bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparative Account of Biogenic Synthesis of Silver Nanoparticles Using Probiotics and Their Antimicrobial Activity Against Challenging Pathogens
Authors: Sharma Shakshi , Sharma Nivedita , Kaushal Neha
Published: July 2022

The present work focusses on development of a safe, inexpensive, and more accessible source for biosynthesis of silver nanoparticles. Four different in-house probiotic isolates, i.e., Lactobacillus pentosus S6, Lactobacillus plantarum F22, Lactobacillus crustorum F11, and Lactobacillus paraplantarum KM1 isolated from different food sources, were used in the current study to check their ability to synthesize silver nanoparticles. All the probiotic-synthesized silver nanoparticles show maximum surface plasmon resonance (SPR) at a peak of 450 nm, which confirms the formation of silver nanoparticles. Scanning electron microscopy (SEM) analysis identified the shape and distribution of silver nanoparticles. Transmission electron microscopy (TEM) revealed the average size of synthesized nanoparticles in the range of 10–50 nm, with the smallest size of 5 nm for silver nanoparticles synthesized by L. crustorum F11. Further, Fourier-transform infrared spectroscopy (FTIR) detected the presence of different functional groups responsible for reduction of silver ion to form silver nanoparticles. The antimicrobial activity of these AgNPs was also found to be effective against different bacterial and fungal pathogens, viz., antibiotic-resistant Staphylococcus aureus, Bacillus cereus, Listeria monocytogenes, Pythium aphanidermatum, Fusarium oxysporum, and Phytopthora parasitica. However, L. crustorum F11–synthesized AgNP showed maximum inhibition against all the bacterial and fungal pathogens, with highest against S. aureus (20 ± 0.61 mm) and F. oxysporum (23 ± 0.37). Findings from this study provide a durable and eco-friendly method for the biosynthesis of silver nanoparticles, having strong antimicrobial activity against different multidrug-resistant microorganisms.

Graphical abstract
Exploring the Links Between Trait Mindfulness and Emotional and Behavioral Responses in the Ultimatum Game
Authors: van der Schans Kim Lien , Kiggen Michiel H. H. , Tziafetas Konstantinos , Holland Rob W. , Karremans Johan C.
Published: July 2022

Objectives

The current study assessed whether trait mindfulness relates to social decision making as increased acceptance rates towards offers in the Ultimatum Game. Mindfulness has been associated to a reduction in emotional reactivity and an increase in emotion regulation once intense emotions do occur. Therefore, we reasoned that trait mindfulness would predict acceptance in the Ultimatum Game, perhaps even in case of unfair offers.

Methods

In two online studies we assessed whether trait mindfulness positively predicts acceptance of offers in the Ultimatum Game among community samples (study 1 N = 107; study 2 N = 118). In study 2, we also assessed participants’ emotional reactions to offers prior to their decision to accept or reject.

Results

Whereas study 1 indeed showed a significant positive relation between trait mindfulness and acceptance of offers (OR = 2.01, p = .05), study 2 did not show this relation (OR = .91, p = .81). Also, the results of study 2 showed that trait mindfulness may moderate emotional responses to offers (β =  − .06, p = .03). Yet, analyses of the pooled data indicated no relation between trait mindfulness and acceptance of offers (p < .15).

Conclusions

Our research provides mixed support regarding the association between trait mindfulness and behavioral acceptance of offers in the Ultimatum Game. We discuss the need for more fine-grained examinations of when and why mindfulness should lead to acceptance of unfairness, and if and when mindfulness would lead to wise responding in social exchange situations.
Beyond Lynn Margulis’ green hydra
Authors: Bosch Thomas C. G.
Published: July 2022

Lynn Margulis has made it clear that in nature partnerships are the predominant form of life; that life processes can only be understood in terms of the interactions of such partnerships; and that their inherent complexity can only be understood by taking a holistic approach. Here I attempt to relate Lynn Margulis´ observations on the freshwater polyp hydra to the perceptions and problems of today’s Hydra research. To accomplish this, I will synthesize our current understanding of how symbionts influence the phenotype and fitness of hydra. Based on this new findings, a fundamental paradigm shift and a new era is emerging in the way that we consider organisms such as hydra as multi-organismic metaorganisms, just as Lynn Margulis may have thought about it.
Cultural ecosystem services in European grasslands: A systematic review of threats
Authors: Pellaton Raoul , Lellei-Kovács Eszter , Báldi András
Published: July 2022

The degradation of ecosystems threatens the provision of ecosystem services and limits human well-being. This systematic literature review evaluates the threats surrounding cultural ecosystem services (CES), namely recreation and landscape aesthetics in European permanent grasslands. We identified underlying causes, direct threats, consequences and suggested solutions for threat mitigation. The most common threats were land-use and management change processes, followed by social attitude, industrial developments and natural threats. However, recreational activities also created negative feedback, affecting the ecosystem, biodiversity and CES, most frequently in the form of various touristic activities. Suggested solutions were most commonly socio-economic and institutional measures to enhance rural communities, as well as improving communication with relevant stakeholders. CES play a crucial role in reconnecting people with nature, and their consequent acknowledgement and incorporation into future ecosystem service frameworks and agri-environmental policy developments are key elements in supporting future sustainable grassland management.
Future agricultural systems and the role of digitalization for achieving sustainability goals. A review
Authors: MacPherson Joseph , Voglhuber-Slavinsky Ariane , Olbrisch Mathias , Schöbel Philipp , Dönitz Ewa , Mouratiadou Ioanna , Helming Katharina
Published: July 2022

By leveraging a wide range of novel, data-driven technologies for agricultural production and agri-food value chains, digital agriculture presents potential enhancements to sustainability across food systems. Accordingly, digital agriculture has received considerable attention in policy in recent years, with emphasis mostly placed on the potential of digital agriculture to improve efficiency, productivity and food security, and less attention given to how digitalization may impact other principles of sustainable development, such as biodiversity conservation, soil protection, and human health, for example. Here, we review high-level policy and law in the German and European context to highlight a number of important institutional, societal, and legal preconditions for leveraging digital agriculture to achieve diverse sustainability targets. Additionally, we combine foresight analysis with our review to reflect on how future frame conditions influencing agricultural digitalization and sustainability could conceivably arise. The major points are the following: (1) some polices consider the benefits of digital agriculture, although only to a limited extent and mostly in terms of resource use efficiency; (2) law as it applies to digital agriculture is emerging but is highly fragmented; and (3) the adoption of digital agriculture and if it is used to enhance sustainability will be dependent on future data ownership regimes.
Ecological engineering for rice pest suppression in China. A review
Authors: Zhu Pingyang , Zheng Xusong , Johnson Anne C. , Chen Guihua , Xu Hongxing , Zhang Facheng , Yao Xiaoming , Heong Kongluen , Lu Zhongxian , Gurr Geoff M.
Published: July 2022

Ecological engineering for pest suppression aimed at promoting ecosystem services of biological control, involves a range of environmentally-benign approaches to conserve and promote arthropod natural enemies and suppress pest populations, and thus reduce the need for insecticide use. Major components in rice pest management involve providing vegetation that favors parasitoid overwintering during the fallow seasons, growing nectar-producing flowering plants on the rice bunds to enhance the biocontrol function, and planting trap plants around rice fields to minimize the initial populations of pests. Complementary tactics involve using sex pheromone traps and mass-releasing Trichogramma spp. parasitoids to reduce the densities of Lepidoptera pests, and synergistically culturing ducks or fish to reduce other planthoppers. After a decade of laboratory and field research accompanied by on-farm demonstrations, ecological engineering for rice pest management has shown growth in both the underlying body of theory and practical adoption, especially in China. Ecological engineering approaches have been listed as a China National Recommendation by the Ministry of Agriculture and Rural Affairs of the People’s Republic of China (MARA) since 2014. We feel this is worth documenting, especially because only a portion of that work has been reported in English-language journals so would otherwise remain “invisible” to the international scientific community. This study is the first time to systematically review the research that has allowed this rapid development and uptake in China, highlighting priorities for future research that will enhance the prospects for ecological engineering in this and other agricultural systems internationally.
Practical Implications of Research on Intimate Partner Violence Experiences for the Mental Health Clinician
Authors: Doyle Kathryn W. , Knetig Jennifer A. , Iverson Katherine M.
Published: July 2022

Purpose of review

Individuals experiencing mental health difficulties are at heightened risk for experiencing past and recent intimate partner violence (IPV), including sexual, psychological, and physical violence and/or stalking, from an intimate partner. Yet, mental health clinicians often report limited knowledge about IPV, especially best clinical practices for identifying and addressing IPV experiences in routine mental health care.

Recent findings

This paper reviews literature on IPV experiences, including prevalence, linkages with mental health problems, considerations for vulnerable populations, and evidence-based practices for screening, assessment, and intervention for IPV in the context of mental health care. These practices are rooted in trauma-informed and person-centered care principles and emphasize safety and empowerment.

We conclude by commenting on common clinician challenges and considerations for case conceptualization for individuals experiencing IPV.
Bots influence opinion dynamics without direct human-bot interaction: the mediating role of recommender systems
Authors: Pescetelli N. , Barkoczi D. , Cebrian M.
Published: July 2022

Bots’ ability to influence public discourse is difficult to estimate. Recent studies found that hyperpartisan bots are unlikely to influence public opinion because bots often interact with already highly polarized users. However, previous studies focused on direct human-bot interactions (e.g., retweets, at-mentions, and likes). The present study suggests that political bots, zealots, and trolls may indirectly affect people’s views via a platform’s content recommendation system's mediating role, thus influencing opinions without direct human-bot interaction. Using an agent-based opinion dynamics simulation, we isolated the effect of a single bot—representing 1% of nodes in a network—on the opinion of rational Bayesian agents when a simple recommendation system mediates the agents’ content consumption. We compare this experimental condition with an identical baseline condition where such a bot is absent. Across conditions, we use the same random seed and a psychologically realistic Bayesian opinion update rule so that conditions remain identical except for the bot presence. Results show that, even with limited direct interactions, the mere presence of the bot is sufficient to shift the average population’s opinion. Virtually all nodes—not only nodes directly interacting with the bot—shifted towards more extreme opinions. Furthermore, the mere bot’s presence significantly affected the internal representation of the recommender system. Overall, these findings offer a proof of concept that bots and hyperpartisan accounts can influence population opinions not only by directly interacting with humans but also by secondary effects, such as shifting platforms’ recommendation engines’ internal representations. The mediating role of recommender systems creates indirect causal pathways of algorithmic opinion manipulation.
Solute dispersion in channels with periodic square boundary roughness
Authors: Haugerud Ivar Svalheim , Linga Gaute , Flekkøy Eirik Grude
Published: July 2022

Transport of solutes through channels with rough boundaries is abundant in natural and engineered settings. However, it is not known currently what the consequences of an abruptly alternating boundary are for the solute dispersion, in particular when advected by inertial fluid flow. To investigate this, we compute numerically the time-asymptotic longitudinal dispersion coefficient of a passive solute advected by fluid flow through a two-dimensional channel with square boundary roughness. We determine how the effective diffusion coefficient depends on the boundary amplitude, Péclet number and Reynolds number. For creeping flow, the effective diffusion coefficient is found to be enhanced significantly through the recirculation zones. Increasing fluid inertia reduces the effective diffusion coefficient by up to a factor of two for high Péclet numbers. We interpret this behaviour by analysing residence times computed from Lagrangian particle simulations.
Stratified turbulent mixing in oscillating shear flows
Authors: Lewin S.F. , Caulfield C.P.
Published: July 2022

Motivated by the variation of local shear produced by internal waves in the ocean, we use direct numerical simulations to investigate the effect of a time-dependent shear forcing on the evolution and mixing of turbulence produced by Kelvin–Helmholtz instability (KHI) at high Reynolds number. The forcing is implemented using a tilting coordinate system which causes the background shear to accelerate and decelerate periodically. We demonstrate that, with suitable timing between development of instability and the shear oscillation cycle, turbulence produced by KHI with a decelerating shear mixes in a distinctly different way from the flow with constant background shear, specifically with the energy for turbulent motions extracted from alternative sources. As a result, the total amount of mixing as measured by the change in background potential energy can in fact be significantly larger for flows in which the shear is decelerated, despite the fact that the total kinetic energy in the flow is significantly smaller. The mixing has characteristics more in common with convectively driven rather than shear-driven flows, supporting the argument for an underlying change in the mechanisms triggering the turbulence.
Multi-decadal elevation changes of the land terminating sector of West Greenland
Authors: Saito Jun , Meierbachtol Toby , Harper Joel
Published: July 2022

Regional assessments of ice elevation change provide insight into the processes controlling an ice sheet's geometric response to climate forcing. In Southwest Greenland's land terminating sector (SWLTS), it is presumed that ice surface elevation changes result solely from changing surface mass balance (SMB). Here we test this assumption by developing a multi-decadal (1985–2017) record of elevation change from digital elevation models (DEMs) and comparing it to regional climate model output and available records of ice speed. The SWLTS thinned by >12 m on average over the full 32-year period, but the change was highly variable in time and space. Thinning was amplified in the central region of the SWLTS, relative to the north and south. During 1985–2007, the north and south regions demonstrated net thickening while the central region thinned. Regional differences in elevation change are inconsistent with SMB anomalies, indicating that enhanced ice flow in the north and south contributed to thickening during this early time interval. While clear validation in the south is prevented by incomplete velocity data, historical surface speeds in the north were elevated. These findings support the interpretation that changing ice flow can influence ice surface elevation in the slow-moving SWLTS.
Identifying Ideologues: A Global Dataset on Political Leaders, 1945–2020
Authors: Herre Bastian
Published: July 2022

Researchers have long studied how the ideology of political leaders affects policymaking and social welfare. The limited coverage of cross-country ideology datasets, however, has meant that researchers have mainly focused on Organisation for Economic Co-operation and Development (OECD) countries. This letter therefore presents the Global Leader Ideology dataset, which vastly expands the scope of previous datasets by classifying chief executives as leftist, centrist, rightist or non-ideological in 182 countries annually from 1945 or independence to 2020. The letter describes the dataset's contents and coding, compares it to existing datasets, and illustrates its uses by exploring how the ideologies of political leaders differ around the world and over time. The letter thereby outlines a research agenda on the global causes of chief executives' ideologies and their effects on policies and socio-economic outcomes.
Endoscopic transoral approach to the parapharyngeal space: technical nuances and preliminary results
Authors: Liu J , Liu Q , Sun X-C , Yu H-M , Wang D-H
Published: July 2022

Objective

Surgical management is the mainstay of treatment for tumours in the parapharyngeal space. This study aimed to evaluate the indications, limits and technical nuances of the endoscopic transoral approach.

Method

Thirteen patients with parapharyngeal space tumours that were treated between May 2017 and November 2020 were included in this retrospective study.

Results

All patients underwent surgery for complete oncological resection except one patient who received treatment for diagnostic purposes. No major complications were reported, with excellent control of the vital structures of the parapharyngeal space.

Conclusion

The endoscopic transoral approach to the parapharyngeal space is a promising alternative approach for selected parapharyngeal space tumours with satisfactory outcomes.
Determination of seasonal changes in phytoplankton community of the coastal waters of Burgaz Island (the Sea of Marmara)
Authors: Kayadelen Yorgo , Balkis-Ozdelice Neslihan , Durmus Turgay
Published: July 2022

The aim of this study is to determine the phytoplankton species found on the shores of Burgaz Island and the basic ecological variables that affect their seasonal distribution between May 2013 and February 2014. Water samples were collected from four stations at six different depths and plankton samples were gathered horizontally and vertically. The analysis of phytoplankton community composition revealed 101 phytoplankton taxa belonging to five classes. As a result of the study, two taxa belonging to the Dinophyceae (Corythodinium frenguellii and Gonyaulax scrippsae) were new records for Turkish coastal waters. Additionally, a taxon belonging to Dinophyceae (Pronoctiluca pelagica) and a taxon belonging to Bacillariophyceae (Nitzschia reversa) were new records for the Sea of Marmara. Prorocentrum micans, was the dominant species throughout all sampling periods. During the study, the highest phytoplankton abundance was observed at 0.5 m depth in May 2013 (138,500 cells l−1) and February 2014 (52,620 cells l−1). Primary ecological variables, such as temperature (9.0–21.5 °C), salinity (15.23–37.22‰) and dissolved oxygen (4.89–15.84 mg l−1), were recorded on each sampling occasion. In addition, nitrite + nitrate–N (NO2 + NO3–N) (0.01–7.37 μg-at N l−1), phosphate (PO4–P) (0.05–51.95 μg-at P l−1) and silicate (SiO4–Si) (0.01–0.20 μg-at Si l−1) concentrations were measured. Chlorophyll a and suspended material values ranged between 0.01–3.17 μg l−1 and 10.0–61.5 mg l−1, respectively. Spearman's rank correlation was used to determine the relationship between phytoplankton species and ecological variables, and Bray–Curtis analysis and Euclidean distance were applied to bring out the similarity between stations.
Taking the Courts to the Fields: Law, Violence, and Agrarian Custom in Colonial Oaxaca, Mexico
Authors: Yannakakis Yanna
Published: July 2022

This article, part of the forum “The Everyday Materials of Colonial Legal Spaces,” analyzes how Spanish law intersected with longue-durée Indigenous histories to pattern performative judicial violence in disputes over boundary lands separating Indigenous communities. During the late seventeenth and eighteenth centuries when population growth and expansion and commercialization of the livestock industry put pressure on Indigenous lands, Native judicial officers used their coercive power and symbols of judicial authority to physically enter boundary lands and shape the course of legal disputes. By combining legal and extralegal procedures, Native officials developed customary patterns of judicial practice and performance proper to their own jurisdiction in which objects invested with political, sacred, and quotidian meaning figured centrally. Staffs of office and whips wielded by Native authorities as emblems of Indian administrative and legal jurisdiction represented one category of the everyday materials of law. Clothing, farming implements, and livestock afforded other tools with which Indigenous farmers and authorities made legal claims. When reading land disputes alongside criminal cases of land invasions across Oaxaca’s judicial archives, it becomes clear that Native officials and farmers used these objects to struggle over territory and authority in cycles of litigation, land titling or contracts of joint-possession, and violence that often endured for decades or centuries, forming an enduring facet of agrarian custom in the region.
Development of consensus recommendations for the management of post-operative chylothorax in paediatric CHD
Authors: Lion Richard P. , Winder Melissa M. , Amirnovin Rambod , Fogg Kristi , Bertrandt Rebecca , Bhaskar Priya , Kasmai Cameron , Holmes Kathryn W , Moza Rohin , Vichayavilas Piyagarnt , Gordon Erin E. , Trauth Amiee , Horsley Megan , Frank Deborah U. , Stock Arabela , Adamson Greg , Lyman Alissa , Raymond Tia , Diaz Isaura , DeMarco Alicia , Prodhan Parthak , Fundora Michael , Aljiffry Alaa , Dewitt Aaron G , Kozyak Benjamin W. , Greiten Lawrence , Scahill Carly , Buckley Jason , Bailly David K.
Published: July 2022

Objective:

A standardised multi-site approach to manage paediatric post-operative chylothorax does not exist and leads to unnecessary practice variation. The Chylothorax Work Group utilised the Pediatric Critical Care Consortium infrastructure to address this gap.

Methods:

Over 60 multi-disciplinary providers representing 22 centres convened virtually as a quality initiative to develop an algorithm to manage paediatric post-operative chylothorax. Agreement was objectively quantified for each recommendation in the algorithm by utilising an anonymous survey. “Consensus” was defined as ≥ 80% of responses as “agree” or “strongly agree” to a recommendation. In order to determine if the algorithm recommendations would be correctly interpreted in the clinical environment, we developed ex vivo simulations and surveyed patients who developed the algorithm and patients who did not.

Results:

The algorithm is intended for all children (<18 years of age) within 30 days of cardiac surgery. It contains rationale for 11 central chylothorax management recommendations; diagnostic criteria and evaluation, trial of fat-modified diet, stratification by volume of daily output, timing of first-line medical therapy for “low” and “high” volume patients, and timing and duration of fat-modified diet. All recommendations achieved “consensus” (agreement >80%) by the workgroup (range 81–100%). Ex vivo simulations demonstrated good understanding by developers (range 94–100%) and non-developers (73%–100%).

Conclusions:

The quality improvement effort represents the first multi-site algorithm for the management of paediatric post-operative chylothorax. The algorithm includes transparent and objective measures of agreement and understanding. Agreement to the algorithm recommendations was >80%, and overall understanding was 94%.
Nucleic acids and melanin pigments after exposure to high doses of gamma rays: a biosignature robustness test
Authors: Cassaro A. , Pacelli C. , Baqué M. , Maturilli A. , Boettger U. , Moeller R. , Fujimori A. , de Vera J-P.P. , Onofri S.
Published: July 2022

The question about the stability of certain biomolecules is directly connected to the life-detection missions aiming to search for past or present life beyond Earth. The extreme conditions experienced on extraterrestrial planet surface (e.g. Mars), characterized by ionizing and non-ionizing radiation, CO2-atmosphere and reactive species, may destroy the hypothetical traces of life. In this context, the study of the biomolecules behaviour after ionizing radiation exposure could provide support for the onboard instrumentation and data interpretation of the life exploration missions on other planets. Here, as a part of STARLIFE campaign, we investigated the effects of gamma rays on two classes of fungal biomolecules–nucleic acids and melanin pigments – considered as promising biosignatures to search for during the ‘in situ life-detection’ missions beyond Earth.
Co‐Occurrence of Surface O3, PM2.5 Pollution, and Tropical Cyclones in China
Authors: Shao Min , Yang Jianbo , Wang Jinmei , Chen Pulong , Liu Baoshuang , Dai Qili
Published: July 2022

Extreme weather events are on the rise against the backdrop of climate change. Impact of tropical cyclone (TC) system, one of the extreme weather events, on air pollution remain poorly understood. A total of 103 recorded TCs (tropical storms and stronger) together with the surface air quality data collected from over 2000 observational sites in mainland China in 2014–2020 were utilized to examine the co‐occurrence of TC with continental ozone (O3) and fine particulate matters (PM2.5) pollution. TCs exhibit cleaning effects on PM2.5 within its coverage (typically ∼650 km), but enhance the co‐occurrence of O3 and PM2.5 in an extended region. The co‐occurrence frequencies are greater than 30% for any two co‐occurring events, and ∼8% for TC + PM2.5 + O3. We observed superregional trans‐boundary transportation of air pollutants driven by TC, led to ubiquitous spatial offsets and temporal lags of O3, PM2.5 pollution and TC, which are often inconsistent with traditional mechanisms such as accelerated chemical reactions for O3 formation. O3 pollution tends to occur 1∼2 days after PM2.5 pollution moved west. In contrast, PM2.5 pollution usually occur 4–12 hr following O3 pollution within a day over most regions except the southeast of China. Such spatial and temporal offsets vary with the paths of TCs. Composite analysis shows that temperature, wind field and large pressure systems are the key factors for air pollution formation and transportation over TC periphery. Our results have implications for understanding the interactions between TCs and air pollution, particularly for coastal areas where there are recurring TCs.
How Does Precipitation Variability Control Bedload Response Across a Mountainous Channel Network in a Maritime Climate?
Authors: Keck Jeffrey , Istanbulluoglu Erkan , Lundquist Jessica , Bandaragoda Christina , Jaeger Kristin , Mauger Guillaume , Horner‐Devine Alex
Published: July 2022

Modeled stream discharge is often used to drive sediment transport models across channel networks. Because sediment transport varies non‐linearly with flow rates, discharge modeled from daily total precipitation distributed evenly over 24‐hr may significantly underestimate actual bedload transport capacity. In this study, we assume bedload transport capacity determined from a hydrograph resulting from the use of hourly (1‐hr) precipitation is a close approximation of actual transport capacity and quantify the error introduced into a network‐scale bedload transport model driven by daily precipitation at channel network locations varying from lowland pool‐riffle channels to upland colluvial channels in a watershed where snow accumulation and melt can affect runoff processes. Transport capacity is determined using effective stresses and the Wilcock and Crowe (2003) equations and expressed in terms of transport capacity normalized by the bankfull value. We find that, depending on channel network location, cumulative error can range from 10% to more than two orders of magnitude. Surprisingly, variation in flow rates due to differences in hillslope and channel runoff do not seem to dictate the network locations where the largest errors in predicted bedload transport capacity occur. Rather, spatial variability of the magnitude of the effective‐bankfull‐excess shear stress and changes in runoff due to snow accumulation and melt exert the greatest influence. These findings have implications for flood‐hazard and aquatic habitat models that rely on modeled sediment transport driven by coarse‐temporal‐resolution climate data.
Impacts of Coastal Shrimp Ponds on Saltwater Intrusion and Submarine Groundwater Discharge
Authors: Hou Yuxuan , Yang Jie , Russoniello Christopher J. , Zheng Tianyuan , Wu Mei‐lin , Yu Xuan
Published: July 2022

Shrimp aquaculture has expanded rapidly in coastal zones worldwide over the past few decades. Saline water stored in shrimp farm ponds can infiltrate into the underlying aquifer causing groundwater salinization and increased submarine groundwater discharge (SGD) to coastal water. However, little research has assessed salinization resulting from these shrimp ponds. To understand the impacts of shrimp farm irrigation on groundwater salinization and SGD, we numerically simulated a series of aquaculture management scenarios in a two‐dimensional conceptual coastal aquifer using a coupled surface‐subsurface approach. We characterized sensitivities to pond water salinity, pond water depth, and farm width. Salinization was assessed by three indicators (salinized area, infiltrated salt mass, and recovery rate), and three SGD indicators were evaluated (fresh SGD, saline SGD, and saltwater circulation rate). Our results show that pond water depth is the primary control on the mass of saltwater infiltration while farm width is the primary control for recovery rate. Pond water salinity and depth affect both fresh and saline SGD. We show that aquaculture is a previously unrecognized mechanism of salinization affecting coastal aquifer vulnerability and SGD. A regional graphical information system analysis shows transformation into aquacultural ponds could introduce considerable SGD variability spatially and temporally. These findings will enable coastal managers to better evaluate groundwater vulnerability in regions with expanding onshore aquaculture and demonstrates the impact of aquaculture on coastal groundwater resources and the need for further study to understand the impact of aquaculture across Asia and the globe.
Consolidated Chemical Provinces on Mars: Implications for Geologic Interpretations
Authors: Rani A. , Basu Sarbadhikari A. , Hood D. R. , Gasnault O. , Nambiar S. , Karunatillake S.
Published: July 2022

Chemical provinces were defined on Mars a decade ago using orbital nuclear spectroscopy of K, Th, Fe, Si, Ca, Cl, and H2O. However, past multivariate analyses yielded three sets of provinces, suggesting methodologic variability. Province‐stability to the inclusion of Al and S is also unknown, presenting additional uncertainties for geologic insight. Here we consolidate key multivariate methods to define the first cross‐validated provinces. In southern highlands, the highly incompatible K and Th show non‐uniform distribution with higher values in mid Noachian and Hesperian than late Noachian – early Hesperian volcanic terrains. Silica‐ and Al‐depletion trends from Noachian to Amazonian indicate highly differentiated mantle with variable degree of melting. Late Hesperian lowlands are highly depleted in Al and enriched in K and Th, consistent with volcanic resurfacing from a low‐degree partially melted, garnet‐rich mantle. Furthermore, older volatile‐rich regions such as Medusae Fossae Formation exhibit igneous geochemistry, consistent with water‐limited isochemical weathering throughout Mars's history.
A Raman Spectroscopic and Microimage Analysis Perspective of the Chang'e‐5 Lunar Samples
Authors: Cao Haijun , Wang Chen , Chen Jian , Che Xiaochao , Fu Xiaohui , Shi Yuruo , Liu Dunyi , Ling Zongcheng , Qiao Le , Lu Xuejin , Qi Xiaobin , Yin Chengxiang , Liu Ping , Liu Changqing , Xin Yanqing , Liu Jianzhong
Published: July 2022

The Chang'e‐5 (CE‐5) materials represent the youngest returned lunar samples. We performed a detailed Raman spectroscopic survey (1259‐point Raman modal analysis) to evaluate the mineralogical characteristics of CE‐5 soils, constraining the source materials and shock effects of these unique samples. The mineral chemistry (e.g., Mg#3‐60 for mafic minerals) and modal abundance (first distinguishing basaltic and feldspathic glasses) of CE‐5 mare soils are different from those of Apollo high‐ and low‐Ti basalts, possibly representing an intermediate‐Ti mare basalt. The occurrence of minor Mg‐rich materials (Mg# > 70) provides evidence of contamination from ∼5% to 7% exogenous materials, possibly related to Mg‐suite rocks. The microimage analyses suggest that the CE‐5 soils are fine‐grained, mature, and unimodal particle‐size distribution, highlighting that micrometeorite reworking dominates the CE‐5 regolith evolution with minor mixing from nonmare materials. The pressure‐sensitive minerals (quartz and maskelynite) indicate that 17–25.8 GPa shock pressures might be the higher limit in a relatively young lunar terrain.
Modulation of adipose inflammation by cellular retinoic acid-binding protein 1
Authors: Wei Chin-Wen , Nhieu Jennifer , Lin Yu-Lung , Wei Li-Na
Published: July 2022

Objectives

Obesity, a metabolic syndrome, is known to be related to inflammation, especially adipose tissue inflammation. Cellular interactions within the expanded white adipose tissue (WAT) in obesity contribute to inflammation and studies have suggested that inflammation is triggered by inflamed adipocytes that recruit M1 macrophages into WAT. What causes accumulation of unhealthy adipocytes is an important topic of investigation. This study aims to understand the action of Cellular Retinoic Acid Binding Protein 1 (CRABP1) in WAT inflammation.

Methods

Eight weeks-old wild type (WT) and Crabp1 knockout (CKO) mice were fed with a normal diet (ND) or high-fat diet (HFD) for 8 weeks. Body weight and food intake were monitored. WATs and serum were collected for cellular and molecular analyses to determine affected signaling pathways. In cell culture studies, primary adipocyte differentiation and bone marrow-derived macrophages (BMDM) were used to examine adipocytes’ effects, mediated by CRABP1, in macrophage polarization. The 3T3L1-adipocyte was used to validate relevant signaling pathways.

Results

CKO mice developed an obese phenotype, more severely under high-fat diet (HFD) feeding. Further, CKO’s WAT exhibited a more severe inflammatory state as compared to wild type (WT) WAT, with a significantly expanded M1-like macrophage population. However, this was not caused by intrinsic defects of CKO macrophages. Rather, CKO adipocytes produced a significantly reduced level of adiponectin and had significantly lowered mitochondrial DNA content. CKO adipocyte-conditioned medium, compared to WT control, inhibited M2-like (CD206+) macrophage polarization. Mechanistically, defects in CKO adipocytes involved the ERK1/2 signaling pathway that could be modulated by CRABP1.

Conclusions

This study shows that CRABP1 plays a protective role against HFD-induced WAT inflammation through, in part, its regulation of adiponectin production and mitochondrial homeostasis in adipocytes, thereby modulating macrophage polarization in WAT to control its inflammatory potential.
Application of ATAC-seq in tumor-specific T cell exhaustion
Authors: Chen Chufeng , Liu Jiaying , Chen Yidong , Lin Anqi , Mou Weiming , Zhu Lingxuan , Yang Tao , Cheng Quan , Zhang Jian , Luo Peng
Published: July 2022

Researches show that chronic viral infection and persistent antigen and/or inflammatory signal exposure in cancer causes the functional status of T cells to be altered, mainly by major changes in the epigenetic and metabolic environment, which then leads to T cell exhaustion. The discovery of the immune checkpoint pathway is an important milestone in understanding and reversing T cell exhaustion. Antibodies targeting these pathways have shown superior ability to reverse T cell exhaustion. However, there are still some limitations in immune checkpoint blocking therapy, such as the short-term nature of therapeutic effects and high individual heterogeneity. Assay for transposase-accessible chromatin with sequencing(ATAC-seq) is a method used to analyze the accessibility of whole-genome chromatin. It uses hyperactive Tn5 transposase to assess chromatin accessibility. Recently, a growing number of studies have reported that ATAC-seq can be used to characterize the dynamic changes of epigenetics in the process of T cell exhaustion. It has been determined that immune checkpoint blocking can only temporarily restore the function of exhausted T cells because of an irreversible change in the epigenetics of exhausted T cells. In this study, we review the latest developments, which provide a clearer molecular understanding of T cell exhaustion, reveal potential new therapeutic targets for persistent viral infection and cancer, and provide new insights for designing effective immunotherapy for treating cancer and chronic infection.
Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket
Authors: Donoughe Seth , Hoffmann Jordan , Nakamura Taro , Rycroft Chris H. , Extavour Cassandra G.
Published: July 2022

The blastoderm is a broadly conserved stage of early animal development, wherein cells form a layer at the embryo’s periphery. The cellular behaviors underlying blastoderm formation are varied and poorly understood. In most insects, the pre-blastoderm embryo is a syncytium: nuclei divide and move throughout the shared cytoplasm, ultimately reaching the cortex. In Drosophila melanogaster, some early nuclear movements result from pulsed cytoplasmic flows that are coupled to synchronous divisions. Here, we show that the cricket Gryllus bimaculatus has a different solution to the problem of creating a blastoderm. We quantified nuclear dynamics during blastoderm formation in G. bimaculatus embryos, finding that: (1) cytoplasmic flows are unimportant for nuclear movement, and (2) division cycles, nuclear speeds, and the directions of nuclear movement are not synchronized, instead being heterogeneous in space and time. Moreover, nuclear divisions and movements co-vary with local nuclear density. We show that several previously proposed models for nuclear movements in D. melanogaster cannot explain the dynamics of G. bimaculatus nuclei. We introduce a geometric model based on asymmetric pulling forces on nuclei, which recapitulates the patterns of nuclear speeds and orientations of both unperturbed G. bimaculatus embryos, and of embryos physically manipulated to have atypical nuclear densities.
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks
Authors: Voznica J. , Zhukova A. , Boskova V. , Saulnier E. , Lemoine F. , Moslonka-Lefebvre M. , Gascuel O.
Published: July 2022

Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on github.com/evolbioinfo/phylodeep.
Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference
Authors: Wang Zihao , Wang Wenxi , Xie Xiaoming , Wang Yongfa , Yang Zhengzhao , Peng Huiru , Xin Mingming , Yao Yingyin , Hu Zhaorong , Liu Jie , Su Zhenqi , Xie Chaojie , Li Baoyun , Ni Zhongfu , Sun Qixin , Guo Weilong
Published: July 2022

Major crops are all survivors of domestication bottlenecks. Studies have focused on the genetic loci related to the domestication syndrome, while the contribution of ancient haplotypes remains largely unknown. Here, an ancestral genomic haploblock dissection method is developed and applied to a resequencing dataset of 386 tetraploid/hexaploid wheat accessions, generating a pan-ancestry haploblock map. Together with cytoplastic evidences, we reveal that domesticated polyploid wheat emerged from the admixture of six founder wild emmer lineages, which contributed the foundation of ancestral mosaics. The key domestication-related loci, originated over a wide geographical range, were gradually pyramided through a protracted process. Diverse stable-inheritance ancestral haplotype groups of the chromosome central zone are identified, revealing the expanding routes of wheat and the trends of modern wheat breeding. Finally, an evolution model of polyploid wheat is proposed, highlighting the key role of wild-to-crop and interploidy introgression, that increased genomic diversity following bottlenecks introduced by domestication and polyploidization.
Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure
Authors: Gerasimavicius Lukas , Livesey Benjamin J. , Marsh Joseph A.
Published: July 2022

Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we investigate the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors, even those based solely on sequence conservation, underperform on non-LOF mutations. However, we do show that non-LOF mutations could potentially be identified by their tendency to cluster in three-dimensional space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mechanisms are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms.
Hippocampal place cells have goal-oriented vector fields during navigation
Authors: Ormond Jake , O’Keefe John
Published: July 2022

The hippocampal cognitive map supports navigation towards, or away from, salient locations in familiar environments1. Although much is known about how the hippocampus encodes location in world-centred coordinates, how it supports flexible navigation is less well understood. We recorded CA1 place cells while rats navigated to a goal on the honeycomb maze2. The maze tests navigation via direct and indirect paths to the goal and allows the directionality of place cells to be assessed at each choice point. Place fields showed strong directional polarization characterized by vector fields that converged to sinks distributed throughout the environment. The distribution of these ‘convergence sinks’ (ConSinks) was centred near the goal location and the population vector field converged on the goal, providing a strong navigational signal. Changing the goal location led to movement of ConSinks and vector fields towards the new goal. The honeycomb maze allows independent assessment of spatial representation and spatial action in place cell activity and shows how the latter relates to the former. The results suggest that the hippocampus creates a vector-based model to support flexible navigation, allowing animals to select optimal paths to destinations from any location in the environment.
Single-cell roadmap of human gonadal development
Authors: Garcia-Alonso Luz , Lorenzi Valentina , Mazzeo Cecilia Icoresi , Alves-Lopes João Pedro , Roberts Kenny , Sancho-Serra Carmen , Engelbert Justin , Marečková Magda , Gruhn Wolfram H. , Botting Rachel A. , Li Tong , Crespo Berta , van Dongen Stijn , Kiselev Vladimir Yu , Prigmore Elena , Herbert Mary , Moffett Ashley , Chédotal Alain , Bayraktar Omer Ali , Surani Azim , Haniffa Muzlifah , Vento-Tormo Roser
Published: July 2022

Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries1. Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal–mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15+ and TREM2+ fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis.