bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction to Dual Polarization Weather Radar
Authors: Chandrasekar V. , Beauchamp Robert M. , Bechini Renzo
Published: August 2023

An interdisciplinary and easy-to-understand introduction to the subject, covering fundamental theory and practical applications, and using numerous operational examples. This balanced text will allow you to begin from what the radar observes and move deeper through electromagnetic scattering theory and cloud microphysics to understand and interpret data as it appears on the display. It uses illustrations and figures of real radar observations to convey concepts and theory of atmospheric processes typically observed with weather radar, as well presenting a working knowledge of the radar system itself. In addition to covering fundamentals of scattering and atmospheric physics, topics include system hardware, signal processing, and radar networks. This is the perfect tool for scientists and engineers working on weather radars or using radars and their data, as well as senior undergraduate and graduate students studying weather radars.
Market Participation of Small-Scale Rice Farmers in Eastern Bolivia
Authors: Lopera Diana C. , Gonzalez Carolina , Martinez Jose M.
Published: August 2023

Using a double-hurdle approach, we assess factors associated with the extent of participation in the rice market with data for small-scale farmers drawn from a nationally representative dataset. The results suggest that larger endowments and assets, animal farming and commercialization, and alternative off-farm income make farmers less likely to participate. Conversely, having access to credit, larger farm sizes, and being part of a farmers’ association all increase the likelihood of participation. Farms with better technological resources are also those with higher sales volumes. Further understanding market participation dynamics should prove useful for deriving evidence-based policy recommendations to strengthen this Bolivian sector.
Effect on damage of aircraft windshield impacted by light UAV with different postures
Authors: Lu X.H. , Zhang Y.C. , Zhang Z.G.
Published: August 2023

To study the performance of the main windshield of a commercial aircraft that has been verified to be airworthy by bird-strike tests against unmanned aerial vehicle (UAV) impact at high-speed, a typical light UAV with various possible flight postures and the main windshield of a commercial aircraft are considered. The transient impact responses at critical moments, energy change and contact force of a multi-layer windshield impacted by a UAV with different postures are investigated using a simulation method based on the models verified by the high-speed impact test between the whole UAV and the full-size nose. This study shows that the flight posture of the UAV has a significant effect on the damage to the windshield. When the abdomen of a typical light UAV maintains a posture parallel to the plane of the windshield, the high-speed impact would cause catastrophic damage to the windshield and no longer be airworthy. Simultaneously, the damage to the aircraft windshield caused by UAV collision is far more serious than that caused by bird strikes under similar collision conditions. The mass-concentrated components of the UAV and their high-hardness characteristics are the main factors of affecting multi-layer glass of windshield damage. The degree of damage to the windshield is positively related to the absorbed energy rather than the impact contact force. In this study, the impact simulation results between the windshield and UAV with different flight postures are verified qualitatively by testing, which provides a rational understanding and technical pre-research support for emerging and increasingly frequent potential safety hazards in air transport practice.
Control of the boundary layer on compressor blade suction surfaces with the momentum jet
Authors: Zheng H. , Zhou Z. , Liu L.
Published: August 2023

The boundary layer thickness on a compressor blade suction surface increases rapidly under a adverse pressure gradient and even separates from the blade surface. This paper proposes a novel method for developing the slot inside the blade, with the inlet of the slot located at the leading edge of the blade and the outlet located at the suction surface, using the momentum of the incoming flow to form a high velocity jet to control the boundary layer on the suction surface. For a plane cascade with a diffusion factor of 0.45, the effects of the main slot parametres (such as the shape of the slot and the positions of the slot inlet and outlet) on the flow in the slot, the flow field and the aerodynamic performance of the cascade were investigated with a numerical method. When the aerodynamic performance of cascades with slotted and unslotted blades was compared, it was found that a reasonable slot structure can effectively inhibit the development of the boundary layer on the blade suction surface and greatly improve the aerodynamic performance of the cascade. Based on the influence of the slot parametres of the above cascade, the slot of a plane cascade with a diffusion factor of 0.60 was designed. The numerical calculation results show that the slotted cascade with a diffusion factor of 0.60 outperformed the slotted cascade with a diffusion factor of 0.45. This result showed that the higher the cascade load, the greater the performance improvement from slotting. Furthermore, the unslotted and slotted cascades were tested, and the test results agreed well with the calculations. The aerodynamic performance of the slotted cascade was better than that of the unslotted cascade, which verifies the accuracy of the calculation method and the feasibility of blade slotting for suppressing the development of boundary layers on suction surfaces and reducing flow loss.
In a Garden of Forking Maps
Authors: Biedermann Zoltán
Published: August 2023

This article compares the cartographical representations
of the Caspian region produced around 1560 in Goa and Venice, with references to
other centers of mapmaking such as Lisbon, Seville, and Antwerp. It explores the
scientific, cultural, technical, and commercial logics that led to profoundly
dissimilar cartographies of the Caspian and its surroundings in different
centers of map production around the same time. It asks questions about the
contrasts between maritime and terrestrial cartography in the Renaissance, and
the cartographical languages associated with each of these cartographical modes.
The habitus of maritime cartographers in Goa, Lisbon, and Seville differed
profoundly, it is argued, from that of mapmakers in Italy, and particularly
Venice, who aimed for an integration of all available data as part of a
tradition of commenting on Ptolemy, and produced highly desirable printed maps
for a growing consumer audience. The article thus advocates a comparative
approach to maps, and critiques the assumption that knowledge “flows” between
regions. It proposes instead a “(dis)connected history” of knowledge production
and consumption to throw new light on the origins of the cartographical printing
revolution.
Sources of seasonal sea-ice bias for CMIP6 models in the Hudson Bay Complex
Authors: Crawford Alex D. , Rosenblum Erica , Lukovich Jennifer V. , Stroeve Julienne C.
Published: August 2023

The seasonal ice-free period in the Hudson Bay Complex (HBC) has grown longer in recent decades in response to warming, both from progressively earlier sea-ice retreat in summer and later sea-ice advance in fall. Such changes disrupt the HBC ecosystem and ice-based human activities. In this study, we compare 102 simulations from 37 models participating in phase 6 of the Coupled Model Intercomparison Project to the satellite passive microwave record and atmospheric reanalyses. We show that, throughout the HBC, models simulate an ice-free period that averages 30 d longer than in satellite observations. This occurs because seasonal sea-ice advance is unrealistically late and seasonal sea-ice retreat is unrealistically early. We find that much of the ice-season bias can be linked to a warm bias in the atmosphere that is associated with a southerly wind bias, especially in summer. Many models also exhibit an easterly wind bias during winter and spring, which reduces sea-ice convergence on the east side of Hudson Bay and impacts the spatial patterns of summer sea-ice retreat. These results suggest that, for many models, more realistic simulation of atmospheric circulation would improve their simulation of HBC sea ice.
Emotions and the Action Analogy: Prospects for an Agential Theory of Emotions
Authors: NAAR HICHEM
Published: August 2023

According to the action analogy, emotions and actions have certain structural and normative similarities that no theory of emotions should ignore. The action analogy has recently been used in an objection against the so-called perceptual theory of emotions, often defended by means of an analogy between emotion and perception. Beyond the dialectical significance of the action analogy, one might wonder whether it can support a picture of emotions as fundamentally action-like—what I call an agential theory. This article is a first step in answering this question. After discussing various ways to formulate the agential theory, I sketch a version of it.
A systematic review on antimicrobial activities of green synthesised Selaginella silver nanoparticles
Authors: Wadhwa Khushbu , Kaur Hardeep , Kapoor Neha , Ghorai Soma M. , Gupta Renu , Sahgal Arunima
Published: August 2023

Background

Metallic nanoparticles from different natural sources exhibit superior therapeutic options as compared to the conventional methods. Selaginella species have attracted special attention of researchers worldwide due to the presence of bioactive molecules such as flavonoids, biflavonoids, triterpenes, steroids, saponins, tannins and other secondary metabolites that exhibit antimicrobial, antiplasmodial, anticancer and anti-inflammatory activities. Environment friendly green synthesised silver nanoparticles from Selaginella species provide viable, safe and efficient treatment against different fungal pathogens.

Objective

This systematic review aims to summarise the literature pertaining to superior antifungal ability of green synthesised silver nanoparticles using plant extracts of Selaginella spp. in comparison to both aqueous and ethanolic raw plant extracts by electronically collecting articles from databases.

Methods

The recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analysis were taken into consideration while preparing this review. The titles and abstracts of the collected data were stored in Endnote20 based on the inclusion and exclusion criteria. The search strategy included literature from established sources like PubMed, Google Scholar and Retrieval System Online using subject descriptors.

Results

The search yielded 60 articles with unique hits. After removal of duplications, 46 articles were identified, 40 were assessed and only seven articles were chosen and included in this review based on our eligibility criteria.

Conclusion

The physicochemical and preliminary phytochemical investigations of Selaginella suggest higher drug potency of nanoparticles synthesised from plant extract against different diseases as compared to aqueous and ethanolic plant extracts. The study holds great promise as the synthesis of nanoparticles involves low energy consumption, minimal technology and least toxic effects.
When are the natural embeddings of classical invariant rings pure?
Authors: Hochster Melvin , Jeffries Jack , Pandey Vaibhav , Singh Anurag K.
Published: August 2023

Consider a reductive linear algebraic group G acting linearly on a polynomial ring S over an infinite field; key examples are the general linear group, the symplectic group, the orthogonal group, and the special linear group, with the classical representations as in Weyl’s book: For the general linear group, consider a direct sum of copies of the standard representation and copies of the dual; in the other cases, take copies of the standard representation. The invariant rings in the respective cases are determinantal rings, rings defined by Pfaffians of alternating matrices, symmetric determinantal rings and the Plücker coordinate rings of Grassmannians; these are the classical invariant rings of the title, with

$S^G\subseteq S$

being the natural embedding.

Over a field of characteristic zero, a reductive group is linearly reductive, and it follows that the invariant ring

$S^G$

is a pure subring of S, equivalently,

$S^G$

is a direct summand of S as an

$S^G$

-module. Over fields of positive characteristic, reductive groups are typically no longer linearly reductive. We determine, in the positive characteristic case, precisely when the inclusion

$S^G\subseteq S$

is pure. It turns out that if

$S^G\subseteq S$

is pure, then either the invariant ring

$S^G$

is regular or the group G is linearly reductive.
Effect of an initial specimen diversion device on blood-culture contamination rates and vancomycin usage: A quasi-experimental study
Authors: Wilber Eli P. , Babiker Ahmed , Howard-Anderson Jessica , Holdsworth Jill E. , Burd Eileen M. , Eldridge M. Jeremy , Jacob Jesse T.
Published: August 2023

Initial specimen diversion devices (ISDDs) are a potential solution for reducing blood-culture contamination rates. We report the implementation of an ISDD associated with a sustained reduction in blood-culture contamination rates for >18 months after implementation. We did not observe a clinically significant reduction in inpatient vancomycin usage.
Revolt with a Revolutionary Perspective
Authors: Jafari Peyman
Published: August 2023

At the zenith of the Women, Life, Freedom (WLF) protests in October to December 2022, the call for (general) strikes became a rallying point for activists who were seeking to increase the protests’ social reach and political strength in the face of increasing state repression. Therefore labor provides an advantageous analytical lens for exploring some of the constraints and potentials of the social dynamics of the WLF protests.
Art of Protest in Five Acts
Authors: Karimi Pamela
Published: August 2023

The world's first encounter with the tragic murder of the 22-year-old Mahsa Amini by Iran's “morality police” was through her image. As millions around the world browsed through news and social media, they were shocked by the image of the unconscious Amini hooked up to ventilators—her punishment for showing some hair through a loosely worn scarf (Fig. 1). The photograph was so influential that a week after its release, its brave photographer, journalist Niloofar Hamedi, was imprisoned. Despite government pressure, artists began reproducing this horrific image. In stylized reiterations, the portrait of Amini was at times coupled with mourning songs or counterrevolutionary music, as in the colorful animation by Belgium-based Iranian artist Niknaz Khalouzadeh that went viral overnight.
Writing in Turbulent Times. Introduction to the Roundtable on the 2022–23 Iranian Protests
Authors: Rivetti Paola
Published: August 2023

The editorial decision to publish a roundtable on the 2022–23 protests in Iran has come with challenges and obvious limitations due to access and immediacy. The ambition of this intervention is to offer some initial reflections and some analytical instruments in the hope that they will be useful for future publications. We also want to write in this moment because we want to register its characteristics—emotions running high, the quick detours of power relations between the state and the protesters, the uncertainty, the changing political weight of the diaspora—along with the difficulty of doing analytical work in the midst of such processes.
“Don't Let the Boats Pass!” Neo-Elamite Grain Procurement in Times of Famine and Drought
Authors: Gorris Elynn
Published: August 2023

This article is concerned with interregional trade dynamics between Elam and Mesopotamia in the early to mid-first millennium BC. During the seventh century BC, two great famines in the Neo-Elamite kingdom, of which climatological changes were a major cause, were documented in the textual records. An era of megadrought made grain procurement from the neighboring regions essential to feed the Neo-Elamite lowland population. This article further explores the impact of the two Neo-Elamite famines and “drought of the century” on the commercial and political mechanisms in the Upper Persian Gulf region.
Ice-flow perturbation analysis: a method to estimate ice-sheet bed topography and conditions from surface datasets
Authors: Ockenden Helen , Bingham Robert G , Curtis Andrew , Goldberg Daniel
Published: August 2023

One of the largest contributors to uncertainty in predictions of sea-level rise from ice-sheet models is a lack of knowledge about the bed topography beneath ice sheets. Bed topography maps are normally made by interpolating between linear radar surveys using methods that include kriging, mass conservation and flowline diffusion, all of which may miss influential mesoscale (2–30 km) bedforms. Previous works have explored an Ice-Flow Perturbation Analysis (IFPA) approach for estimating bed topography using the surface expression of these mesoscale bedforms. Using regions of Pine Island Glacier that have been intensively surveyed by ice-penetrating radar as test sites, and a refined IFPA methodology, we find that IFPA detects bedforms capable of influencing ice flow which are not represented in Bedmachine Antarctica and other interpolated bed products. We further explore the ability of IFPA to estimate relative bed slipperiness, finding higher slipperiness in the main trunk and tributaries. Alongside other methods which estimate ice thickness, bed topography maps from IFPA have the potential to constrain projections of future sea-level rise, especially where radar data are sparse.
The relationship between reading and listening anxieties in EFL classrooms: Exploring the mediating effect of foreign language classroom anxiety
Authors: Öztürk Gökhan
Published: August 2023

The purpose of the current study is threefold: (a) to present a descriptive picture of classroom anxiety (FLCA), reading anxiety (FLRA), and listening anxiety (FLLA) in foreign language classrooms; (b) to explore the association between FLCA, FLRA, and FLLA; and (c) to test the mediating effect of FLCA on the relationship between FLRA and FLLA. The participants included 341 tertiary-level students studying at the English Preparatory Program of four public universities in the Turkish EFL context. The data were collected at the beginning of the 2022 fall semester through the Foreign Language Classroom Anxiety Scale, Foreign Language Reading Anxiety Scale, and Foreign Language Listening Anxiety Scale. The descriptive findings indicated a moderate level of FLCA, FLRA, and FLLA among the participants. In addition, significant and positive correlations were found between these three types of anxieties, with the strongest correlation between FLRA and FLLA. In the last stage of the analysis, it was found that FLCA partially and significantly mediated the relationship between FLRA and FLLA. Finally, directions for further research on investigating skill-based anxieties are presented.
Integrating Research Methods Training into Elective Courses in an Undergraduate Curriculum
Authors: Arikan Gizem , Milosav Ðorđe
Published: August 2023

This article discusses the integration of research methods training into a third-year elective undergraduate course. We suggest that the building blocks of research design can be embedded in courses without compromising their content. This introduces research methods to students who have no prior methods training or gives students with methods training more opportunities to engage in research design. We present evidence that this approach increased students’ self-assessed knowledge of and confidence with research-related skills, especially among those without prior methods training. Additionally, the analysis of research proposals—the final assignment of the course—revealed that most students were able to apply core research design skills. These findings demonstrate that progress in research methods skills is possible across the curriculum.
Separation of powers in a globalized democratic society: Theorizing the human rights treaty organs’ interactions with various state organs
Authors: Takata Hinako
Published: August 2023

As part of their continuous effort to enhance the effectiveness and democratic legitimacy of human rights treaties, human rights treaty organs have increasingly fostered a direct relationship with various state organs, thereby penetrating the ‘states’ that traditionally have been treated as monolithic legal entities. Treaty organs review the decision-making process of each type of state organ – courts, parliaments and administrative organs – and make remedial orders that are substantially addressed to specific state organs. Such phenomena go hand in hand with the relativization of the distinction between the legal spheres in which human rights treaty organs and state organs operate. This is the first study to address such phenomena as a totality. It constructs the ‘separation of powers in a globalized democratic society’ theory, thereby proposing how each type of state organ and the treaty organs should interact under human rights treaties. Its findings contribute, first, to the harmonious achievement of the effectiveness and democratic legitimacy of human rights treaties; second, to the reform of the classical paradigm of international law, in which monolithic states are the only relevant legal entities; and third, to the long-standing debates on the relationship between international and national laws from a new angle.
The Active Suppression of a Distractor’s Location Can Be Elusive
Authors: Taylor Jillian R. , Ivanoff Jason
Published: August 2023

Abstract. Our visual system is inundated with distracting objects that vie for our attention. While visual attention selects relevant information, inhibitory mechanisms might be useful to suppress the locations occupied by irrelevant distractors. Yet, there is a dearth of behavioral evidence for the active suppression of a distractor’s location (ASDL) using central cues that provide preliminary information about a distractor’s location. In the first two experiments, we attempt to conceptually replicate, using an online platform, experiments that provide evidence of the ASDL. We replicate the distractor cueing effect in a localization task (Experiment 1) wherein responses to targets were faster when a central arrow cued the location of an impending distractor than an empty location. This effect was larger in the first block of trials than it was in the second. In a discrimination task (Experiment 2), unlike previous studies, we found no evidence for an effect of distractor cueing. In Experiment 3, we replaced the central arrow cues with central number cues because arrow cues may elicit a symbolic shift of attention that might offset the ASDL. Once again, the best model was one in which the distractor cueing effect was absent. We replicate these failures to find evidence of the ASDL in two more experiments. The results suggest that the ASDL can be elusive and may be tied to the response system, not attention.
Atmospheric Rivers and Weather Types in Aotearoa New Zealand: A Two‐Way Story
Authors: Pohl Benjamin , Prince Hamish D. , Wille Jonathan , Kingston Daniel G. , Cullen Nicolas J. , Fauchereau Nicolas
Published: August 2023

Here, we analyze the inter‐relationships between weather types (WTs) and atmospheric rivers (ARs) around Aotearoa New Zealand (ANZ), their respective properties, as well as their combined and separate influence on daily precipitation amounts and extremes. Results show that ARs are often associated with 3–4 WTs, but these WTs change depending on the regions where ARs landfall. The WTs most frequently associated with ARs generally correspond to those favoring anomalously strong westerly wind in the mid‐latitudes, especially for southern regions of ANZ, or northwesterly anomalies favoring moisture export from the lower latitudes, especially for the northern regions. WTs and ARs show strong within‐type and inter‐event diversity. The synoptic patterns of the WTs significantly differ when they are associated with AR occurrences, with atmospheric centers of actions being shifted so that moisture fluxes toward ANZ are enhanced. The location, angle, and persistence of ARs appear strongly driven by the synoptic configurations of the WTs. Although total moisture transport shows weaker WT‐dependency, it appears strongly related to zonal wind speed to the south of ANZ, or the moisture content of the air mass to the north. Finally, WT influence on daily precipitation may completely change depending on their association, or lack thereof, with AR events. WTs traditionally considered as favorable to wet conditions may conceal daily precipitation extremes occurring during AR days, and anomalously dry days or near‐climatological conditions during non‐AR days.
Statistics of Isolated Deep Convection Initiation and Its Relation to Topography in the North China Area
Authors: Lu Guilin , Ren Yangze , Fu Shizuo , Xue Huiwen
Published: August 2023

This study investigates the statistical characteristics of isolated deep convection initiation (DCI) and its relation to topography in the North China area during the summer season of 2017–2019. A total of 2,534 isolated DCI events are identified using the infrared brightness temperature data from Himawari‐8 satellite with a resolution of 0.05° × 0.05°. The spatial distribution of DCI shows clustering over mountains and hills, indicating that the local topography may be critical for DCI. Topography is described with elevation and relief amplitude in this study. Results show that normalized DCI counts increase with elevation and relief amplitude. For the regime characterized by fewer morning clouds (regime one), DCI strongly depends on elevation and relief amplitude, while for the regime with more morning clouds (regime two), topography only moderately impacts DCI. Linear regression analyses suggest the existence of significant linear relationships between DCI and relief amplitude when elevation is relatively high. Topography is also categorized into four types: plain/sea areas, plateaus, hilly areas, and mountains. Normalized DCI counts show that mountains and hilly areas are more favorable for initiating isolated deep convection, especially for regime one. Moreover, DCI counts in regime one show a stronger diurnal variation and a peak occurring 2 hr earlier than that of regime two. We suggest that special attention should be paid to elevation and relief amplitude, as well as morning cloud cover condition when forecasting DCI in the North China area. Further study is necessary to understand this DCI occurrence preference on specific topography.
Two Small Volcanoes, One Inside the Other: Geophysical and Drilling Investigation of Bažina Maar in Western Eger Rift
Authors: Hrubcová Pavla , Fischer Tomáš , Rapprich Vladislav , Valenta Jan , Tábořík Petr , Mrlina Jan , Dahm Torsten , Vylita Tomáš , Beránek Roman , Klanica Radek , Vlček Josef , Turjaková Veronika
Published: August 2023

Maar‐diatreme volcanoes are small volcanic structures with a funnel‐shaped crater surrounded by a tephra‐ring. They are usually formed by the explosive phreatomagmatic eruptions when groundwater comes into the contact with magma. We focus on such a structure in the geodynamically active western Eger Rift (Czech Republic) and present results from multidisciplinary geophysical investigation calibrated by drilling in the newly discovered Pleistocene Bažina maar. We evaluated morphological (LiDAR‐based DEM) data and confirmed the existence of a maar‐diatreme structure by combined geophysical methods. In the map view, they revealed circular negative gravity anomaly, funnel‐shape low‐resistivity anomaly, and strong magnetic anomaly. These results allowed for the optimal location of two boreholes in the maar crater, which evinced its contact with country rocks and lithologies of the maar‐diatreme filling. The drilling revealed coherent volcanic rocks and volcaniclastic deposits, moreover, it revealed a presence of a pyroclastic cone with the olivine nephelinite feeding conduit. Further investigations disclosed maar structure and subsequent pyroclastic cone(s) with several generations of eruptions and systematic decrease of water influence on the eruption style. Different eruption styles suggest a unique evolution of two volcanoes, one inside the other. The age of the Bažina maar eruption, estimated from the reverse polarity of the detected magnetic anomaly, implies that the effusion and solidification of the lava during the eruption must be older than 0.78 Ma (Pleistocene). This points to an active volcanism in the western Eger Rift in a span of ∼0.5 Ma, where Bažina represents the oldest (maybe opening) phase.
Sub‐Grid Representation of Vegetation Cover in Land Surface Schemes Improves the Modeling of How Climate Responds to Deforestation
Authors: Qin Yingzuo , Wang Dashan , Cao Ye’er , Cai Xitian , Liang Shijing , Beck Hylke E. , Zeng Zhenzhong
Published: August 2023

Understanding the regional climate response to land cover change requires a realistic sub‐grid representation of vegetation cover in the land surface scheme (LSS) of climate models. The Community Land Model (CLM) is considered one of the most advanced LSSs; however, when coupled with the Weather Research and Forecasting (WRF) model, the tiling vegetation cover approach was deactivated. Here, we reactivated the theoretical sub‐grid vegetation cover representation in WRF‐CLM and applied it to assess the impacts of deforestation on regional climate in the Southeast Asian Massif region. We found that CLM‐tiling performs more accurate simulations of surface air temperature and precipitation compared to other LSSs using the in situ observations. Importantly, CLM‐tiling successfully captures the theoretical sensitivity of evapotranspiration (ET) and temperature to sub‐grid deforestation, aligning with Noah‐mosaic, and it substantially improves the spatial pattern responses of simulated ET and temperature to regional deforestation.
A Strengthened Teleconnection of the Quasi‐Biennial Oscillation and Tropical Easterly Jet in the Past Decades in E3SMv1
Authors: Li Yuanpu , Richter Jadwiga H. , Chen Chih‐Chieh , Tang Qi
Published: August 2023

The Energy Exascale Earth System Model version 1 (E3SMv1) is a new global model that can generate a weakened tropical easterly jet (TEJ) during the easterly quasi‐biennial oscillation (EQBO) and a strengthened TEJ during the westerly QBO (WQBO), which is referred to as the QBO‐TEJ teleconnection. Although the longitudinal structure of the QBO‐TEJ teleconnection is different between reanalysis and simulations, we hypothesize that simulations can still provide insights into the observed long‐term changes in the QBO‐TEJ teleconnection. The Atmospheric Model Intercomparison Project historical simulations (AMIP‐historical) generate a strengthened trend in the correlation between the QBO and TEJ indices in the period of 1950–2014 as in reanalysis. The comparison of the AMIP‐historical and the Coupled Model Intercomparison Project coupled historical simulations (coupled‐historical) shows that the warming of the Indian Ocean has played a vital role in the strengthened QBO‐TEJ teleconnection over the past six decades.
Conserved role for PCBP1 in altered RNA splicing in the hippocampus after chronic alcohol exposure
Authors: Carvalho Luana , Chen Hu , Maienschein-Cline Mark , Glover Elizabeth J. , Pandey Subhash C. , Lasek Amy W.
Published: August 2023

We previously discovered using transcriptomics that rats undergoing withdrawal after chronic ethanol exposure had increased expression of several genes encoding RNA splicing factors in the hippocampus. Here, we examined RNA splicing in the rat hippocampus during withdrawal from chronic ethanol exposure and in postmortem hippocampus of human subjects diagnosed with alcohol use disorder (AUD). We found that expression of the gene encoding the splicing factor, poly r(C) binding protein 1 (PCBP1), was elevated in the hippocampus of rats during withdrawal after chronic ethanol exposure and AUD subjects. We next analyzed the rat RNA-Seq data for differentially expressed (DE) exon junctions. One gene,Hapln2, had increased usage of a novel 3′ splice site in exon 4 during withdrawal. This splice site was conserved in humanHAPLN2and was used more frequently in the hippocampus of AUD compared to control subjects. To establish a functional role for PCBP1 inHAPLN2splicing, we performed RNA immunoprecipitation (RIP) with a PCBP1 antibody in rat and human hippocampus, which showed enriched PCBP1 association near theHAPLN2exon 4 3′ splice site in the hippocampus of rats during ethanol withdrawal and AUD subjects. Our results indicate a conserved role for the splicing factor PCBP1 in aberrant splicing ofHAPLN2after chronic ethanol exposure. As theHAPLN2gene encodes an extracellular matrix protein involved in nerve conduction velocity, use of this alternative splice site is predicted to result in loss of protein function that could negatively impact hippocampal function in AUD.
Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model
Authors: Liaudanskaya Volha , Fiore Nicholas J. , Zhang Yang , Milton Yuka , Kelly Marilyn F. , Coe Marly , Barreiro Ariana , Rose Victoria K. , Shapiro Matthew R. , Mullis Adam S. , Shevzov-Zebrun Anna , Blurton-Jones Mathew , Whalen Michael J. , Symes Aviva J. , Georgakoudi Irene , Nieland Thomas J. F. , Kaplan David L.
Published: August 2023

Traumatic Brain injury-induced disturbances in mitochondrial fission-and-fusion dynamics have been linked to the onset and propagation of neuroinflammation and neurodegeneration. However, cell-type-specific contributions and crosstalk between neurons, microglia, and astrocytes in mitochondria-driven neurodegeneration after brain injury remain undefined. We developed a human three-dimensional in vitro triculture tissue model of a contusion injury composed of neurons, microglia, and astrocytes and examined the contributions of mitochondrial dysregulation to neuroinflammation and progression of injury-induced neurodegeneration. Pharmacological studies presented here suggest that fragmented mitochondria released by microglia are a key contributor to secondary neuronal damage progression after contusion injury, a pathway that requires astrocyte-microglia crosstalk. Controlling mitochondrial dysfunction thus offers an exciting option for developing therapies for TBI patients.
ERFVII action and modulation through oxygen-sensing in Arabidopsis thaliana
Authors: Zubrycka Agata , Dambire Charlene , Dalle Carbonare Laura , Sharma Gunjan , Boeckx Tinne , Swarup Kamal , Sturrock Craig J. , Atkinson Brian S. , Swarup Ranjan , Corbineau Françoise , Oldham Neil J. , Holdsworth Michael J.
Published: August 2023

Oxygen is a key signalling component of plant biology, and whilst an oxygen-sensing mechanism was previously described in Arabidopsis thaliana, key features of the associated PLANT CYSTEINE OXIDASE (PCO) N-degron pathway and Group VII ETHYLENE RESPONSE FACTOR (ERFVII) transcription factor substrates remain untested or unknown. We demonstrate that ERFVIIs show non-autonomous activation of root hypoxia tolerance and are essential for root development and survival under oxygen limiting conditions in soil. We determine the combined effects of ERFVIIs in controlling gene expression and define genetic and environmental components required for proteasome-dependent oxygen-regulated stability of ERFVIIs through the PCO N-degron pathway. Using a plant extract, unexpected amino-terminal cysteine sulphonic acid oxidation level of ERFVIIs was observed, suggesting a requirement for additional enzymatic activity within the pathway. Our results provide a holistic understanding of the properties, functions and readouts of this oxygen-sensing mechanism defined through its role in modulating ERFVII stability.
A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models
Authors: Faure Léon , Mollet Bastien , Liebermeister Wolfram , Faulon Jean-Loup
Published: August 2023

Constraint-based metabolic models have been used for decades to predict the phenotype of microorganisms in different environments. However, quantitative predictions are limited unless labor-intensive measurements of media uptake fluxes are performed. We show how hybrid neural-mechanistic models can serve as an architecture for machine learning providing a way to improve phenotype predictions. We illustrate our hybrid models with growth rate predictions of Escherichia coli and Pseudomonas putida grown in different media and with phenotype predictions of gene knocked-out Escherichia coli mutants. Our neural-mechanistic models systematically outperform constraint-based models and require training set sizes orders of magnitude smaller than classical machine learning methods. Our hybrid approach opens a doorway to enhancing constraint-based modeling: instead of constraining mechanistic models with additional experimental measurements, our hybrid models grasp the power of machine learning while fulfilling mechanistic constrains, thus saving time and resources in typical systems biology or biological engineering projects.
Theoretical assessment of persistence and adaptation in weeds with complex life cycles
Authors: Lauenroth Dana , Gokhale Chaitanya S.
Published: August 2023

Herbicide-resistant weeds pose a substantial threat to global food security. Perennial weed species are particularly troublesome. Such perennials as Sorghum halepense spread quickly and are difficult to manage due to their ability to reproduce sexually via seeds and asexually through rhizomes. Our theoretical study of S. halepense incorporates this complex life cycle with control measures of herbicide application and tillage. Rooted in the biology and experimental data of S. halepense, our population-based model predicts population dynamics and target-site resistance evolution in this perennial weed. We found that the resistance cost determines the standing genetic variation for herbicide resistance. The sexual phase of the life cycle, including self-pollination and seed bank dynamics, contributes substantially to the persistence and rapid adaptation of S. halepense. While self-pollination accelerates target-site resistance evolution, seed banks considerably increase the probability of escape from control strategies and maintain genetic variation. Combining tillage and herbicide application effectively reduces weed densities and the risk of control failure without delaying resistance adaptation. We also show how mixtures of different herbicide classes are superior to rotations and mono-treatment in controlling perennial weeds and resistance evolution. Thus, by integrating experimental data and agronomic views, our theoretical study synergistically contributes to understanding and tackling the global threat to food security from resistant weeds.
Autonomous quantum error correction and fault-tolerant quantum computation with squeezed cat qubits
Authors: Xu Qian , Zheng Guo , Wang Yu-Xin , Zoller Peter , Clerk Aashish A. , Jiang Liang
Published: August 2023

We propose an autonomous quantum error correction scheme using squeezed cat (SC) code against excitation loss in continuous-variable systems. Through reservoir engineering, we show that a structured dissipation can stabilize a two-component SC while autonomously correcting the errors. The implementation of such dissipation only requires low-order nonlinear couplings among three bosonic modes or between a bosonic mode and a qutrit. While our proposed scheme is device independent, it is readily implementable with current experimental platforms such as superconducting circuits and trapped-ion systems. Compared to the stabilized cat, the stabilized SC has a much lower dominant error rate and a significantly enhanced noise bias. Furthermore, the bias-preserving operations for the SC have much lower error rates. In combination, the stabilized SC leads to substantially better logical performance when concatenating with an outer discrete-variable code. The surface-SC scheme achieves more than one order of magnitude increase in the threshold ratio between the loss rate κ1 and the engineered dissipation rate κ2. Under a practical noise ratio κ1/κ2 = 10−3, the repetition-SC scheme can reach a 10−15 logical error rate even with a small mean excitation number of 4, which already suffices for practically useful quantum algorithms.
An intestinal sphingolipid confers intergenerational neuroprotection
Authors: Wang Wenyue , Sherry Tessa , Cheng Xinran , Fan Qi , Cornell Rebecca , Liu Jie , Xiao Zhicheng , Pocock Roger
Published: August 2023

In animals, maternal diet and environment can influence the health of offspring. Whether and how maternal dietary choice impacts the nervous system across multiple generations is not well understood. Here we show that feeding Caenorhabditis elegans with ursolic acid, a natural plant product, improves axon transport and reduces adult-onset axon fragility intergenerationally. Ursolic acid provides neuroprotection by enhancing maternal provisioning of sphingosine-1-phosphate, a bioactive sphingolipid. Intestine-to-oocyte sphingosine-1-phosphate transfer is required for intergenerational neuroprotection and is dependent on the RME-2 lipoprotein yolk receptor. Sphingosine-1-phosphate acts intergenerationally by upregulating the transcription of the acid ceramidase-1 (asah-1) gene in the intestine. Spatial regulation of sphingolipid metabolism is critical, as inappropriate asah-1 expression in neurons causes developmental axon outgrowth defects. Our results show that sphingolipid homeostasis impacts the development and intergenerational health of the nervous system. The ability of specific lipid metabolites to act as messengers between generations may have broad implications for dietary choice during reproduction.
Systematic benchmarking of single-cell ATAC-sequencing protocols
Authors: De Rop Florian V. , Hulselmans Gert , Flerin Chris , Soler-Vila Paula , Rafels Albert , Christiaens Valerie , González-Blas Carmen Bravo , Marchese Domenica , Caratù Ginevra , Poovathingal Suresh , Rozenblatt-Rosen Orit , Slyper Michael , Luo Wendy , Muus Christoph , Duarte Fabiana , Shrestha Rojesh , Bagdatli S. Tansu , Corces M. Ryan , Mamanova Lira , Knights Andrew , Meyer Kerstin B. , Mulqueen Ryan , Taherinasab Akram , Maschmeyer Patrick , Pezoldt Jörn , Lambert Camille Lucie Germaine , Iglesias Marta , Najle Sebastián R. , Dossani Zain Y. , Martelotto Luciano G. , Burkett Zach , Lebofsky Ronald , Martin-Subero José Ignacio , Pillai Satish , Sebé-Pedrós Arnau , Deplancke Bart , Teichmann Sarah A. , Ludwig Leif S. , Braun Theodore P. , Adey Andrew C. , Greenleaf William J. , Buenrostro Jason D. , Regev Aviv , Aerts Stein , Heyn Holger
Published: August 2023

Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
Unique functional responses differentially map onto genetic subtypes of dopamine neurons
Authors: Azcorra Maite , Gaertner Zachary , Davidson Connor , He Qianzi , Kim Hailey , Nagappan Shivathmihai , Hayes Cooper K. , Ramakrishnan Charu , Fenno Lief , Kim Yoon Seok , Deisseroth Karl , Longnecker Richard , Awatramani Rajeshwar , Dombeck Daniel A.
Published: August 2023

Dopamine neurons are characterized by their response to unexpected rewards, but they also fire during movement and aversive stimuli. Dopamine neuron diversity has been observed based on molecular expression profiles; however, whether different functions map onto such genetic subtypes remains unclear. In this study, we established that three genetic dopamine neuron subtypes within the substantia nigra pars compacta, characterized by the expression of Slc17a6 (Vglut2), Calb1 and Anxa1, each have a unique set of responses to rewards, aversive stimuli and accelerations and decelerations, and these signaling patterns are highly correlated between somas and axons within subtypes. Remarkably, reward responses were almost entirely absent in the Anxa1+ subtype, which instead displayed acceleration-correlated signaling. Our findings establish a connection between functional and genetic dopamine neuron subtypes and demonstrate that molecular expression patterns can serve as a common framework to dissect dopaminergic functions.
Sialic acids Neu5Ac and KDN in adipose tissue samples from individuals following habitual vegetarian or non-vegetarian dietary patterns
Authors: Guerrero-Flores Gerardo N. , Pacheco Fabio J. , Boskovic Danilo S. , Pacheco Sandaly O. S. , Zhang Guangyu , Fraser Gary E. , Miles Fayth L.
Published: August 2023

Sialic acids (Sias) are a class of sugar molecules with a parent nine-carbon neuraminic acid, generally present at the ends of carbohydrate chains, either attached to cellular surfaces or as secreted glycoconjugates. Given their position and structural diversity, Sias modulate a wide variety of biological processes. However, little is known about the role of Sias in human adipose tissue, or their implications for health and disease, particularly among individuals following different dietary patterns. The goal of this study was to measure N-Acetylneuraminic acid (Neu5Ac), N-Glycolylneuraminic acid (Neu5Gc), and 2-keto-3-deoxy-d-glycero-d-galacto-nononic acid (KDN) concentrations in adipose tissue samples from participants in the Adventist Health Study-2 (AHS-2) and to compare the abundance of these Sias in individuals following habitual, long-term vegetarian or non-vegetarian dietary patterns. A method was successfully developed for the extraction and detection of Sias in adipose tissue. Sias levels were quantified in 52 vegans, 56 lacto-vegetarians, and 48 non-vegetarians using LC–MS/MS with Neu5Ac-D-1,2,3-13C3 as an internal standard. Dietary groups were compared using linear regression. Vegans and lacto-ovo-vegetarians had significantly higher concentrations of Neu5Ac relative to non-vegetarians. While KDN levels tended to be higher in vegans and lacto-ovo-vegetarians, these differences were not statistically significant. However, KDN levels were significantly inversely associated with body mass index. In contrast, Neu5Gc was not detected in human adipose samples. It is plausible that different Neu5Ac concentrations in adipose tissues of vegetarians, compared to those of non-vegetarians, reflect a difference in the baseline inflammatory status between the two groups. Epidemiologic studies examining levels of Sias in human adipose tissue and other biospecimens will help to further explore their roles in development and progression of inflammatory conditions and chronic diseases.