform one of the linear POD techniques. On the other hand, the supremacy of the GAN approach is shown when the statistical multi-scale properties are compared. Similarly, extreme events in the gap region are better predicted when using GAN. The balance between point-wise error and statistical properties is controlled by the adversarial ratio, which determines the relative importance of the generator and the discriminator in the GAN training.
The ethical challenges of diversifying genomic data: A qualitative evidence synthesis
Authors: Hardcastle Faranak , Lyle Kate , Horton Rachel , Samuel Gabrielle , Weller Susie , Ballard Lisa , Thompson Rachel , De Paula Trindade Luiz Valerio , Gómez Urrego José David , Kochin Daniel , Johnson Tess , Tatz-Wieder Nechama , Redrup Hill Elizabeth , Robinson Adams Florence , Eskandar Yoseph , Harriss Eli , Tsosie Krystal S. , Dixon Padraig , Mackintosh Maxine , Nightingale Lyra , Lucassen Anneke
Published: September 2023

This article aims to explore the ethical issues arising from attempts to diversify genomic data and include individuals from underserved groups in studies exploring the relationship between genomics and health. We employed a qualitative synthesis design, combining data from three sources: 1) a rapid review of empirical articles published between 2000 and 2022 with a primary or secondary focus on diversifying genomic data, or the inclusion of underserved groups and ethical issues arising from this, 2) an expert workshop and 3) a narrative review. Using these three sources we found that ethical issues are interconnected across structural factors and research practices. Structural issues include failing to engage with the politics of knowledge production, existing inequities, and their effects on how harms and benefits of genomics are distributed. Issues related to research practices include a lack of reflexivity, exploitative dynamics and the failure to prioritise meaningful co-production. Ethical issues arise from both the structure and the practice of research, which can inhibit researcher and participant opportunities to diversify data in an ethical way. Diverse data are not ethical in and of themselves, and without being attentive to the social, historical and political contexts that shape the lives of potential participants, endeavours to diversify genomic data run the risk of worsening existing inequities. Efforts to construct more representative genomic datasets need to develop ethical approaches that are situated within wider attempts to make the enterprise of genomics more equitable.
Technical conferences as a technique of internationalism
Authors: Reinisch Jessica
Published: September 2023

This paper looks at a genre of meetings that, while neither purely ‘scientific’ nor ‘diplomatic’, drew on elements from both professional spheres and gained prominence in the interwar decades and during the Second World War. It proposes to make sense of ‘technical conferences’ as a phenomenon that was made by and through scientific experts and politicians championing the organizing power of rationality, science and liberal internationalism. Against the background of swelling ranks of state-employed scientists, this paper documents the emergence of technical conferences as the forums where they got down to work. To make this case the paper traces the influence of a new way of thinking about the function and organization of conferences, originating in the time around the First World War, on one international organization in particular: the United Nations Relief and Rehabilitation Administration (UNRRA), as a new hub of scientists and technicians.
WHY CAN'T TELEMACHUS BE KING? THE GROWTH OF A YOUNG BASILEUS
Authors: Valle Salazar Luca
Published: September 2023

This article seeks to offer some considerations on Telemachus’ journey to Pylos and Sparta (Hom. Od. 1–4), interpreting it in the light of his social position as heir of a basileus. Can the beginning of the Odyssey represent a sort of formation for the young prince? And how does the text support this reading? After a brief review of the features of a Homeric basileus, it will be argued that the narrative presents the growth of Telemachus as that of a young prince who needs to comply with those features, and become acquainted with the heroic world he lives in at peace.
Oblique predicative constructions in English withforandas:quavsqualitate qua
Authors: AARTS BAS
Published: September 2023

English has anoblique predicative constructionin which the prepositionsforandaslicense anoblique predicative complementthat is predicated of a noun phrase, as inWe took herfor a friendandI regarded heras a genius. The construction withforis the oldest, and is found in many other languages. This article traces the history of oblique predicative constructions involvingforandas, and a number of other prepositions, from Old English to Present-Day English (PDE). Visser (1963–73) has suggested that predicativeforandaswere rivals, and that in PDEasis now dominant at the expense offor. I will argue instead that since around 1900 predicativeforandascan clearly be distinguished semantically as expressing the meaningsqua(‘as being’) andqualitate qua(‘in the capacity of’), respectively, and that the existence of these distinct meanings explains why constructions with both prepositions still survive in PDE.
Transitioning to sustainable academic conferences needs more experimentation and reflection
Authors: Raven Rob , Hadfield Paris , Butler Brianna , Eagleton Jennifer , Giraud Gael , Jacob Merin , Markard Jochen , Schiller Katharina , Swilling Mark , Tshangela Mapula
Published: September 2023

Non-technical summary

Accelerated decarbonization of academic conferences is necessary and urgent. Despite the window of opportunity that COVID-19 created for rethinking conferences, there is a risk of slipping back into old habits now that restrictions are lifted. This commentary reports on recent experiences with a unique, sustainable approach to academic conferencing involving an international partnership and hub model across three continents. There is a need to continue to experiment with and implement new modes of sustainable academic conferencing.

Technical summary

In response to increasing demands to move away from carbon-intensive academic conferences, and a need to address social justice issues, the author-team designed, implemented, and experimented with a new conference model. Three key-design choices informed the model. First, instead of the common single-host-single-location approach, we established a partnership between three universities across three continents. Second, we adopted a hub model of three online conference days, followed by three non-hybrid, in-person only conference days. Third, we sought to accommodate global participation by organizing each of the online conference days during daylight hours in the respective time zones. We find that the model promotes less air travel and improved global south participation. Our approach adds to a growing number of experiments with new modes of academic conferencing in a world that is facing climate and inequality crises.

Social media summary

Decarbonizing academic conferences is necessary and urgent. This commentary reveals experiences with a hub-based format.
Moho Inversion by Gravity Anomalies in the South China Sea: Updates and Improved Iteration of the Parker‐Oldenburg Algorithm
Authors: Rao Weibo , Yu Nan , Chen Gang , Xu Xinyu , Zhao Simin , Song Zhaoqi , Liu Jiazheng , Wan Longtu , Hu Changhong
Published: September 2023

The Moho is the interface between crust and mantle, and accurate location of the Moho is important for both resource exploration and deep earth condition and structural change investigations. The theory of the traditional Parker‐Oldenburg (P‐O) method is quite simple and it is widely applied in the frequency domain of Moho depth inversion. However, Moho fluctuation simulations using the P‐O method are not reliable because of the lack of field geographic data constraints during the inversion process and the excessively smoothing of data details caused by using filters to correct the source data signals. To solve those problems, we propose an improved iteration P‐O method with a variable density contrast model, the iterative process is constrained by geological data in the inversion parameters, and the variable depth of the gravity interface is iterated using an equivalent form of upward continuation in the Fourier domain, which is more stable and convergent than downward continuation term in original P‐O method. Synthetic experiments indicate that improved method has the better consistency among the simulations than original method, and our improved method has the smallest root mean square (RMS) of 0.59 km. In a real case, we employed the improved method to invert for the Moho depth of the South China Sea (SCS), and the RMS between our Moho depth model and the seismological data is the smallest value of 2.27 km. The synthetic experiments and application of the model to the SCS further prove that our method is practical and efficient.
Modeling Wavelength Dependent Mid‐Infrared (5.5–25 μm) Optical Constants of Silicate Glasses: A Genetic Algorithm Approach
Authors: Varatharajan I. , Sklute E. , Glotch T. D. , Dyar M. D.
Published: September 2023

Wavelength‐dependent mid‐infrared (400–1,800 cm−1; 5.56–25 μm) optical constants (real and imaginary indices of refraction; n and k) are determined using reflectance spectra at a spectral sampling of 4 cm−1 for several silicate glasses of varying SiO2 wt% which include (a) basaltic volcanic glass from Kīlauea, Hawaii, (b) synthetic andesite, (c) two synthetic dacites, (d) obsidian volcanic glass from Mount Lassen, California, (e) synthetic rhyodacite, and (f) rhyolitic volcanic glass from Mexico. Because glasses are optically isotropic, no specific orientation was required for spectral measurements, and polished glass samples were measured at random orientations using micro‐FTIR spectrometer. Lorentz‐Lorenz dispersion theory and Fresnel reflectance model for high symmetry materials were used to model the optical constants by optimizing oscillator parameters in modeled spectra to match laboratory spectra. A genetic algorithm (GA) approach automatically finds the natural oscillators and their parameters for each spectrum, and then uses these parameters in a non‐linear least squares optimization routine. The study compared spectral parameters such as Christiansen feature, reststrahlen bands (RBs), and the peaks centered around 860–1,100 (peak 1) and 400–480 cm−1 (peak 2) of n and k to their respective SiO2 wt% of the glasses. CF, RBs, peak 1 of n and k, and peak 2 of n shift to higher wavenumbers with increased SiO2 wt%, whereas peak 2 of k shifts to lower wavenumbers with increased SiO2 wt%. Derived optical constants of these glasses will improve quantitative abundance mapping of volcanic materials on the surfaces of silicate targets in the Solar System.
Submarine Groundwater Discharge Strengthens Acidification in the Coastal Semi‐Closed Bays
Authors: Liu Yi , Song Yurong , Jiao Jiu Jimmy
Published: September 2023

Coastal ocean acidification is a worldwide problem associated with anthropogenic activity and climate change. In this study, a close relationship between submarine groundwater discharge (SGD) and coastal ocean acidification in Hong Kong's coastal waters is discovered. We for the first time evaluated the direct influence of SGD on seawater pH decline. Results show that SGD can contribute to up to 48% of seawater pH variation among terrestrial water input, air‐sea CO2 exchange, photosynthesis/respiration, and bay‐open water exchange in semi‐closed bays through direct input of carbonate species. Local air‐sea CO2 exchange has negligible influences on the seawater pH. In the semi‐closed bay areas, SGD and aerobic respiration are major contributors to seawater pH variation but in areas with open space, the exchange process with open waters is more important. In addition to the direct input of carbonate species (total alkalinity and dissolved inorganic carbon), SGD also influences the seawater pH via considerable nutrient loadings. The findings highlight the importance of the investigation and management of groundwater to alleviate the fast coastal ocean acidification.
Polarity Asymmetries in Rocket‐Triggered Lightning
Authors: da Silva C. L. , Winn W. P. , Taylor M. C. , Aulich G. D. , Hunyady S. J. , Eack K. B. , Edens H. E. , Sonnenfeld R. G. , Krehbiel P. R. , Eastvedt E. M. , Trueblood J. J.
Published: September 2023

The dissonant development of positive and negative lightning leaders is a central question in atmospheric electricity. It is also the likely root cause of other reported asymmetries between positive and negative lightning flashes, including the ones regarding: stroke multiplicity, recoil activity, leader velocities, and emission of energetic radiation. In an effort to contrast lightning leaders of different polarities, we highlight the staggering differences between two rocket‐triggered lightning flashes. The flash beginning with upward positive leaders exhibits an initial continuous current stage followed by multiple sequences of dart leaders and return strokes. On the other, in its opposite‐polarity counterpart, the upward development of negative leaders is by itself the entire flash. As a result, the flash with negative leaders is faster, briefer, transfers less charge to the ground, has lower currents, and smaller spatial extent. We conclude by presenting a discussion on the three fundamental leader propagation modes.
Abnormal Sub‐Auroral Ion Drifts (ASAID) Developed in the Postmidnight (1–4) Magnetic Local Time Sector in 2013
Authors: Horvath Ildiko , Lovell Brian C.
Published: September 2023

We investigate the Abnormal Sub‐Auroral Ion Drifts (ASAID) developed in the postmidnight (1–4) magnetic local time sector in 2013. Shown by the Defense Meteorological Satellite Program F15 horizontal ion velocity measurements, we specified 21 antisunward (eastward) ASAID flow channels (FCs) based on their respective underlying polar convections. Overall, the polar convection formed a two‐cell pattern with its convection axis tilted in the morning‐evening direction because of the underlying BY < 0 conditions. Its dawn cell intruded into the duskside from the dawnside where the eastward ASAID flows were streaming antisunward, opposite to the dawn cell sunward convection flows. Mostly, the ASAID FC appeared in the coinciding ring‐current–related ionospheric trough and flow‐stagnation–related main ionospheric trough in the South American sector because of the favorable conditions created by the South Atlantic Magnetic Anomaly promoting also the development of Stable Auroral Red (SAR) arc. Rarely observed, the ASAID FC was associated with the SAR arc detected over Rothera. Detected in the Mid Pacific longitude sector, a pair of northern‐southern ASAID FCs demonstrated northern‐southern conjugacy. With correlated observations, demonstrating magnetosphere‐ionosphere conjugacy, the inward (earthward) ASAID electric (E) field could also be investigated. These reveal the ASAID E field's fast‐time development by short‐circuiting when the hot‐ring‐current—cold‐plasmasphere interface developed and became impacted by finite Larmor radius effects because of the earthward intrusion of hot ring current protons. The ASAID E field's inner‐magnetosphere environment was characterized by the hot zone where heating was generated by low‐frequency waves and auroral kilometric radiations.
Characterizing Ozone Sensitivity to Urban Greening in Los Angeles Under Current Day and Future Anthropogenic Emissions Scenarios
Authors: Schlaerth Hannah L. , Silva Sam J. , Li Yun
Published: September 2023

Cities are simultaneously implementing urban greening and reducing anthropogenic emissions to combat climate change, but these strategies can have complex and potentially counteracting effects on regional atmospheric chemistry. Urban greening can increase emissions of volatile organic compounds (BVOCs), while climate change mitigation strategies reduce co‐emitted pollutants such as nitrogen oxides (NOx). The nonlinear relationship between ozone (O3) and BVOC and NOx concentrations makes it crucial to investigate potential interactions between urban greening and anthropogenic emissions reductions. Here, we use regional atmospheric chemistry modeling to assess O3 sensitivity to a 50% increase in urban vegetation in the Los Angeles Basin. We evaluated potential interactions between urban greening and climate change mitigation by running urban greening simulations with current day and future anthropogenic emissions that reflect renewable energy adoption and electrification in Los Angeles, CA. Our model results show that urban greening increased daily maximum 8‐hr ozone concentrations with higher increases modeled under current day anthropogenic emissions. Urban greening had complex effects on hourly O3 concentrations, with increased O3 concentrations up to 0.95 ppb during the day following increased biogenic emissions and reduced urban O3 concentrations up to 0.41 ppb at night following reduced ventilation of NOx. Under the future anthropogenic emissions scenario, reductions in NOx somewhat mitigated the daytime O3 penalties of urban greening but also dampened nighttime O3 reductions. Our results suggest that urban greening will likely have regional O3 penalties if new vegetation is high isoprene emitting, even as NOx emissions are drastically reduced following climate change mitigation.
Non‐Thermal Escape of Sulfur and Oxygen on Io Driven by Photochemistry
Authors: Huang Xu , Gu Hao , Cui Jun , Sun Mingyang , Ni Yangxin
Published: September 2023

Io, the closest of Jupiter's four Galileo moons, experiences intense volcanic activity that is induced by Jupiter's powerful tidal forces. The active volcanisms consequently create a tenuous SO2‐dominated atmosphere on Io, from which energetic particles can be easily lost due to the weak gravity field. The photolysis of SO2 triggers a complicated network of chemical reactions, which may be a significant source of atmospheric escape on Io. This study, for the first time, is devoted to evaluating the role of the chemically induced escape of S‐ and O‐containing species on Io by combining previous photochemical results and Monte Carlo model calculations. Different atmospheric conditions are compared, including high‐density volcanic and low‐density quiet scenarios, in which various chemical channels are considered. Our calculations suggest that the escape rates driven by photochemistry on Io are (1.1 − 2.0) × 1027 s−1 for total O and (1.5 − 6.7) × 1026 s−1 for total S, occurring mainly in the atomic form. The escape rates are found to vary extensively with the atmospheric conditions, especially in terms of the intensity of volcanic eruption. In general, photochemical escape is more important than Jeans escape for both atomic O and S for the quiet atmosphere scenario, whereas for the volcanic scenario, it is likely important for atomic S only.
Reconnaissance Basement Geology and Tectonics of North Zealandia
Authors: Mortimer Nick , Williams Simon , Seton Maria , Calvert Andy , Waight Tod , Turnbull Rose , Nelson Demian , Palin Mike , Ramezani Jahandar , Sagar Matthew W. , Tulloch Andy , Stratford Wanda , Collot Julien , Etienne Samuel
Published: September 2023

New rock dredge samples supply key information to establish the tectonic and geological framework of the northern two‐thirds of the 95% submerged Zealandia continent. The R/V Investigator voyage IN2016T01 to the Fairway Ridge, Coral Sea, obtained poorly sorted poly‐lithologic pebbly to cobbly sandstones, well sorted fine grained sandstones, mudstones, bioclastic limestones, and basaltic lavas. Post‐cruise analytical work comprised petrography, whole rock geochemical and Sr and Nd isotopic analyses, and U‐Pb zircon, Rb‐Sr, and Ar‐Ar geochronology. A Fairway Ridge cobbly sandstone has a ∼95 Ma (early Late Cretaceous) depositional age; two biotite granite cobbles are 111 ± 1 and 128 ± 1 Ma in age, and some volcanic pebbles are also likely Early Cretaceous. Fairway Ridge basalts have intraplate alkaline chemistry and are of Late Eocene age (∼40–36 Ma). By analogy with South Zealandia, we interpret strong positive continental magnetic anomalies of North Zealandia to mainly result from Late Cretaceous to Cenozoic intraplate basalts, many of them rift‐related lavas. A new basement geological map of North Zealandia shows the position of the Mesozoic Gondwana magmatic arc axis (Median Batholith) and other major geological units. This study completes onland and offshore reconnaissance geological mapping of the entire 5 Mkm2 Zealandia continent.
Generalizing Reservoir Operations Using a Piecewise Classification and Regression Approach
Authors: Ford Lucas , Sankarasubramanian A.
Published: September 2023

Inflow anomalies at varying temporal scales, seasonally varying storage mandates, and multipurpose allocation requirements contribute to reservoir operational decisions. The difficulty of capturing these constraints across many basins in a generalized framework has limited the accuracy of streamflow estimates in land‐surface models for locations downstream of reservoirs. We develop a Piecewise Linear Regression Tree to learn generalized daily operating policies from 76 reservoirs from four major basins across the coterminous US. Reservoir characteristics, such as residence time and maximum storage, and daily state variables, such as storage and inflow, are used to group similar observations across all reservoirs. Linear regression equations are then fit between daily state variables and release for each group. We recommend two models—Model 1 (M1) that performs the best when simulating untrained records but is complex and Model 2 (M2) that is nearly as performant as M1 but more parsimonious. The simulated release median root mean squared error is 49.7% (53.2%) of mean daily release with a median Nash‐Sutcliffe efficiency of 0.62 (0.52) for M1 (M2). Long‐term residence time is shown to be useful in grouping similar operating reservoirs. Release from low residence time reservoirs can be mostly described using inflow‐based variables. Operations at higher residence time reservoirs are more related to previous release variables or storage variables, depending on the current inflow. The ability of the models presented to capture operational dynamics of many types of reservoirs indicates their potential to be used for untrained and limited data reservoirs.
Artemisinins inhibit oral candidiasis caused by Candida albicans through the repression on its hyphal development
Authors: Liang Xiaoyue , Chen Ding , Wang Jiannan , Liao Binyou , Shen Jiawei , Ye Xingchen , Wang Zheng , Zhu Chengguang , Gou Lichen , Zhou Xinxuan , Cheng Lei , Ren Biao , Zhou Xuedong
Published: September 2023

Candida albicans is the most abundant fungal species in oral cavity. As a smart opportunistic pathogen, it increases the virulence by switching its forms from yeasts to hyphae and becomes the major pathogenic agent for oral candidiasis. However, the overuse of current clinical antifungals and lack of new types of drugs highlight the challenges in the antifungal treatments because of the drug resistance and side effects. Anti-virulence strategy is proved as a practical way to develop new types of anti-infective drugs. Here, seven artemisinins, including artemisinin, dihydroartemisinin, artemisinic acid, dihydroartemisinic acid, artesunate, artemether and arteether, were employed to target at the hyphal development, the most important virulence factor of C. albicans. Artemisinins failed to affect the growth, but significantly inhibited the hyphal development of C. albicans, including the clinical azole resistant isolates, and reduced their damage to oral epithelial cells, while arteether showed the strongest activities. The transcriptome suggested that arteether could affect the energy metabolism of C. albicans. Seven artemisinins were then proved to significantly inhibit the productions of ATP and cAMP, while reduced the hyphal inhibition on RAS1 overexpression strain indicating that artemisinins regulated the Ras1-cAMP-Efg1 pathway to inhibit the hyphal development. Importantly, arteether significantly inhibited the fungal burden and infections with no systemic toxicity in the murine oropharyngeal candidiasis models in vivo caused by both fluconazole sensitive and resistant strains. Our results for the first time indicated that artemisinins can be potential antifungal compounds against C. albicans infections by targeting at its hyphal development.
Unveiling the inner structure of electron pulses generated from a laser-wakefield accelerator
Authors: Kaluza Malte C.
Published: September 2023

A novel diagnostic method has been used to gain deeper insight into the transverse structure and its evolution of electron pulses generated from a laser-wakefield accelerator.
Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli
Authors: Matamouros Susana , Gensch Thomas , Cerff Martin , Sachs Christian C. , Abdollahzadeh Iman , Hendriks Johnny , Horst Lucas , Tenhaef Niklas , Tenhaef Julia , Noack Stephan , Graf Michaela , Takors Ralf , Nöh Katharina , Bott Michael
Published: September 2023

Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h−1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries
Authors: Chang Li-Hsin , Ghosh Sourav , Papale Andrea , Luppino Jennifer M. , Miranda Mélanie , Piras Vincent , Degrouard Jéril , Edouard Joanne , Poncelet Mallory , Lecouvreur Nathan , Bloyer Sébastien , Leforestier Amélie , Joyce Eric F. , Holcman David , Noordermeer Daan
Published: September 2023

Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.
Metabolic heterogeneity of tissue-resident macrophages in homeostasis and during helminth infection
Authors: Heieis Graham A. , Patente Thiago A. , Almeida Luís , Vrieling Frank , Tak Tamar , Perona-Wright Georgia , Maizels Rick M. , Stienstra Rinke , Everts Bart
Published: September 2023

Tissue-resident macrophage populations constitute a mosaic of phenotypes, yet how their metabolic states link to the range of phenotypes and functions in vivo is still poorly defined. Here, using high-dimensional spectral flow cytometry, we observe distinct metabolic profiles between different organs and functionally link acetyl CoA carboxylase activity to efferocytotic capacity. Additionally, differences in metabolism are evident within populations from a specific site, corresponding to relative stages of macrophage maturity. Immune perturbation with intestinal helminth infection increases alternative activation and metabolic rewiring of monocyte-derived macrophage populations, while resident TIM4+ intestinal macrophages remain immunologically and metabolically hyporesponsive. Similar metabolic signatures in alternatively-activated macrophages are seen from different tissues using additional helminth models, but to different magnitudes, indicating further tissue-specific contributions to metabolic states. Thus, our high-dimensional, flow-based metabolic analyses indicates complex metabolic heterogeneity and dynamics of tissue-resident macrophage populations at homeostasis and during helminth infection.
High-efficiency green management of potato late blight by a self-assembled multicomponent nano-bioprotectant
Authors: Wang Yuxi , Li Mingshan , Ying Jiahan , Shen Jie , Dou Daolong , Yin Meizhen , Whisson Stephen C. , Birch Paul R. J. , Yan Shuo , Wang Xiaodan
Published: September 2023

Potato late blight caused by Phytophthora infestans is a devastating disease worldwide. Unlike other plant pathogens, double-stranded RNA (dsRNA) is poorly taken up by P. infestans, which is a key obstacle in using dsRNA for disease control. Here, a self-assembled multicomponent nano-bioprotectant for potato late blight management is designed based on dsRNA and a plant elicitor. Nanotechnology overcomes the dsRNA delivery bottleneck for P. infestans and extends the RNAi protective window. The protective effect of nano-enabled dsRNA against infection arises from a synergistic mechanism that bolsters the stability of dsRNA and optimizes its effective intracellular delivery. Additionally, the nano-enabled elicitor enhances endocytosis and amplifies the systemic defense response of the plants. Co-delivery of dsRNA and an elicitor provides a protective effect via the two aspects of pathogen inhibition and elevated plant defense mechanisms. The multicomponent nano-bioprotectant exhibits superior control efficacy compared to a commercial synthetic pesticide in field conditions. This work proposes an eco-friendly strategy to manage devastating plant diseases and pests.
Searching the chemical space for effective magnesium dissolution modulators: a deep learning approach using sparse features
Authors: Schiessler Elisabeth J. , Würger Tim , Vaghefinazari Bahram , Lamaka Sviatlana V. , Meißner Robert H. , Cyron Christian J. , Zheludkevich Mikhail L. , Feiler Christian , Aydin Roland C.
Published: September 2023

Small organic molecules can alter the degradation rates of the magnesium alloy ZE41. However, identifying suitable candidate compounds from the vast chemical space requires sophisticated tools. The information contained in only a few molecular descriptors derived from recursive feature elimination was previously shown to hold the potential for determining such candidates using deep neural networks. We evaluate the capability of these networks to generalise by blind testing them on 15 randomly selected, completely unseen compounds. We find that their generalisation ability is still somewhat limited, most likely due to the relatively small amount of available training data. However, we demonstrate that our approach is scalable; meaning deficiencies caused by data limitations can presumably be overcome as the data availability increases. Finally, we illustrate the influence and importance of well-chosen descriptors towards the predictive power of deep neural networks.
Neurofilament light chain as a mediator between LRRK2 mutation and dementia in Parkinson’s disease
Authors: Yang Dehao , Xie Haobo , Wu Sheng , Ying Chenxin , Chen Yiqun , Ge Yaoying , Yao Ruotong , Li Kun , Jiang Zihan , Chen Guangyong
Published: September 2023

Elevated neurofilament light chain (NfL) levels have been associated with dementia in idiopathic Parkinson’s disease (iPD). To examine the baseline and longitudinal changes in NfL levels in GBA-PD, SNCA-PD, and LRRK2-PD and further investigate the association between these genetic mutations, NfL, and dementia in PD. We analyzed data from the Parkinson’s Progression Markers Initiative (PPMI), including 184 healthy controls (HC) and 617 PD categorized as iPD (n = 381), LRRK2-PD (n = 142), GBA-PD (n = 76) and SNCA-PD (n = 18). Analysis of covariance (ANCOVA) or linear mixed-effect models were used to compare the baseline or dynamic NfL levels between groups. We then explored the relationship between genetic mutations, serum NfL levels, and conversion to dementia using mediation analysis. After adjusting for confounding factors, SNCA-PD exhibited higher baseline serum NfL levels than iPD. Regarding longitudinal changes, SNCA-PD showed the highest increase rate in estimated NfL levels (2.43 pg/mL per year), while LRRK2-PD experienced the slowest increase rate (0.52 pg/mL per year). Mediation analysis indicated that higher estimated NfL level changes were associated with faster cognitive decline (β = 0.591, p = 0.026). Specifically, the relationship between LRRK2 and dementia was mediated by the estimated NfL level change (β = −0.717, p < 0.05). Longitudinal changes in serum NfL levels may serve as a biomarker for cognitive decline in Parkinson’s disease. Moreover, compared to iPD, the slower progression of dementia in LRRK2-PD may be partially attributed to a slower increase in NfL levels.
Review of visual analytics methods for food safety risks
Authors: Chen Yi , Wu Caixia , Zhang Qinghui , Wu Di
Published: September 2023

With the availability of big data for food safety, more and more advanced data analysis methods are being applied to risk analysis and prewarning (RAPW). Visual analytics, which has emerged in recent years, integrates human and machine intelligence into the data analysis process in a visually interactive manner, helping researchers gain insights into large-scale data and providing new solutions for RAPW. This review presents the developments in visual analytics for food safety RAPW in the past decade. Firstly, the data sources, data characteristics, and analysis tasks in the food safety field are summarized. Then, data analysis methods for four types of analysis tasks: association analysis, risk assessment, risk prediction, and fraud identification, are reviewed. After that, the visualization and interaction techniques are reviewed for four types of characteristic data: multidimensional, hierarchical, associative, and spatial-temporal data. Finally, opportunities and challenges in this area are proposed, such as the visual analysis of multimodal food safety data, the application of artificial intelligence techniques in the visual analysis pipeline, etc.
A quantum chemical interaction energy dataset for accurately modeling protein-ligand interactions
Authors: Spronk Steven A. , Glick Zachary L. , Metcalf Derek P. , Sherrill C. David , Cheney Daniel L.
Published: September 2023

Fast and accurate calculation of intermolecular interaction energies is desirable for understanding many chemical and biological processes, including the binding of small molecules to proteins. The Splinter [“Symmetry-adapted perturbation theory (SAPT0)protein-ligandinteraction”] dataset has been created to facilitate the development and improvement of methods for performing such calculations. Molecular fragments representing commonly found substructures in proteins and small-molecule ligands were paired into >9000 unique dimers, assembled into numerous configurations using an approach designed to adequately cover the breadth of the dimers’ potential energy surfaces while enhancing sampling in favorable regions. ~1.5 million configurations of these dimers were randomly generated, and a structurally diverse subset of these were minimized to obtain an additional ~80 thousand local and global minima. For all >1.6 million configurations, SAPT0 calculations were performed with two basis sets to complete the dataset. It is expected that Splinter will be a useful benchmark dataset for training and testing various methods for the calculation of intermolecular interaction energies.
Improved patient mortality predictions in emergency departments with deep learning data-synthesis and ensemble models
Authors: Son Byounghoon , Myung Jinwoo , Shin Younghwan , Kim Sangdo , Kim Sung Hyun , Chung Jong-Moon , Noh Jiyoung , Cho Junho , Chung Hyun Soo
Published: September 2023

The triage process in emergency departments (EDs) relies on the subjective assessment of medical practitioners, making it unreliable in certain aspects. There is a need for a more accurate and objective algorithm to determine the urgency of patients. This paper explores the application of advanced data-synthesis algorithms, machine learning (ML) algorithms, and ensemble models to predict patient mortality. Patients predicted to be at risk of mortality are in a highly critical condition, signifying an urgent need for immediate medical intervention. This paper aims to determine the most effective method for predicting mortality by enhancing the F1 score while maintaining high area under the receiver operating characteristic curve (AUC) score. This study used a dataset of 7325 patients who visited the Yonsei Severance Hospital’s ED, located in Seoul, South Korea. The patients were divided into two groups: patients who deceased in the ED and patients who didn’t. Various data-synthesis techniques, such as SMOTE, ADASYN, CTGAN, TVAE, CopulaGAN, and Gaussian Copula, were deployed to generate synthetic patient data. Twenty two ML models were then utilized, including tree-based algorithms like Decision tree, AdaBoost, LightGBM, CatBoost, XGBoost, NGBoost, TabNet, which are deep neural network algorithms, and statistical algorithms such as Support Vector Machine, Logistic Regression, Random Forest, k-nearest neighbors, and Gaussian Naive Bayes, as well as Ensemble Models which use the results from the ML models. Based on 21 patient information features used in the pandemic influenza triage algorithm (PITA), the models explained previously were applied to aim for the prediction of patient mortality. In evaluating ML algorithms using an imbalanced medical dataset, conventional metrics like accuracy scores or AUC can be misleading. This paper emphasizes the importance of using the F1 score as the primary performance measure, focusing on recall and specificity in detecting patient mortality. The highest-ranked model for predicting mortality utilized the Gaussian Copula data-synthesis technique and the CatBoost classifier, achieving an AUC of 0.9731 and an F1 score of 0.7059. These findings highlight the effectiveness of machine learning algorithms and data-synthesis techniques in improving the prediction performance of mortality in EDs.
36Cl, a new tool to assess soil carbon dynamics
Authors: Grapeloup Cécile , Cornu Sophie , Giraud Xavier , Pupier Julie , Team Aster , Guillou Valery , Ciffroy Philippe , Cabana Beatriz Lourino , Couegnas Cécile , Hatté Christine , Benedetti Lucilla
Published: September 2023

Soil organic carbon is one of the largest surface pools of carbon that humans can manage in order to partially mitigate annual anthropogenic CO2 emissions. A significant element to assess soil sequestration potential is the carbon age, which is evaluated by modelling or experimentally using carbon isotopes. Results, however, are not consistent. The 14C derived approach seems to overestimate by a factor of 6–10 the average carbon age in soils estimated by modeling and 13C approaches and thus the sequestration potential. A fully independent method is needed. The cosmogenic chlorine nuclide, 36Cl, is a potential alternative. 36Cl is a naturally occurring cosmogenic radionuclide with a production that increased by three orders of magnitude during nuclear bomb tests. Part of this production is retained by soil organic matter in organochloride form and hence acts as a tracer of the fate of soil organic carbon. We here quantify the fraction and the duration of 36Cl retained in the soil and we show that retention time increases with depth from 20 to 322 years, in agreement with both modelling and 13C-derived estimates. This work demonstrates that 36Cl retention duration can be a proxy for the age of soil organic carbon.
miRNA-126a plays important role in myoblast and endothelial cell interaction
Authors: Mierzejewski Bartosz , Ciemerych Maria Anna , Streminska Wladyslawa , Janczyk-Ilach Katarzyna , Brzoska Edyta
Published: September 2023

Muscle satellite cells (SCs) are stem cells and the main players in skeletal muscle reconstruction. Since satellite cells are located near or in direct contact with blood vessels their niche is formed, inter alia, by endothelial cells. The cross-talk between satellite cells and endothelial cells determines quiescence or proliferation of these cells. However, little is known about the role of miRNA in these interactions. In the present study we identified miRNA that were up-regulated in SC-derived myoblasts treated with stromal derived factor-1 (SDF-1) and/or down-regulated in cells in which the expression of CXCR4 or CXCR7, that is, SDF-1 receptors, was silenced. SDF-1 is one of the important regulators of cell migration, mobilization, skeletal muscle regeneration, and angiogenesis. We hypothesized that selected miRNAs affect SC-derived myoblast fate and interactions with endothelial cells. We showed that miR-126a-3p inhibited both, myoblast migration and fusion. Moreover, the levels of Cxcl12, encoding SDF-1 and Ackr3, encoding CXCR7, were reduced by miR-126a-3p mimic. Interestingly, the miR-126a-3p mimic significantly decreased the level of numerous factors involved in myogenesis and the miR-126a-5p mimic increased the level of Vefga. Importantly, the treatment of endothelial cells with medium conditioned by miR-126-5p mimic transfected SC-derived myoblasts promoted tubulogenesis.
Fatty acid challenge shifts cellular energy metabolism in a substrate-specific manner in primary bovine neonatal hepatocytes
Authors: Chandler T. L. , Kendall S. J. , White H. M.
Published: September 2023

Adipose tissue mobilization increases circulating fatty acid (FA) concentrations, leads to increased hepatic FA uptake, and influences hepatic metabolism. Our objective was to trace carbon flux through metabolic pathways in primary bovine neonatal hepatocytes challenged with FA, and to examine the effect of FA challenge on oxidative stress. Primary bovine neonatal hepatocytes were isolated from 4 Holstein bull calves and maintained for 24 h before treatment with either 0 or 1 mM FA cocktail. After 21 h, either [1-14C]C16:0 or [2-14C]sodium pyruvate was added to measure complete and incomplete oxidation and cellular glycogen. Cellular and media triglyceride (TG), and glucose and ß-hydroxybutyrate (BHB) export were quantified, as well as reactive oxygen species and cellular glutathione (GSH/GSSH). Fatty acid treatment increased cellular, but not media TG, and although complete oxidation of [1-14C]C16:0 was not affected by FA, BHB export was increased. Reactive oxygen species were increased with FA treatment and GSSH was marginally increased such that the ratio of GSH:GSSG was marginally decreased. Glucose export increased, and cellular glycogen marginally increased with FA treatment while [2-14C]sodium pyruvate oxidation was decreased. These data suggest that FA treatment shifts cellular energy metabolism in a substrate-specific manner, spares pyruvate carbon from oxidation, and stimulates glucose synthesis.
Mine or my neighbours’ offspring: an experimental study on parental discrimination of offspring in a colonial seabird, the little auk Alle alle
Authors: Kidawa Dorota , Wojczulanis-Jakubas Katarzyna , Jakubas Dariusz , Palme Rupert , Barcikowski Mateusz
Published: September 2023

Individual recognition (IR) abilities may result from various ecological and naturally selected features of a species. Complex IR mechanisms should develop when the risk of misidentification of a chick is high. For colonial seabirds, the ability to identify their own brood is crucial to ensure parental fitness. Vocalizations seem to be a key component of most parent–offspring interactions, although few studies have assessed the interindividual differences in seabird chick calls and their potential usage in IR. The little auk (Allealle), which breeds in dense colonies, constitutes a perfect model for testing IR. In this study, we (1) examined chick calls at different stages of the nesting period, and (2) cross-fostered chicks to examine the rate of acceptance/nonacceptance of chicks by parents. We found significant interindividual differences in chick begging and fledging calls. Surprisingly, all cross-fostered chicks in our experiments were accepted by their foster parents, and male parents were as equally likely to accept cross-fostered chicks as females, even though the sexes would be expected to differ in offspring recognition due to different postfledging interactions with the chick. The revealed individuality of chick calls suggests the potential for chick vocal recognition in the studied species, but parent birds may disregard the individual characteristics enabling chick discrimination. This may take place as long as the chick is found in the nest because of the high likelihood that the chick present there is the focal one. However, IR during and after fledging requires further study. Studying the complexity of IR mechanisms is important for better understanding various avian social relationships and interactions.