bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effect of Compressibility on the Shear-Stress Distribution in Turbulent Pipe Flow
Authors: Durst F. , Launder B. E. , Kjellstrom B.
Published: March 2023

For flows at Mach numbers much less than unity the fully-developed wall shear stress in a circular pipe may be determined directly from a knowledge of the pipe radius, R, and the measured gradient in static pressure along the pipe, dp/dx. At higher subsonic Mach numbers it is conventional to apply a one-dimensional compressibility correction to make allowance for the acceleration of the fluid arising from the progressive decrease in density along the pipe. The correction procedure is to determine a “frictional” pressure gradient, dpf/dx, associated with wall shear stresses alone.
Wire Saving Techniques
Authors: Wakefield G.
Published: March 2023

On 22nd October, 1969, a joint meeting was held between The Royal Aeronautical Society and the Institution of Electrical Engineers, at 4 Hamilton Place, London, W.l. The subject under discussion was methods for reducing the large numbers of wires used in present day aircraft.

Mr. Ruy de Barras—Sabena Airline, read a paper on new wiring techniques using flat strip wires. The paper was awe inspiringly entitled “System of Interface Matrix of Parallel Lines” (SIMPL), although the technique proved to be most simple.
Aircraft Maintenance
Authors: Norberg J. W.
Published: March 2023

The aircraft maintenance function is a vital element of airline operations. The achievement and sustaining of the airworthiness standard throughout the life of an aircraft is its prime concern and responsibility. There are many approaches one may take in describing the maintenance function, no one of which is complete in itself, but when considered collectively as a reference framework, can provide a comprehensive insight into the rather complex and dynamic process involved.

The generally steadily rising costs of labour and material, together with lagging or level fare structures, are demanding even greater gains in productivity and utilisation of resources to maintain profit margins and adequate returns on investments. The productivity gains made possible by introduction of jet aircraft are being exhausted and new ways must be found to achieve lower operating costs. At the outset I think it might be reasonable to ask ourselves the simple question “Why aircraft maintenance?” From an airline corporate or operating viewpoint it certainly conflicts with the objectives of attaining low operating costs, low material inventory levels, high utilisation of aircraft. I have stated on several occasions that “we are the trouble department—and when we have no trouble we are really in trouble”.
The Civil Aircraft Market: An Examination of the Replacement Order Cycle and the Used Aircraft Market
Authors: Ellison A. P.
Published: March 2023

The aviation industry over the past twenty years has experienced rapid growth and also considerable fluctuations about this growing trend. It is fluctuations about this trend, even though they may be of relatively short duration, which make or break airlines. In Table I(a) for instance, are shown the fluctuations about the trend of fares, load factor, international airline operating projects, aircraft investment and output. The institutional structure within which air travel operates is shown by the small variation in fares, while aircraft investment and profits show wide fluctuation. Reference to the last three columns shows the synchronised cycle in aircraft producer profits. We shall enquire into some possible courses of these fluctuations, and then examine the consequences of these fluctuations on used aircraft prices and financial performance of the airlines.
STOL Aircraft in Future Transport Systems
Authors: Marshall E. E.
Published: March 2023

In the author's R. J. Mitchell Memorial Lecture, presented to the Southampton Branch of the Royal Aeronautical Society in March 1969, the role of aircraft in future transport systems was examined. Since that time, three important trends or events have taken place. First and probably the most important, the environmental problems arising from the use of aircraft—noise, pollution and land use—have come to be major parameters in the design of new airliners. This trend has been highlighted by the recent issue of noise regulations by the Federal Aviation Administration (FAA) which new airliners have to meet before they can be certificated. These limits can be expected to become more stringent in future years. Secondly, the economic effects of congestion—both in the air and on the ground, at and around airports—have begun to be felt at major airports, especially at those in the Northeast Corridor of the United States. Finally, in the United Kingdom the Roskill Commission on the Third London Airport has recently issued its report.
The American Legal View
Authors: Kreindler Lee S.
Published: March 2023

I had thought that perhaps, one time I could appear here and say something without being contentious but I must immediately start off with a significant argument. I think that as a plantiff's lawyer in the United States I am one of a large number of responsible members of the Bar, and I say this in all innocence, doing a responsible job which I am sorry to say is frequently misunderstood here. I do not think we set out to bankrupt the British or American aviation industries. I do not think we set out to make fortunes for ourselves, or our clients. I think sincerely, that the objectives of the typical plaintiff's lawyer is to get reasonable redress for the poor victims of tragic accidents.
Aviation Products Liability—A Technical Viewpoint
Authors: Hunter Alan B.
Published: March 2023

The modern jet transport has established an excellent safety record of which the industry can justly be proud, but with the airlines soon to be flying something of the order of a million hours per month, the potential exposure to accident in the years ahead is considerable.

The first 50M hours of jet flight took 12 years to achieve and—excluding the wanton destruction of aircraft in the Middle East—involved the loss of 132 aircraft and the deaths of 3800 passengers, or an average of aircraft and 76 passengers per million hours. Isolation of the past three years of this record to detect the later trend reveals an improvement to an average of 2 aircraft and 51 passengers per million hours. Given no further improvement this would soon become the average monthly rate of loss, but because of the uncertainty as to the passenger load factor in any particular accident, consideration must now be given to the realistic possibility of losing at least 20 aircraft and perhaps 1000 or more passengers in any one year. Given the validity of this concept, then over the next five years whatever dollar figure is chosen to represent the financial problem involved, the first digit is likely to be followed by nine noughts!
Looking ahead with hindsight
Authors: Edwards George
Published: March 2023

It is a great honour for me to be invited to give this lecture but it has been rather a problem to know how best to tackle it. It is a great temptation when you are my age, and you have been in the aerospace business as long as I have, to reminisce about the things that you have done in the past—and it is one that, in part, I could not resist. If by any chance any of the younger members of the community that still have their working lifetime in front of them can discern any sort of a message here and there in what I say, then I hope they will do so and that they will have the courage to do something about it.
Factors affecting host plant selection in alfalfa aphids
Authors: Radonjić Andja , Jovičić Ivana , Lalićević Ivana , Petrović-Obradović Olivera
Published: March 2023

Alfalfa (Medicago sativa L.) hosts several species of aphid, Acyrthosiphon pisum (Harris), Aphis craccivora Koch and Therioaphis trifolii (Monell). The preference of the aphids of alfalfa plants for dense assemblies or individual plants, as well as for healthy or infested plants, was investigated in the field as in the laboratory. Years of field research have revealed the specific preferences of all three species of aphid. A. pisum and T. trifolii are most commonly found in alfalfa crops, while A. craccivora is mostly found on alfalfa weeds. Also, a single species of aphid alone is usually present on a plant. In order to determine the reason for this clear preference and to establish whether at the very beginning, i.e. at the stage of choosing a host, aphid species distance themselves from each other, we tested the effect of the volatiles of healthy and infested plants on their attractiveness to aphids. A. craccivora is repelled by the volatiles of dense crops and plants previously infested with one of the other two species. A. pisum and T. trifolii choose a dense assembly of plants, repelled by the volatiles of plants previously infested with A. craccivora. A. pisum displays the weakest competitive traits, and A. craccivora the strongest. This research showed that competition between aphid species does not occur only when they find themselves on the same plant at the same time, fighting for resources, but also in the choice of plant, in order to avoid later competition.
Sisterhood in the City: Creating Community through Lion Dance
Authors: Avaunt Casey
Published: March 2023

This article examines notions of “sisterhood” by focusing on an all-women's lion dance company called Gund Kwok, based in Boston's Chinatown. Gund Kwok, which limits membership to those who identify as female and Asian American, provides a space for women to perform this traditional male-only dance style. Company members have created a community of “sisters” to address layers of gendered and racial oppression. Despite concerns that scholars have raised about how community formations, such as sisterhoods, can be overly idealistic and potentially harmful, this study highlights the role of sisterhood in Gund Kwok and the important functions it serves for the group. It argues that Gund Kwok is a diverse community that draws from the ideology of sisterhood as a way of articulating Asian American cultural identity outside the scope of Western cultural frameworks and the dance's patriarchal tradition.
What Are the Most Effective Proxies in Identifying Storm‐Surge Deposits in Paleotempestology? A Quantitative Evaluation From the Sand‐Limited, Peat‐Dominated Environment of the Florida Coastal Everglades
Authors: Yao Qiang , Liu Kam‐biu , Zhang Zhenqing , Rodrigues Erika , Cohen Marcelo , Maiti Kanchan , Yang Yang
Published: March 2023

Although many studies have attempted to reconstruct millennial‐scale hurricane patterns using various proxy‐based methods, it is still unclear what the most effective proxies are to identify storm surge deposits in different environmental settings. This study quantitatively compares the application of grain‐size, loss‐on‐ignition, stable isotopes, X‐ray fluorescence, and palynological proxies in paleotempestology from an organic‐rich environment in the Florida Everglades. The nonparametric tests indicate that only 9 among the 27 parameters (mean diameter, %water, %organic, %carbonate, Ca, Sr, Ca/Ti, Cl/Br, and marine microfossils) exhibited significant differences between storm‐surge and in situ deposits. The principal component analysis shows that five marine indicators (Sr, Ca, Ca/Ti, %Carbonate, and Marine microfossils) have the closest association with the allochthonous samples, while Cl/Br and Mz are the most sensitive proxies in low‐ and high‐energy environments, respectively. Moreover, organic geochemical proxies (e.g., δ13C and δ15N of bulk sedimentary organic matter) are ineffective for identifying storm‐surge deposits in organic‐rich mangrove environments.
The Effect of Shear Displacement and Wear on Fault Stability: Laboratory Constraints
Authors: Noël Corentin , Giorgetti Carolina , Scuderi Marco M. , Collettini Cristiano , Marone Chris
Published: March 2023

Faults are composed of a damage zone and a fault core with wear material that has accumulated during sliding. Fault zone width and structural complexity have been suggested as key factors that dictate the stability of fault slip and the transition from stable to unstable motion. Here we address the role of fault rock wear rate and the presence of gouge on the stability of frictional sliding. We performed biaxial shear experiments on quartz‐rich bare rock surfaces having different resistances to abrasion (i.e., wear production with slip), as well as simulated quartz gouge. To characterize the influence of shear displacement on fault stability, constant velocity and velocity step experiments were performed to displacements up to 30 mm. Mechanical data are analyzed within the rate‐and‐state framework, and integrated with post‐mortem microscopic analyses of the samples. For initially bare surfaces a shear displacement threshold is required to transition from stable to unstable sliding. Stick‐slip events (laboratory earthquakes) evolve systematically as a function of fault slip. Shear displacement has a clear effect on the rate‐and‐state parameters (a‐b) and Dc. For all our tests, (a‐b) decreases with increasing shear displacement, implying enhanced velocity weakening and potential unstable behavior for larger fault slip. For high wear rates and simulated gouge, Dc decreases with increasing slip. However, for low wear rate faults, changes in Dc are negligible. Our results demonstrate that, fault stability varies systematically with fault slip and in particular that shear displacement and strain localization are dominant parameters controlling fault stability.
Assessment of increased knowledge about traffic accidents prevention, one month after a presentation included in the program “it can happen to you” of AESLEME
Authors: Cogollos-Paja Mar , García-Reneses Juan Angel , Herruzo Rafael
Published: March 2023

Road traffic accidents are a real pandemic and incur expenses amounting to 1–2% of every country’s GDP. AESLEME (Association for the Study of Spinal Cord Injuries) has celebrated its 30th anniversary here in Spain. AESLEME’s instructors are health workers and people with spinal cord injuries caused by road accidents: their presentations—teaching road safety and sharing information on irreversible injuries—are enhanced by personal stories that help schoolchildren to acquire knowledge on this matter.

Study design

Pre and post-quasi-experimental study.

Objective

To assess the increase in knowledge about road safety following a school-based road safety campaign.

Methods

Two multiple-choice tests were given to each of the 8106 students taking part, who were 12–14 years old. Of the four possible answers, only one of them was correct. The first multiple-choice test was taken before the presentation and the second was taken one month later.

Results

After assessing the answers, there was a change in the tendency of the number of correct before/after answers for the multiple-choice test, and the number of correct ones rose one month after the presentation. This increase is statistically significant (p < 0.01) and represents a national increase of 61% in the probability of correct answers, although this varies from 8% to 278% depending on the region.

Conclusions

The assessment, involving over 8000 people, showed that there has been an improvement in road safety knowledge thanks to education provided by AESLEME’s instructors, and a statistically significant increase was obtained throughout Spain and different regions.
Isolation of phages infecting the abundant freshwater Actinobacteriota order ‘Ca. Nanopelagicales’
Authors: Kavagutti Vinicius S , Chiriac Maria-Cecilia , Ghai Rohit , Salcher Michaela M , Haber Markus
Published: March 2023

Low-GC Actinobacteriota of the order ‘Ca. Nanopelagicales’ (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of ‘Ca. Nanopelagicales’ we isolated a novel species of its genus ‘Ca. Planktophila’. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host’s metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting ‘Ca. Nanopelagicales’. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.
Food hypersensitivity: an examination of factors influencing symptoms and temporal changes in the prevalence of sensitization in an adult sample
Authors: Lam Holly C. Y. , Neukirch Catherine , Janson Christer , Garcia-Aymerich Judith , Clausen Michael , Idrose N. Sabrina , Demoly Pascal , Bertelsen Randi J. , Ruiz Lidia C. , Raherison Chantal , Jarvis Deborah L.
Published: March 2023

Background/Objectives

Food hypersensitivity (FHS) is common, but little is known about the factors associated with severe reactions, age of onset and whether sensitization persists. This study examines the factors associated with self-reported severe food reactions, onset age and the changes in prevalence of sensitization to foods over time in an adult sample.

Subjects/Methods

We used data from adults taking part in the European Community Respiratory Health Survey (ECRHS) III (2010–2014) who provided information on food hypersensitivity, including symptoms, suspected culprit food and onset age (n = 4865). A subsample from six countries had serum food-specific IgE tested for 25 core foods and also in 10 years earlier (ECRHS II). We applied logistic regression and McNemar’s test for analyses.

Results

The prevalence of self-reported FHS was 13.5% at ECRHS III. Of those providing information on symptoms (n = 611), 26.4% reported severe reactions. About 80% of 1033 reported food-specific reactions (reported by 596 participants) began after age 15. History of asthma (odds ratio OR 2.12 95% confidence interval CI 1.13–3.44) and a younger age of onset of FHS (OR 1.02, 95% CI 1.01–1.03, per year) were associated with higher risks of a lifetime experience of severe food reactions. In the subsample with IgE tested in both surveys (n = 1612), the overall prevalence of sensitization to foods did not change over 10 years.

Conclusion

Our findings support previous observations of more severe food reactions in people with asthma and that most FHS reported by this sample started after age 15. We found no evidence of changes in the prevalence of sensitization to food in adults followed for 10 years.
Monocyte-derived macrophages contain persistent latent HIV reservoirs
Authors: Veenhuis Rebecca T. , Abreu Celina M. , Costa Pedro A. G. , Ferreira Edna A. , Ratliff Janaysha , Pohlenz Lily , Shirk Erin N. , Rubin Leah H. , Blankson Joel N. , Gama Lucio , Clements Janice E.
Published: March 2023

The development of persistent cellular reservoirs of latent human immunodeficiency virus (HIV) is a critical obstacle to viral eradication since viral rebound takes place once anti-retroviral therapy (ART) is interrupted. Previous studies show that HIV persists in myeloid cells (monocytes and macrophages) in blood and tissues in virologically suppressed people with HIV (vsPWH). However, how myeloid cells contribute to the size of the HIV reservoir and what impact they have on rebound after treatment interruption remain unclear. Here we report the development of a human monocyte-derived macrophage quantitative viral outgrowth assay (MDM-QVOA) and highly sensitive T cell detection assays to confirm purity. We assess the frequency of latent HIV in monocytes using this assay in a longitudinal cohort of vsPWH (n = 10, 100% male, ART duration 5–14 yr) and find half of the participants showed latent HIV in monocytes. In some participants, these reservoirs could be detected over several years. Additionally, we assessed HIV genomes in monocytes from 30 vsPWH (27% male, ART duration 5–22 yr) utilizing a myeloid-adapted intact proviral DNA assay (IPDA) and demonstrate that intact genomes were present in 40% of the participants and higher total HIV DNA correlated with reactivatable latent reservoirs. The virus produced in the MDM-QVOA was capable of infecting bystander cells resulting in viral spread. These findings provide further evidence that myeloid cells meet the definition of a clinically relevant HIV reservoir and emphasize that myeloid reservoirs should be included in efforts towards an HIV cure.
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas
Authors: Herr Bruce W. , Hardi Josef , Quardokus Ellen M. , Bueckle Andreas , Chen Lu , Wang Fusheng , Caron Anita R. , Osumi-Sutherland David , Musen Mark A. , Börner Katy
Published: March 2023

The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and ontology annotations for 26 organs. Experts access the HRA annotations via spreadsheets and view reference object models in 3D editing tools. This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCF Ontology design and implementation, present CCF Ontology classes and properties together with exemplary usage, and report on validation methods. The CCF Ontology graph database and API are used in the HuBMAP portal, HRA Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources.
The HAInich: A multidisciplinary vision data-set for a better understanding of the forest ecosystem
Authors: Milz Stefan , Wäldchen Jana , Abouee Amin , Ravichandran Ashwanth A. , Schall Peter , Hagen Chris , Borer John , Lewandowski Benjamin , Wittich Hans-Christian , Mäder Patrick
Published: March 2023

We present a multidisciplinary forest ecosystem 3D perception dataset. The dataset was collected in the Hainich-Dün region in central Germany, which includes two dedicated areas, which are part of the Biodiversity Exploratories - a long term research platform for comparative and experimental biodiversity and ecosystem research. The dataset combines several disciplines, including computer science and robotics, biology, bio-geochemistry, and forestry science. We present results for common 3D perception tasks, including classification, depth estimation, localization, and path planning. We combine the full suite of modern perception sensors, including high-resolution fisheye cameras, 3D dense LiDAR, differential GPS, and an inertial measurement unit, with ecological metadata of the area, including stand age, diameter, exact 3D position, and species. The dataset consists of three hand held measurement series taken from sensors mounted on a UAV during each of three seasons: winter, spring, and early summer. This enables new research opportunities and paves the way for testing forest environment 3D perception tasks and mission set automation for robotics.
Physical modeling and geometric shape simulation for one-dimensional flexible objects with cylindrical surface constraints
Authors: Mei Yuhang , Du Hongwang , Jiang Qinwen , Xiong Wei
Published: March 2023

This study develops forces equilibrium differential equations for the geometric modeling of 1D flexible objects with surface constraints. These second-order equations are an extension of the Cosserat elastic rod theory and include both bending and torsion. Variables were established for the centerline and attitude in the Cartesian coordinate system of the cross section. This paper specifically investigates the case of a 1D flexible object constrained by a cylindrical surface. To solve this problem, a novel hybrid semi-analytical numerical method is proposed. In this process, a Hamiltonian function and an initial integral operator are introduced in a cylindrical coordinate system. The analytical solution, decoupled in polar coordinates, is then derived. The improved finite difference method was then used to obtain three cylindrical coordinates, which ensured numerical stability and efficiency. The results of a geometric shape simulation with differing boundary conditions demonstrate that this proposed method is capable of real-time modeling. As such, this technique could be a promising new tool for use in graphics simulations of elongated structures, such as DNA molecules, drill pipes, and submarine cables.
Homologous recombination deficiency signatures in gastrointestinal and thoracic cancers correlate with platinum therapy duration
Authors: Tsang Erica S. , Csizmok Veronika , Williamson Laura M. , Pleasance Erin , Topham James T. , Karasinska Joanna M. , Titmuss Emma , Schrader Intan , Yip Stephen , Tessier-Cloutier Basile , Mungall Karen , Ng Tony , Sun Sophie , Lim Howard J. , Loree Jonathan M. , Laskin Janessa , Marra Marco A. , Jones Steven J. M. , Schaeffer David F. , Renouf Daniel J.
Published: March 2023

There is emerging evidence about the predictive role of homologous recombination deficiency (HRD), but this is less defined in gastrointestinal (GI) and thoracic malignancies. We reviewed whole genome (WGS) and transcriptomic (RNA-Seq) data from advanced GI and thoracic cancers in the Personalized OncoGenomics trial (NCT02155621) to evaluate HRD scores and single base substitution (SBS)3, which is associated withBRCA1/2mutations and potentially predictive of defective HRD. HRD scores were calculated by sum of loss of heterozygosity, telomeric allelic imbalance, and large-scale state transitions scores. Regression analyses examined the association between HRD and time to progression on platinum (TTPp). We included 223 patients with GI (n = 154) or thoracic (n = 69) malignancies. TTPp was associated with SBS3 (p < 0.01) but not HRD score in patients with GI malignancies, whereas neither was associated with TTPp in thoracic malignancies. Tumors with gBRCA1/2mutations and a somatic second alteration exhibited high SBS3 and HRD scores, but these signatures were also present in several tumors with germline but no somatic second alterations, suggesting silencing of the wild-type allele orBRCA1/2haploinsufficiency. Biallelic inactivation of an HR gene, including loss ofXRCC2andBARD1, was identified inBRCA1/2wild-type HRD tumors and these patients had prolonged response to platinum. Thoracic cases with high HRD score were associated with highRECQL5expression (p ≤ 0.025), indicating another potential mechanism of HRD. SBS3 was more strongly associated with TTPp in patients with GI malignancies and may be complementary to using HRD andBRCAstatus in identifying patients who benefit from platinum therapy.
Prediction model for drug response of acute myeloid leukemia patients
Authors: Trac Quang Thinh , Pawitan Yudi , Mou Tian , Erkers Tom , Östling Päivi , Bohlin Anna , Österroos Albin , Vesterlund Mattias , Jafari Rozbeh , Siavelis Ioannis , Bäckvall Helena , Kiviluoto Santeri , Orre Lukas M. , Rantalainen Mattias , Lehtiö Janne , Lehmann Sören , Kallioniemi Olli , Vu Trung Nghia
Published: March 2023

Despite some encouraging successes, predicting the therapy response of acute myeloid leukemia (AML) patients remains highly challenging due to tumor heterogeneity. Here we aim to develop and validate MDREAM, a robust ensemble-based prediction model for drug response in AML based on an integration of omics data, including mutations and gene expression, and large-scale drug testing. Briefly, MDREAM is first trained in the BeatAML cohort (n = 278), and then validated in the BeatAML (n = 183) and two external cohorts, including a Swedish AML cohort (n = 45) and a relapsed/refractory acute leukemia cohort (n = 12). The final prediction is based on 122 ensemble models, each corresponding to a drug. A confidence score metric is used to convey the uncertainty of predictions; among predictions with a confidence score >0.75, the validated proportion of good responders is 77%. The Spearman correlations between the predicted and the observed drug response are 0.68 (95% CI: [0.64, 0.68]) in the BeatAML validation set, –0.49 (95% CI: [–0.53, –0.44]) in the Swedish cohort and 0.59 (95% CI: [0.51, 0.67]) in the relapsed/refractory cohort. A web-based implementation of MDREAM is publicly available at https://www.meb.ki.se/shiny/truvu/MDREAM/.
Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome
Authors: Revolinski Samuel R. , Maughan Peter J. , Coleman Craig E. , Burke Ian C.
Published: March 2023

Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.
Direct reprogramming of human fibroblasts into insulin-producing cells using transcription factors
Authors: Fontcuberta-PiSunyer Marta , García-Alamán Ainhoa , Prades Èlia , Téllez Noèlia , Alves-Figueiredo Hugo , Ramos-Rodríguez Mireia , Enrich Carlos , Fernandez-Ruiz Rebeca , Cervantes Sara , Clua Laura , Ramón-Azcón Javier , Broca Christophe , Wojtusciszyn Anne , Montserrat Nuria , Pasquali Lorenzo , Novials Anna , Servitja Joan-Marc , Vidal Josep , Gomis Ramon , Gasa Rosa
Published: March 2023

Direct lineage reprogramming of one somatic cell into another without transitioning through a progenitor stage has emerged as a strategy to generate clinically relevant cell types. One cell type of interest is the pancreatic insulin-producing β cell whose loss and/or dysfunction leads to diabetes. To date it has been possible to create β-like cells from related endodermal cell types by forcing the expression of developmental transcription factors, but not from more distant cell lineages like fibroblasts. In light of the therapeutic benefits of choosing an accessible cell type as the cell of origin, in this study we set out to analyze the feasibility of transforming human skin fibroblasts into β-like cells. We describe how the timed-introduction of five developmental transcription factors (Neurog3, Pdx1, MafA, Pax4, and Nkx2-2) promotes conversion of fibroblasts toward a β-cell fate. Reprogrammed cells exhibit β-cell features including β-cell gene expression and glucose-responsive intracellular calcium mobilization. Moreover, reprogrammed cells display glucose-induced insulin secretion in vitro and in vivo. This work provides proof-of-concept of the capacity to make insulin-producing cells from human fibroblasts via transcription factor-mediated direct reprogramming.
Common seed dispersers contribute most to the persistence of a fleshy-fruited tree
Authors: Rehling Finn , Jongejans Eelke , Schlautmann Jan , Albrecht Jörg , Fassbender Hubert , Jaroszewicz Bogdan , Matthies Diethart , Waldschmidt Lina , Farwig Nina , Schabo Dana G.
Published: March 2023

Mutualistic interactions are by definition beneficial for each contributing partner. However, it is insufficiently understood how mutualistic interactions influence partners throughout their lives. Here, we used animal species-explicit, microhabitat-structured integral projection models to quantify the effect of seed dispersal by 20 animal species on the full life cycle of the treeFrangula alnusin Białowieża Forest, Eastern Poland. Our analysis showed that animal seed dispersal increased population growth by 2.5%. The effectiveness of animals as seed dispersers was strongly related to the interaction frequency but not the quality of seed dispersal. Consequently, the projected population decline due to simulated species extinction was driven by the loss of common rather than rare mutualist species. Our results support the notion that frequently interacting mutualists contribute most to the persistence of the populations of their partners, underscoring the role of common species for ecosystem functioning and nature conservation.
A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration
Authors: Löffler Julia , Noom Anne , Ellinghaus Agnes , Dienelt Anke , Kempa Stefan , Duda Georg N.
Published: March 2023

Bone regeneration after fracture is a complex process with high and dynamic energy demands. The impact of metabolism on bone healing progression and outcome, however, is so far understudied. Our comprehensive molecular profiling reveals that central metabolic pathways, such as glycolysis and the citric acid cycle, are differentially activated between rats with successful or compromised bone regeneration (young versus aged female Sprague-Dawley rats) early in the inflammatory phase of bone healing. We also found that the citric acid cycle intermediate succinate mediates individual cellular responses and plays a central role in successful bone healing. Succinate induces IL-1β in macrophages, enhances vessel formation, increases mesenchymal stromal cell migration, and potentiates osteogenic differentiation and matrix formation in vitro. Taken together, metabolites—here particularly succinate—are shown to play central roles as signaling molecules during the onset of healing and in steering bone tissue regeneration.
Host-driven temperature dependence of Deformed wing virus infection in honey bee pupae
Authors: Palmer-Young Evan C. , Ryabov Eugene V. , Markowitz Lindsey M. , Boncristiani Dawn L. , Grubbs Kyle , Pawar Asha , Peterson Raymond , Evans Jay D.
Published: March 2023

The temperature dependence of infection reflects changes in performance of parasites and hosts. High temperatures often mitigate infection by favoring heat-tolerant hosts over heat-sensitive parasites. Honey bees exhibit endothermic thermoregulation—rare among insects—that can favor resistance to parasites. However, viruses are heavily host-dependent, suggesting that viral infection could be supported—not threatened—by optimum host function. To understand how temperature-driven changes in performance of viruses and hosts shape infection, we compared the temperature dependence of isolated viral enzyme activity, three honey bee traits, and infection of honey bee pupae. Viral enzyme activity varied <2-fold over a > 30 °C interval spanning temperatures typical of ectothermic insects and honey bees. In contrast, honey bee performance peaked at high (≥ 35 °C) temperatures and was highly temperature-sensitive. Although these results suggested that increasing temperature would favor hosts over viruses, the temperature dependence of pupal infection matched that of pupal development, falling only near pupae’s upper thermal limits. Our results reflect the host-dependent nature of viruses, suggesting that infection is accelerated—not curtailed—by optimum host function, contradicting predictions based on relative performance of parasites and hosts, and suggesting tradeoffs between infection resistance and host survival that limit the viability of bee ‘fever’.
Interspecies interaction reduces selection for antibiotic resistance in Escherichia coli
Authors: Nair Ramith R. , Andersson Dan I.
Published: March 2023

Evolution of microbial traits depends on the interaction of a species with its environment as well as with other coinhabiting species. However, our understanding of the evolution of specific microbial traits, such as antibiotic resistance in complex environments is limited. Here, we determine the role of interspecies interactions on the dynamics of nitrofurantoin (NIT) resistance selection among Escherichia coli. We created a synthetic two-species community comprised of two variants of E. coli (NIT susceptible and resistant) and Bacillus subtilis in minimal media with glucose as the sole carbon source. We show that the presence of B. subtilis significantly slows down the selection for the resistant E. coli mutant when NIT is present and that this slowdown is not due to competition for resources. Instead, the dampening of NIT resistance enrichment is largely mediated by extracellular compounds produced by B. subtilis with the peptide YydF playing a significant role. Our results not only demonstrate the impact of interspecies interactions on the evolution of microbial traits but also show the importance of using synthetic microbial systems in unravelling relevant interactions and mechanisms affecting the evolution of antibiotic resistance. This finding implies that interspecies interactions should be considered to better understand and predict resistance evolution in the clinic as well as in nature.
Rising water-use efficiency in European grasslands is driven by increased primary production
Authors: Poppe Terán Christian , Naz Bibi S. , Graf Alexander , Qu Yuquan , Hendricks Franssen Harrie-Jan , Baatz Roland , Ciais Phillipe , Vereecken Harry
Published: March 2023

Water-use efficiency is the amount of carbon assimilated per water used by an ecosystem and a key indicator of ecosystem functioning, but its variability in response to climate change and droughts is not thoroughly understood. Here, we investigated trends, drought response and drivers of three water-use efficiency indices from 1995–2018 in Europe with remote sensing data that considered long-term environmental effects. We show that inherent water-use efficiency decreased by −4.2% in Central Europe, exhibiting threatened ecosystem functioning. In European grasslands it increased by +24.2%, by regulated transpiration and increased carbon assimilation. Further, we highlight modulation of water-use efficiency drought response by hydro-climate and the importance of adaptive canopy conductance on ecosystem function. Our results imply that decoupling carbon assimilation from canopy conductance and efficient water management strategies could make the difference between threatened and well-coping ecosystems with ongoing climate change, and provide important insights for land surface model development.
Linking prokaryotic genome size variation to metabolic potential and environment
Authors: Rodríguez-Gijón Alejandro , Buck Moritz , Andersson Anders F , Izabel-Shen Dandan , Nascimento Francisco J A , Garcia Sarahi L
Published: March 2023

While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
Fundamentals of MOF Mechanics & Structure–Mechanical Property Relationships
Authors: Tan Jin-Chong
Published: March 2023

The first chapter addresses the basic mechanical properties of metal-organic framework (MOFs). The Young’s modulus, hardness, mechanical anisotropy, interfacial adhesion, and fracture toughness of MOF crystals, monoliths, thin films and membranes are presented. Furthermore, the discussion is extended to encompass the terahertz framework dynamics, soft modes, and shear deformation mechanisms omnipresent in MOFs that control framework functions and could mechanically destabilise the structure. Ashby-style materials selection charts are constructed employing the latest data, unravelling the trends and vast opportunities in the field of MOF mechanics.
Computational Modelling of MOF Mechanics: From Elastic Behaviour to Phase Transformations
Authors: Rogge Sven M. J.
Published: March 2023

This chapter critically reviews the computational tools for the in silico modelling of MOF mechanics from the atomic level onwards. To this end, the macroscopic properties describing the mechanical behaviour of these materials – such as stress and strain – are formulated in terms of atomistic information that can be readily extracted from quantum mechanical or classical computer simulations. This immediately reveals the fundamental challenges that arise when attempting to computationally predict the wide array of responses which MOFs exhibit under mechanical stimuli. The different techniques to extract the mechanical behaviour of MOFs near equilibrium – especially the elastic constants – are contrasted with one another through representative literature examples. While these elastic constants capture the response of a material to small mechanical stimuli, different approaches are required to computationally predict how MOFs respond to larger stresses. A distinction is made between those techniques suitable to describe single-crystal-to-single-crystal phase transitions on the one hand, and those applicable to describe single-crystal-to-amorphous phase transitions, a field that currently remains in its infancy, on the other hand. Through various illustrations from literature, this chapter highlights the open questions arising in each of these topics and explores how ongoing research aims to tackle these challenges.
An Introduction to Motility-induced Phase Separation
Authors: O'Byrne Jérémy , Solon Alexandre , Tailleur Julien , Zhao Yongfeng
Published: March 2023

Active particles may undergo phase separation when interactions oppose self-propulsion, in the absence of any cohesive forces. The corresponding Motility-Induced Phase Separation (MIPS) is arguably the simplest non-trivial collective feature that distinguishes active from passive particles. It is observed in a large variety of systems which we review in this chapter. We describe in depth the case of motile particles interacting via quorum-sensing interactions, whose theoretical framework is by now well-established. We close the chapter by discussing the features observed in systems undergoing MIPS that still challenge our understanding.
Motility and Self-propulsion of Active Droplets
Authors: Carenza L. N. , Gonnella G. , Negro G.
Published: March 2023

In the last few years, self-motile droplets have attracted the attention of scientists from different fields ranging from applied biology to theoretical physics, because of their promising technological applications and important biological implications. In this chapter we review the state of the art of the research on active droplets with a particular focus on theoretical and numerical studies. In particular, we review the active gel theory, namely a generalization of the standard Landau–de Gennes theory for liquid crystals adapted to take into account internal active injection due to the presence of self-motile constituents. When confined in finite geometries, liquid crystalline-like systems are also subject to topological constraints. Because of the relevance of topology in many different realizations of active droplets, we also reviewed some fundamental topological concepts. We review how motility arises in different realizations of active droplet both in 2D and 3D as the result of the breaking of specific symmetries, by looking in particular detail at the case of polar and nematic droplets and shells of active liquid crystal.
Computational Physics of Active Matter
Authors: Sabass Benedikt , Winkler Roland G. , Auth Thorsten , Elgeti Jens , Fedosov Dmitry A. , Ripoll Marisol , Vliegenthart Gerard A. , Gompper Gerhard
Published: March 2023

From cytoskeletal macromolecules and micron-sized bacteria to giant fish swarms, active-matter systems occur on all scales throughout nature. These systems are internally driven out of equilibrium and therefore allow for the emergence of a plethora of complex phenomena that are essential for life. In this chapter, we illustrate the unique power of computer simulations to provide a quantitative understanding of active matter. First, basic active-matter model systems are described, including biological and synthetic self-propelled objects, where the driving mechanism is modeled on different levels of abstraction. Second, focusing on bacterial motion, we will discuss the role of hydrodynamic interactions for collective swimming and the role of activity for the rheology of dense bacterial colonies. Third, we will provide examples of active agents that are coupled together by interacting with deformable manifolds such as filaments and membranes. This leads to diverse non-equilibrium shapes, deformations, and motility modes. Finally, some results of simulations of active gels, multicellular growing structures and artificial phoretic swimmers are shown, illustrating the extraordinary diversity of computational active-matter systems.