bluuebunny/crossref_metadata_2025 huggingface dataset:
Conceptualizing organizational culture and business-IT alignment: a systematic literature review
Authors: Sieber Marcel R. , Malý Milan , Liška Radek
Published: August 2022

For decades, business and information technology alignment has fascinated scholars and practitioners. However, understanding these alignment mechanisms is challenging. The significant role of information technology (IT) in digitalization and agile transformation calls for targeted management of the readiness and capability of IT as an enabler and strategic business partner. This paper assumes that organizational culture is a success factor for business-IT alignment. Therefore, it aims to explore the culture-alignment relationship by the following research questions: What are typical IT management organizational culture characteristics, and how do they contribute to business-IT alignment? The study conducts a systematic literature review. First, after defining the critical terms, it searches the databases indexed in the Web of Science, Scopus, and Google Scholar. Then, the study uses bibliometrics to get quantitative insights into the research topic. Finally, it investigates the key arguments and findings of the selected papers. The analyzed literature depicts the relationship between an IT management culture and business-IT alignment elements. However, the research lacks concrete modeling and conception. This article contributes to a better culture-alignment relationship interpretation and closes a gap in the body of knowledge by combining quantitative and qualitative literature review methods.
The six-functor formalism for rigid analytic motives
Authors: Ayoub Joseph , Gallauer Martin , Vezzani Alberto
Published: August 2022

We offer a systematic study of rigid analytic motives over general rigid analytic spaces, and we develop their six-functor formalism. A key ingredient is an extended proper base change theorem that we are able to justify by reducing to the case of algebraic motives. In fact, more generally, we develop a powerful technique for reducing questions about rigid analytic motives to questions about algebraic motives, which is likely to be useful in other contexts as well. We pay special attention to establishing our results without noetherianity assumptions on rigid analytic spaces. This is indeed possible using Raynaud’s approach to rigid analytic geometry.
Lateral motion of a solid with a heterogeneous wettability surface driven by impacting droplets
Authors: Zhang Tongwei , Wu Jie , Lin Xingjian
Published: August 2022

When a droplet impacts a solid with a heterogeneous wettability surface, the generated asymmetric forces can manipulate the droplet, and its counterforces can also actuate the solid in theory. In this study, a water droplet impacting a movable hydrophobic substrate, which is decorated with a hydrophilic stripe and restrained by two linear dampers, is studied numerically. After preliminarily checking the effects of the solid mass and damping coefficient of linear dampers, the dynamic mechanisms of solid motion are explored by analysing the variations in the lateral force and instantaneous displacement distance of the solid. After that, the effects of the impact parameters on the solid lateral motion are mainly investigated, including the initial droplet diameter, impact velocity and offset distance between the impact point and hydrophilic stripe. On this basis, the reciprocating solid motion under successive droplet impacts is studied, and periodic motion with different amplitudes can be realized under appropriate impact conditions. The obtained results can shed some fresh insight into the potential applications of droplet–solid interactions, which are valuable for the collection and utilization of energy from natural environments.
Evolutionary genomic insights into cyanobacterial symbioses in plants
Authors: de Vries Sophie , de Vries Jan
Published: August 2022

Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria–plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.
ON FRACTAL DIMENSIONS OF FRACTAL FUNCTIONS USING FUNCTION SPACES
Authors: CHANDRA SUBHASH , ABBAS SYED
Published: August 2022

Based on the work of Mauldin and Williams [‘On the Hausdorff dimension of some graphs’,Trans. Amer. Math. Soc.298(2) (1986), 793–803] on convex Lipschitz functions, we prove that fractal interpolation functions belong to the space of convex Lipschitz functions under certain conditions. Using this, we obtain some dimension results for fractal functions. We also give some bounds on the fractal dimension of fractal functions with the help of oscillation spaces.
Visual duplication: specimens, works of art and photographs at the Musée d'ethnographie du Trocadéro (1928–1935)
Authors: Mauuarin Anaïs
Published: August 2022

The article considers how the use of duplicates and the practice of photography interacted in museums of ethnography, contributing to the ambivalent framing of ethnographic objects as items that can be both scientific specimens and works of art. It focuses on the Musée d'ethnographie du Trocadéro in Paris and on the key period of its reorganization between 1928 and 1935, which was central to the institutionalization of French ethnology. By examining the place of duplicates in this museum, as well as the major role attributed to photographs of objects and their materiality, the paper shows that these others of the ethnographic artefacts, often considered separately from their originals, still participated in the same project: the development of the museum and its growing cultural influence. While the duplicates positioned the museum in the various networks of the scientific community, the photographs appealed to the avant-garde, amateurs, African and Oceanian art dealers and the general public.
Sterility ofCydia pomonellaby X ray irradiation as an alternative to gamma radiation for the sterile insect technique
Authors: Zhang Jing-Han , Li Na , Zhao Hui-Yuan , Wang Ya-Qi , Yang Xue-Qing , Wu Kong-Ming
Published: August 2022

The codling mothCydia pomonellais a major pest of global significance impacting pome fruits and walnuts. It threatens the apple industry in the Loess Plateau and Bohai Bay in China. Sterile insect technique (SIT) could overcome the limitations set by environmentally compatible area-wide integrated pest management (AW-IPM) approaches such as mating disruption and attract-kill that are difficult to suppress in a high-density pest population, as well as the development of insecticide resistance. In this study, we investigated the effects of X-ray irradiation (183, 366, 549 Gy) on the fecundity and fertility of a laboratory strain ofC. pomonella, using a newly developed irradiator, to evaluate the possibility of X-rays as a replacement for Cobalt60(60Co-γ) and the expanded future role of this approach in codling moth control. Results show that the 8th-day is the optimal age for irradiation of male pupae. The fecundity decreased significantly as the dosage of radiation increased. The mating ratio and mating number were not influenced. However, treated females were sub-sterile at a radiation dose of 183 Gy (20.93%), and were almost 100% sterile at a radiation dose of 366 Gy or higher. Although exposure to a radiation dose of 366 Gy resulted in a significant reduction in the mating competitiveness of male moths, our radiation biology results suggest that this new generation of X-ray irradiator has potential applications in SIT programs for future codling moth control.
Use of an aridity index to classify season with an application in genetic evaluation of Braunvieh cattle
Authors: Herrera-Ojeda J. B. , Ramírez-Valverde R. , Núñez-Domínguez R. , Lopez-Villalobos N. , Vázquez-Armijo J. F. , Orozco-Durán K. E. , Parra-Bracamonte G. M.
Published: August 2022

One of the most important aspects of genetic evaluation (GE) is the definition of contemporary groups (CG), commonly defined as animals of the same sex born in the same herd, year and season. The objective of this study was to use an aridity index (AI) to classify season and evaluate the implications on the GE of Braunvieh cattle. A data set with 32 777 and 22 448 birth weight (BW) and weaning weight adjusted to 240 days (WW) records, respectively, was used to compare two methods of classification of climatic seasons to be used in the definition of CG for GE models. The first method considered rain season criterion (RC), and the second method is a proposed classification using an AI. Both methods were compared using two approaches. The first approach examined differences in mixed models using the RC and AI season to select the best model for BW and WW, evaluated by different goodness of fit measures. The second approach considered fitting a GE model including the season classifications into the CG structure. Lower probability values for season effect and better goodness of fit measures were obtained when the season was classified according to the AI. Results showed that although differences are small, the AI allows a better model fitting for live-weight traits than RC and revealed a re-ranking effect on expected progeny differences data. Further analysis with other traits would demonstrate the extended utility of AI indicators to be considered for fitting models under a climatic change environment.
Procedure for assessing the quality of explanations in failure analysis
Authors: González Barman Kristian
Published: August 2022

This paper outlines a procedure for assessing the quality of failure explanations in engineering failure analysis. The procedure structures the information contained in explanations such that it enables to find weak points, to compare competing explanations, and to provide redesign recommendations. These features make the procedure a good asset for critical reflection on some areas of the engineering practice of failure analysis and redesign. The procedure structures relevant information contained in an explanation by means of structural equations so as to make the relations between key elements more salient. Once structured, the information is examined on its potential to track counterfactual dependencies by offering answers torelevantwhat-if-things-had-been-different questions. This criterion for explanatory goodness derives from the philosophy of science literature on scientific explanation. The procedure is illustrated by applying it to two case studies, one on Failure Analysis in Mechanical Engineering (a broken vehicle shaft) and one on Failure Analysis in Civil Engineering (a collapse in a convention center). The procedure offers failure analysts a practical tool for critical reflection on some areas of their practice while offering a deeper understanding of the workings of failure analysis (framing it as an explanatory practice). It, therefore, allows to improve certain aspects of the explanatory practices of failure analysis and redesign, but it also offers a theoretical perspective that can clarify important features of these practices. Given the programmatic nature of the procedure and its object (assessing and refining explanations), it extends work on the domain of computational argumentation.
Parametric optimization of FDM using the ANN-based whale optimization algorithm
Authors: Kumar Praveen , Gupta Pardeep , Singh Indraj
Published: August 2022

Surface roughness (SR) is one of the major parameters used to govern the quality of the fused deposition modeling (FDM)-printed products, and the FDM process parameters can be easily regulated in order to obtain a good surface finish. The surface quality of the product produced by the FDM is generally affected by the staircase effect that needs to be managed. Also, the production time (PT) to fabricate the product and volume percentage error (VPE) should be minimized to make the FDM process more efficient. The aim of this paper is to accomplish these three objectives with the use of the parametric optimization technique integrating the artificial neural network (ANN) and the whale optimization algorithm (WOA). The FDM parameters which have been taken into consideration are layer thickness, nozzle temperature, printing speed, and raster width. Experimentation has been conducted on printed samples to examine the impact of the input parameters on SR, VPE, and PT according to Taguchi's L27 orthogonal array. The ANN model has been built up using the experimental data, which was further used as an objective function in the WOA with an aim to minimize output responses. The robustness of the proposed method has been validated on the optimal combinations of FDM process parameters.
Differentiation strategies in coffee farms: opportunities for Costa Rican growers
Authors: Valenciano-Salazar Jorge A. , André Francisco J. , Díaz-Porras Rafael
Published: August 2022

This study investigates the determinants of coffee prices received by growers in Costa Rica, paying attention to the impact of environmental, regional, quality, and international aspects in a panel data set for the period 2008–2016. We identify three groups of variables that affect domestic coffee prices. Some of them are external to the control of the coffee growers, such as the international price of green coffee or the power of multinationals; others, such as the altitude where the coffee is harvested or the berries' yield, are related to coffee quality but difficult to modify by coffee growers. The focus of our study is on the third group, which refers to differentiation strategies related to environmental certifications. More specifically, we consider two particularly relevant certifications, which are Fairtrade mills and organic coffee. We find that organic coffee berries received higher prices, but Fairtrade mills report lower average prices than other, non-certified, buyers.
A Hybrid Dynamical Approach for Seasonal Prediction of Sea‐Level Anomalies: A Pilot Study for Charleston, South Carolina
Authors: Frederikse Thomas , Lee Tong , Wang Ou , Kirtman Ben , Becker Emily , Hamlington Ben , Limonadi Daniel , Waliser Duane
Published: August 2022

Using Earth system models for seasonal sea‐level prediction remains challenging due to model biases and initialization shocks. Here we present a hybrid dynamical approach for seasonal sea‐level prediction to alleviate some of these issues. The approach is based on convolving atmospheric forcings with sea‐level sensitivities to these forcings. The sensitivities are pre‐computed by the adjoint model of the Estimating Circulation and Climate of the Ocean (ECCO) system. The forcings are a concatenation of ECCO forcings before prediction initialization and a 10‐member predicted atmospheric forcing ensemble from the Community Climate System Model version 4 (CCSM4) after initialization, with offline forcing bias corrections applied using the observationally‐constrained ECCO seasonal forcing climatology. As a pilot study, we conducted 12‐month hindcasts from 1995 to 2016 in Charleston (United States East Coast). Our approach avoids drifts in CCSM4 sea‐level predictions and beats seasonal climatology and damped persistence as predictors up to a 6‐month lead time. The prediction skill comes from two factors: (a) ECCO forcings prior to prediction initialization influence sea level after initialization through delayed oceanic adjustments (e.g., coastally‐trapped waves, open‐ocean Rossby waves, and advection of steric anomalies) leading to skillful predictions beyond 2 months after initialization, and (b) the 10‐member CCSM4 ensemble forcing predictions have relatively good skill at 1–2 months lead times. Our method is computationally efficient for operational sea‐level prediction at specific locations and can attribute sea‐level prediction skill and uncertainty to specific forcings or forcing from particular regions, thereby providing useful information to seasonal prediction centers for improving their prediction systems.
A Physically Based Model of Deposition, Re‐Entrainment, and Transport of Fine Sediment in Gravel‐Bed Rivers
Authors: Haddadchi Arman , Rose Calvin W.
Published: August 2022

Interpreting the links between transient in‐channel fine sediment storage and the dynamics of suspended sediment transport during flood events helps the understanding of river geomorphology, and also the impacts of fine sediment on water quality and bed habitats of rivers and downstream receiving environments. We present a unique physically based model of suspended sediment transport which is intimately coupled with fine sediment deposition and re‐entrainment processes within the gravel bed. This multi‐size fraction theory provides unique information about the effect of fine sediment size classes due to their dynamics and associated river bed changes in net deposition. The data from a series of flood events from the Oreti River, located in Southland, New Zealand were used to test the ability of this theory to provide a description of the dynamics of the fine sediment size distribution, their concentration, load, and rate of river bed deposition and re‐entrainment. After calibration of the model using the data from one flood event, the model provides good agreement between observed and modeled fine sediment concentration and event load for seven subsequent test events. One of the main applications of this theory in future is for routing suspended sediment concentration and changes on fine sediment deposition down a river network.
Magnetostratigraphic Evidence From the Gengma Basin for the Fast Response of the Crustal Rotation of the Northern Part of the Shan‐Thai Block to the India‐Eurasia Convergence
Authors: Sun Xinxin , Tong Yabo , Yang Zhenyu , Pei Junling , Pu Zongwen , Hou Lifu , Jin Shuchen , Zhang Zijian , Li Xinyue
Published: August 2022

The Cenozoic tectonic evolution of the southeastern edge of the Tibetan Plateau is interpreted in terms of two alterative dynamic mechanisms: lateral extrusion of coherent lithospheric blocks and viscous lower crustal flow. To contribute to this debate, we conducted a magnetostratigraphic study of the Early Miocene sedimentary strata of the Gengma Basin, in the northern part of the Shan‐Thai Block (STB). The results show that variations in the deposition rate were synchronous with the rate of clockwise rotation during ∼18.05–15.93 Ma, indicating that the crustal clockwise rotation of the northern STB was the driver of the tectonic transformation of the NE‐SW trending strike‐slip system within the STB by at least ∼18.05 Ma. The rapid decrease in the clockwise rotational rate of the Gengma Basin was also synchronous with the sharp decrease in the convergence rate between the Indian Plate (IDP) and Eurasia at ∼17.23 Ma, which is similar to that occurred in the interior of the Tibetan Plateau during the Paleocene and Eocene, demonstrating the fast response of the southeastern edge of the Tibetan Plateau to the convergence of the IDP and Eurasia, in the form of the continuous upper crustal ductile deformation of the Tibetan Plateau and its periphery. The lateral flow of the viscous lower crust beneath the southeastern edge of the Tibetan Plateau may be the predominant driver of the tectonic evolution of the southeastern edge of the Tibetan Plateau since the Early Miocene.
What Is Unusual About the Third Largest Geomagnetic Storm of Solar Cycle 24?
Authors: Gopalswamy N. , Yashiro S. , Akiyama S. , Xie H. , Mäkelä P. , Fok M.‐C. , Ferradas C. P.
Published: August 2022

We report on the solar and interplanetary (IP) causes of the third largest geomagnetic storm (26 August 2018) in solar cycle 24. The underlying coronal mass ejection (CME) originating from a quiescent filament region becomes a 440 km/s magnetic cloud (MC) at 1 au after ∼5 days. The prolonged CME acceleration (for ∼24 hr) coincides with the time profiles of the post‐eruption arcade intensity and reconnected flux. Chen et al. (2019, https://doi.org/10.3847/1538-4357/ab3f36) obtain a lower speed since they assumed that the CME does not accelerate after ∼12 hr. The presence of multiple coronal holes near the filament channel and the high‐speed wind from them seem to have the combined effect of producing complex rotation in the corona and IP medium resulting in a high‐inclination MC. The Dst time profile in the main phase steepens significantly (rapid increase in storm intensity) coincident with the density increase (prominence material) in the second half of the MC. Simulations using the Comprehensive Inner Magnetosphere‐Ionosphere model show that a higher ring current energy results from larger dynamic pressure (density) in MCs. Furthermore, the Dst index is highly correlated with the main‐phase time integral of the ring current injection that includes density, consistent with the simulations. A complex temporal structure develops in the storm main phase if the underlying MC has a complex density structure during intervals of southward IP magnetic field. We conclude that the high intensity of the storm results from the prolonged CME acceleration, complex rotation of the CME flux rope, and the high density in the 1‐au MC.
A Climatology of Long‐Duration High 2‐MeV Electron Flux Periods in the Outer Radiation Belt
Authors: Mourenas D. , Agapitov O. V. , Artemyev A. V. , Zhang X.‐J.
Published: August 2022

Since the advent of the Space Age, the importance of understanding and forecasting relativistic electron fluxes in the Earth’s radiation belts has been steadily growing due to the threat that such particles pose to satellite electronics. Here, we provide a model of long‐duration periods of high time‐integrated 2‐MeV electron flux deep inside the outer radiation belt, based on the significant correlation obtained in 2001–2017 between time‐integrated electron flux measured by satellites and a measure of the preceding time‐integrated homogenized aaH geomagnetic index. We show that this correlation is likely due to a stronger cumulative chorus wave‐driven acceleration of relativistic electrons and a stronger cumulative inward radial diffusion of such electrons during periods of higher time‐integrated geomagnetic activity. Return levels of 2‐MeV electron flux are provided based on Extreme Value analysis of time‐integrated geomagnetic activity over 1868–2017, in rough agreement with estimates based on 20‐year data sets of measured flux. A high correlation is also found between our measure of time‐integrated geomagnetic activity averaged over each solar cycle and averaged sunspot numbers, potentially paving the way for forecasts of time‐integrated relativistic electron flux during future solar cycles based on predictions of solar activity.
The Effect of Regional Winds on Subtidal Along‐Inlet Currents at Oregon Inlet, NC
Authors: Humberston J. L. , Lippmann T. C.
Published: August 2022

Wind influence on tidal inlet hydrodynamics is examined using 40 days of wind, water level, and current observations collected in Spring 2019 at Oregon Inlet, NC, a large (1 km wide, 1–13 m deep) meso‐tidal inlet with complex delta systems. Wind velocities through the inlet (ranging 0–18 m/s) are modulated at subtidal timescales and are well correlated (R = 0.87) to a subtidal component of the water level slope through the inlet. The subtidal wind and water level slope are also well correlated to the subtidal current along the principal flow axis in the main inlet channel (R = 0.92 and 0.96, respectively). In combination with findings from previous studies, these findings suggest that regional winds induce the subtidal water level slope through the inlet by causing opposing setup/setdown to either side of the inlet. A force balance at the inlet demonstrates that the wind‐induced pressure gradient forces the subtidal currents, with wave forcing and local wind shear acting as lower‐order influences. The magnitude of the subtidal current is substantial, exceeding that of the tidal currents 45% of the time. Cumulatively, these findings indicate that regional winds exert a first‐order control on the currents at Oregon Inlet and cause irregular hydrodynamic patterns not well described by the traditional inlet classification scheme. Regional geographic characteristics may contribute to the high level of wind influence at Oregon Inlet, but similar processes are likely to be important to net flow dynamics at other inlets with large, shallow inland water bodies.
Entrainment and Transport of Well‐Sorted and Mixed Sediment Under Wave Motion
Authors: Rafati Yashar , Hsu Tian‐Jian , Calantoni Joseph , Puleo Jack
Published: August 2022

Entrainment and suspension of sediment particles with the size distribution similar to a range of natural sands were simulated with a focus on the vertical size sorting and transport dynamics in response to different wave conditions. The simulations were performed using a two‐phase Eulerian‐Lagrangian model by combining the LIGGGHTS discrete element method solver for sediment and SedFoam solver for the fluid phase. The model was first validated for a range of sand grain sizes from 0.21 to 0.97 mm having well‐sorted and mixed (bimodal) size distributions using laboratory oscillatory flow data. Three sediment bed configurations were studied under a wide range of velocity‐skewed waves with different wave intensity and skewness. It was found that the bimodal distribution having only 30% of coarse fraction and 70% of medium fraction responds similar to a well‐sorted coarse sand configuration. Sediment fluxes of the bimodal distribution were slightly higher than those of well‐sorted coarse sand because of the pronounced inverse grading in the bimodal distribution. Furthermore, for the bimodal distribution the medium fraction acted as a relatively smooth foundation underneath the coarse fraction which facilitated the mobilization of the coarser particles. Under high energy wave conditions, the smoothing feature was exacerbated and further caused the formation of plug flow where a thick layer of intense sediment flux was observed. Model results also showed that under high skewness waves, phase‐lag effect occurred in well‐sorted medium sand which caused lower net onshore sediment transport rates but the effect was significantly reduced for mixed sediments.
Structural Characterization of a Toppling Rock Slab From Array‐Based Ambient Vibration Measurements and Numerical Modal Analysis
Authors: Bessette‐Kirton E. K. , Moore J. R. , Geimer P. R. , Finnegan R. , Häusler M. , Dzubay A.
Published: August 2022

Accurate assessments of the internal structure and boundary conditions of unstable rock slopes are imperative for evaluating landslide hazard scenarios. However, instability characterization at depth remains challenging and is often limited by costly or invasive subsurface investigations. Here, we develop a new approach coupling array‐based ambient vibration modal analysis and numerical modeling to improve structural characterization of rock slope instabilities at depth. We used ambient noise cross‐correlation on 4 hr of seismic data recorded by an array of 30 nodal geophones at a 500‐m‐long toppling rock slab in Utah, USA to identify modal frequencies between 0.8 and 3.5 Hz and derive modal displacements. We show that transverse and longitudinal bending modes span the length of the instability, indicating an interconnected slab. Statistical comparison of field results with outputs from >1,000 finite element models with varying boundary conditions showed that the instability depth varies between 40–70 and 10–20 m in the middle and lateral regions, respectively. Our approach yields new information on the structural conditions of rock cliff and column instabilities at depth, which is not easily obtained by other means but is imperative for change detection monitoring and improved hazard assessments.
Efficient Numerical Simulation of Density‐Driven Flows: Application to the 2‐ and 3‐D Elder Problem
Authors: Bahlali Meissam L. , Salinas Pablo , Jackson Matthew D.
Published: August 2022

Modeling density‐driven flow in porous media is challenging due to the nonlinear coupling between flow and transport equations, the large domains of interest and the wide range of time and space scales involved. Solving this type of problem numerically using a fixed mesh can be prohibitively expensive. Here, we apply a dynamic mesh optimization (DMO) technique along with a control‐volume‐finite element method to simulate density‐driven flows. DMO allows the mesh resolution and geometry to vary during a simulation to minimize an error metric for one or more solution fields of interest, refining where needed and coarsening elsewhere. We apply DMO to the Elder problem for several Rayleigh numbers. It is demonstrated that DMO accurately reproduces the unique two‐dimensional (2D) solutions for low Rayleigh number cases at significantly lower computational cost compared to an equivalent fixed mesh, with speedup of order ×16. For unstable, high Rayleigh number 2D cases, multiple steady‐state fingering solutions exist and are all captured by our approach with high accuracy and significantly reduced computational cost, with speedup of order ×6. Velocity‐dependent dispersion is shown to have a small impact on the 2D numerical solutions. The lower computational cost of simulations using DMO allows extension of the high Rayleigh number case to a three dimensional (3D) configuration. We demonstrate new 3D fingering patterns that have not been observed previously. Early time, transient 3D patterns represent combinations of the previously observed, steady‐state 2D solutions, but all evolve to a single, steady‐state finger in the late time limit.
Parasite reliance on its host gut microbiota for nutrition and survival
Authors: Zhou Sicong , Lu Yueqi , Chen Jiani , Pan Zhongqiu , Pang Lan , Wang Ying , Zhang Qichao , Strand Michael R , Chen Xue-Xin , Huang Jianhua
Published: August 2022

Studying the microbial symbionts of eukaryotic hosts has revealed a range of interactions that benefit host biology. Most eukaryotes are also infected by parasites that adversely affect host biology for their own benefit. However, it is largely unclear whether the ability of parasites to develop in hosts also depends on host-associated symbionts, e.g., the gut microbiota. Here, we studied the parasitic wasp Leptopilina boulardi (Lb) and its host Drosophila melanogaster. Results showed that Lb successfully develops in conventional hosts (CN) with a gut microbiota but fails to develop in axenic hosts (AX) without a gut microbiota. We determined that developing Lb larvae consume fat body cells that store lipids. We also determined that much larger amounts of lipid accumulate in fat body cells of parasitized CN hosts than parasitized AX hosts. CN hosts parasitized by Lb exhibited large increases in the abundance of the bacterium Acetobacter pomorum in the gut, but did not affect the abundance of Lactobacillus fructivorans which is another common member of the host gut microbiota. However, AX hosts inoculated with A. pomorum and/or L. fructivorans did not rescue development of Lb. In contrast, AX larvae inoculated with A. pomorum plus other identified gut community members including a Bacillus sp. substantially rescued Lb development. Rescue was further associated with increased lipid accumulation in host fat body cells. Insulin-like peptides increased in brain neurosecretory cells of parasitized CN larvae. Lipid accumulation in the fat body of CN hosts was further associated with reduced Bmm lipase activity mediated by insulin/insulin-like growth factor signaling (IIS). Altogether, our results identify a previously unknown role for the gut microbiota in defining host permissiveness for a parasite. Our findings also identify a new paradigm for parasite manipulation of host metabolism that depends on insulin signaling and the gut microbiota.
Identification of activity-induced Egr3-dependent genes reveals genes associated with DNA damage response and schizophrenia
Authors: Marballi Ketan K. , Alganem Khaled , Brunwasser Samuel J. , Barkatullah Arhem , Meyers Kimberly T. , Campbell Janet M. , Ozols Annika B. , Mccullumsmith Robert E. , Gallitano Amelia L.
Published: August 2022

Bioinformatics and network studies have identified the immediate early gene transcription factor early growth response 3 (EGR3) as a master regulator of genes differentially expressed in the brains of patients with neuropsychiatric illnesses ranging from schizophrenia and bipolar disorder to Alzheimer’s disease. However, few studies have identified and validatedEgr3-dependent genes in the mammalian brain. We have previously shown thatEgr3is required for stress-responsive behavior, memory, and hippocampal long-term depression in mice. To identifyEgr3-dependent genes that may regulate these processes, we conducted an expression microarray on hippocampi from wildtype (WT) andEgr3−/−mice following electroconvulsive seizure (ECS), a stimulus that induces maximal expression of immediate early genes includingEgr3. We identified 69 genes that were differentially expressed between WT andEgr3−/−mice one hour following ECS. Bioinformatic analyses showed that many of these are altered in, or associated with, schizophrenia, includingMef2candCalb2. Enrichr pathway analysis revealed the GADD45 (growth arrest and DNA-damage-inducible) family (Gadd45b,Gadd45g) as a leading group of differentially expressed genes. Together with differentially expressed genes in the AP-1 transcription factor family genes (Fos,Fosb), and the centromere organization proteinCenpa, these results revealed thatEgr3is required for activity-dependent expression of genes involved in the DNA damage response. Our findings show thatEGR3is critical for the expression of genes that are mis-expressed in schizophrenia and reveal a novel requirement for EGR3 in the expression of genes involved in activity-induced DNA damage response.
Predictors of emotional distress in uveal melanoma survivors: a systematic review
Authors: Davies Cari , Brown Stephen Lloyd , Fisher Peter , Hope-Stone Laura , Fisher Debra , Morgan Andrew , Cherry Mary Gemma
Published: August 2022

Uveal melanoma (UM) survivors can experience significant emotional distress, although the factors underpinning this are poorly understood. Systematic reviews of distress in UM only include cross-sectional studies, thereby limiting our understanding of causal factors. This review identified prospective clinical, demographic, social and psychological predictors of distress in UM survivors. A systematic search of the literature for English language prospective studies was conducted. Thirteen papers, reporting data from seven unique datasets were included in a narrative synthesis of the results. Younger age (3 studies from 3 datasets), physical health (including visual impairment, ocular symptoms, and other UM-related factors; 3 studies from 3 datasets), and psychological factors (mainly baseline distress; 3 studies from 3 datasets and worry about recurrence; 2 studies from 2 datasets), significantly predicted distress. There was no consistent evidence for other demographic, clinical or social variables (significant in <50% of datasets). Generally, the quality of the papers was adequate. However, attrition rates were high or not reported in over half of the included studies. The findings of this review emphasise the importance of attempts to prevent and recognise distress immediately post-diagnosis of UM. Particular focus should be given to younger patients, those with physical and psychological health difficulties at the time of diagnosis, and those who develop adverse treatment symptoms during survivorship. More research into potential social and psychological variables and their role in predicting distress in survivors is recommended.
RALY regulate the proliferation and expression of immune/inflammatory response genes via alternative splicing of FOS
Authors: Liang Zhao , Rehati Aliya , Husaiyin Erhati , Chen Dong , Jiyuan Zhang , Abuduaini Buzukela
Published: August 2022

RALY is a multifunctional RNA-binding protein involved in cancer metastasis, prognosis, and chemotherapy resistance in various cancers. However, the molecular mechanism of which is still unclear. We have established RALY overexpression cell lines and studied the effect of RALY on proliferation and apoptosis in HeLa cells. Then we used RNA-seq to analyze the transcriptomes data. Lastly, RT-qPCR experiments had performed to confirm the RNA-seq results. We found that the overexpression of RALY in HeLa cells inhibited proliferation. Moreover, the overexpression of RALY changed the gene expression profile, and the significant upregulation of genes involved immune/inflammatory response related biological process by NOD-like receptor signaling pathway cytokine-cytokine receptor interaction. The significant downregulation genes involved innate immune response by the Primary immunodeficiency pathway. Notably, IFIT1, IFIT2, IFTI3, IFI44, HERC4, and OASL expression had inhibited by the overexpression of RALY. Furthermore, RALY negatively regulates the expression of transcription factors FOS and FOSB. Notably, we found that 645 alternative splicing events had regulated by overexpression of RALY, which is highly enriched in transcription regulation, RNA splicing, and cell proliferation biological process by the metabolic pathway. We show that RALY regulates the expression of immune/inflammatory response-related genes via alternative splicing of FOS in HeLa cells. The novel role of RALY in regulating immune/inflammatory gene expression may explain its function in regulating chemotherapy resistance and provides novel insights into further exploring the molecular mechanism of RALY in regulating cancer immunity and chemo/immune therapies.
Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis
Authors: Koren Elle , Feldman Alona , Yusupova Marianna , Kadosh Avihay , Sedov Egor , Ankawa Roi , Yosefzon Yahav , Nasser Waseem , Gerstberger Stefanie , Kimel Liam B. , Priselac Noa , Brown Samara , Sharma Sam , Gorenc Travis , Shalom-Feuerstein Ruby , Steller Hermann , Shemesh Tom , Fuchs Yaron
Published: August 2022

The presence of distinct stem cells that maintain the interfollicular epidermis is highly debated. Here, we report a population of keratinocytes, marked by Thy1, in the basal layer of the interfollicular epidermis. We find that epidermal cells expressing differential levels of Thy1 display distinct transcriptional signatures. Thy1+ keratinocytes do not express T cell markers, express a unique transcriptional profile, cycle significantly slower than basal epidermal progenitors and display significant expansion potential in vitro. Multicolor lineage tracing analyses and mathematical modeling reveal that Thy1+ basal keratinocytes do not compete neutrally alike interfollicular progenitors and contribute long-term to both epidermal replenishment and wound repair. Importantly, ablation of Thy1+ cells strongly impairs these processes, thus indicating the non-redundant function of Thy1+ stem cells in the epidermis. Collectively, these results reveal a distinct stem cell population that plays a critical role in epidermal homeostasis and repair.
Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data
Authors: Dhapola Parashar , Rodhe Johan , Olofzon Rasmus , Bonald Thomas , Erlandsson Eva , Soneji Shamit , Karlsson Göran
Published: August 2022

As the scale of single-cell genomics experiments grows into the millions, the computational requirements to process this data are beyond the reach of many. Herein we present Scarf, a modularly designed Python package that seamlessly interoperates with other single-cell toolkits and allows for memory-efficient single-cell analysis of millions of cells on a laptop or low-cost devices like single-board computers. We demonstrate Scarf’s memory and compute-time efficiency by applying it to the largest existing single-cell RNA-Seq and ATAC-Seq datasets. Scarf wraps memory-efficient implementations of a graph-based t-stochastic neighbour embedding and hierarchical clustering algorithm. Moreover, Scarf performs accurate reference-anchored mapping of datasets while maintaining memory efficiency. By implementing a subsampling algorithm, Scarf additionally has the capacity to generate representative sampling of cells from a given dataset wherein rare cell populations and lineage differentiation trajectories are conserved. Together, Scarf provides a framework wherein any researcher can perform advanced processing, subsampling, reanalysis, and integration of atlas-scale datasets on standard laptop computers. Scarf is available on Github: https://github.com/parashardhapola/scarf.
Unified classification and risk-stratification in Acute Myeloid Leukemia
Authors: Tazi Yanis , Arango-Ossa Juan E. , Zhou Yangyu , Bernard Elsa , Thomas Ian , Gilkes Amanda , Freeman Sylvie , Pradat Yoann , Johnson Sean J. , Hills Robert , Dillon Richard , Levine Max F. , Leongamornlert Daniel , Butler Adam , Ganser Arnold , Bullinger Lars , Döhner Konstanze , Ottmann Oliver , Adams Richard , Döhner Hartmut , Campbell Peter J. , Burnett Alan K. , Dennis Michael , Russell Nigel H. , Devlin Sean M. , Huntly Brian J. P. , Papaemmanuil Elli
Published: August 2022

Clinical recommendations for Acute Myeloid Leukemia (AML) classification and risk-stratification remain heavily reliant on cytogenetic findings at diagnosis, which are present in <50% of patients. Using comprehensive molecular profiling data from 3,653 patients we characterize and validate 16 molecular classes describing 100% of AML patients. Each class represents diverse biological AML subgroups, and is associated with distinct clinical presentation, likelihood of response to induction chemotherapy, risk of relapse and death over time. Secondary AML-2, emerges as the second largest class (24%), associates with high-risk disease, poor prognosis irrespective of flow Minimal Residual Disease (MRD) negativity, and derives significant benefit from transplantation. Guided by class membership we derive a 3-tier risk-stratification score that re-stratifies 26% of patients as compared to standard of care. This results in a unified framework for disease classification and risk-stratification in AML that relies on information from cytogenetics and 32 genes. Last, we develop an open-access patient-tailored clinical decision support tool.
Tectonically-driven oxidant production in the hot biosphere
Authors: Stone Jordan , Edgar John O. , Gould Jamie A. , Telling Jon
Published: August 2022

Genomic reconstructions of the common ancestor to all life have identified genes involved in H2O2 and O2 cycling. Commonly dismissed as an artefact of lateral gene transfer after oxygenic photosynthesis evolved, an alternative is a geological source of H2O2 and O2 on the early Earth. Here, we show that under oxygen-free conditions high concentrations of H2O2 can be released from defects on crushed silicate rocks when water is added and heated to temperatures close to boiling point, but little is released at temperatures <80 °C. This temperature window overlaps the growth ranges of evolutionary ancient heat-loving and oxygen-respiring Bacteria and Archaea near the root of the Universal Tree of Life. We propose that the thermal activation of mineral surface defects during geological fault movements and associated stresses in the Earth’s crust was a source of oxidants that helped drive the (bio)geochemistry of hot fractures where life first evolved.
Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer
Authors: Queiroz Andre Lima , Dantas Ezequiel , Ramsamooj Shakti , Murthy Anirudh , Ahmed Mujmmail , Zunica Elizabeth R. M. , Liang Roger J. , Murphy Jessica , Holman Corey D. , Bare Curtis J. , Ghahramani Gregory , Wu Zhidan , Cohen David E. , Kirwan John P. , Cantley Lewis C. , Axelrod Christopher L. , Goncalves Marcus D.
Published: August 2022

Cancer cachexia is a common, debilitating condition with limited therapeutic options. Using an established mouse model of lung cancer, we find that cachexia is characterized by reduced food intake, spontaneous activity, and energy expenditure accompanied by muscle metabolic dysfunction and atrophy. We identify Activin A as a purported driver of cachexia and treat with ActRIIB-Fc, a decoy ligand for TGF-β/activin family members, together with anamorelin (Ana), a ghrelin receptor agonist, to reverse muscle dysfunction and anorexia, respectively. Ana effectively increases food intake but only the combination of drugs increases lean mass, restores spontaneous activity, and improves overall survival. These beneficial effects are limited to female mice and are dependent on ovarian function. In agreement, high expression of Activin A in human lung adenocarcinoma correlates with unfavorable prognosis only in female patients, despite similar expression levels in both sexes. This study suggests that multimodal, sex-specific, therapies are needed to reverse cachexia.
Space-time monitoring of groundwater fluctuations with passive seismic interferometry
Authors: Mao Shujuan , Lecointre Albanne , van der Hilst Robert D. , Campillo Michel
Published: August 2022

Historic levels of drought, globally, call for sustainable freshwater management. Under pressing demand is a refined understanding of the structures and dynamics of groundwater systems. Here we present an unconventional, cost-effective approach to aquifer monitoring using seismograph arrays. Employing advanced seismic interferometry techniques, we calculate the space-time evolution of relative changes in seismic velocity, as a measure of hydrological properties. During 2000–2020 in basins near Los Angeles, seismic velocity variations match groundwater tables measured in wells and surface deformations inferred from satellite sensing, but the seismological approach adds temporal and depth resolutions for deep structures and processes. Maps of long-term seismic velocity changes reveal distinct patterns (decline or recovery) of groundwater storage in basins that are adjacent but adjudicated to water districts conducting different pumping practices. This pilot application bridges the gap between seismology and hydrology, and shows the promise of leveraging seismometers worldwide to provide 4D characterizations of groundwater and other near-surface systems.