bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity
Authors: Prasad Bodhayan , Bjourson Anthony J , Shukla Priyank
Published: October 2022

Multimorbidity generally refers to concurrent occurrence of multiple chronic conditions. These patients are inherently at high risk and often lead a poor quality of life due to delayed treatments. With the emergence of personalized medicine and stratified healthcare, there is a need to stratify patients right at the primary care setting. Here we developed multimorbidity analysis pipeline (MulMorPip), which can stratify patients into multimorbid subgroups or endotypes based on their lifetime disease diagnosis and characterize them based on demographic features and underlying disease–disease interaction networks. By implementing MulMorPip on UK Biobank cohort, we report five distinct molecular subclasses or endotypes of multimorbidity. For each patient, we calculated the existence of broad disease classes defined by Charlson's comorbidity classification using the International Classification of Diseases-10 encoding. We then applied multiple correspondence analysis in 77 524 patients from UK Biobank, who had multimorbidity of more than one disease, which resulted in five multimorbid clusters. We further validated these clusters using machine learning and were able to classify 20% model-blind test set patients with an accuracy of 97% and an average Jaccard similarity of 84%. This was followed by demographic characterization and development of interlinking disease network for each cluster to understand disease–disease interactions. Our identified five endotypes of multimorbidity draw attention to dementia, stroke and paralysis as important drivers of multimorbidity stratification. Inclusion of such patient stratification at the primary care setting can help general practitioners to better observe patients’ multiple chronic conditions, their risk stratification and personalization of treatment strategies.
NetTDP: permutation-based true discovery proportions for differential co-expression network analysis
Authors: Cai Menglan , Vesely Anna , Chen Xu , Li Limin , Goeman Jelle J
Published: October 2022

Existing methods for differential network analysis could only infer whether two networks of interest have differences between two groups of samples, but could not quantify and localize network differences. In this work, a novel method, permutation-based Network True Discovery Proportions (NetTDP), is proposed to quantify the number of edges (correlations) or nodes (genes) for which the co-expression networks are different. In the NetTDP method, we propose an edge-level statistic and a node-level statistic, and detect true discoveries of edges and nodes in the sense of differential co-expression network, respectively, by the permutation-based sumSome method. Furthermore, the NetTDP method could further localize the differences by inferring the TDPs for edge or gene subsets of interest, which can be selected post hoc. Our NetTDP method allows inference on data-driven modules or biology-driven gene sets, and remains valid even when these sub-networks are optimized using the same data. Experimental results on both simulation data sets and five real data sets show the effectiveness of the proposed method in inferring the quantification and localization of differential co-expression networks. The R code is available at https://github.com/LiminLi-xjtu/NetTDP.
PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
Authors: Ji Jiahui , Anwar Maryam , Petretto Enrico , Emanueli Costanza , Srivastava Prashant Kumar
Published: October 2022

Motivation

Single-cell/nuclei RNA-sequencing (scRNA-seq) technologies can simultaneously quantify gene expression in thousands of cells across the genome. However, the majority of the noncoding RNAs, such as microRNAs (miRNAs), cannot currently be profiled at the same scale. MiRNAs are a class of small noncoding RNAs and play an important role in gene regulation. MiRNAs originate from the processing of primary transcripts, known as primary-microRNAs (pri-miRNAs). The pri-miRNA transcripts, independent of their cognate miRNAs, can also function as long noncoding RNAs, code for micropeptides or even interact with DNA, acting like enhancers. Therefore, it is apparent that the significance of scRNA-seq pri-miRNA profiling expands beyond using pri-miRNA as proxies of mature miRNAs. However, there are no computational methods that allow profiling and quantification of pri-miRNAs at the single-cell-type resolution.

Results

We have developed a simple yet effective computational framework to profile pri-MiRNAs from single-cell RNA-sequencing datasets (PPMS). Based on user input, PPMS can profile pri-miRNAs at cell-type resolution. PPMS can be applied to both newly produced and publicly available datasets obtained via single cell or single-nuclei RNA-seq. It allows users to (i) investigate the distribution of pri-miRNAs across cell types and cell states and (ii) establish a relationship between the number of cells/reads sequenced and the detection of pri-miRNAs. Here, to demonstrate its efficacy, we have applied PPMS to publicly available scRNA-seq data generated from (i) individual chambers (ventricles and atria) of the human heart, (ii) human pluripotent stem cells during their differentiation into cardiomyocytes (the heart beating cells) and (iii) hiPSCs-derived cardiomyocytes infected with severe acute respiratory syndrome coronavirus 2.
PLEX in AAV-GN: insights from the meta-analysis results and impact on remission induction treatment recommendations
Authors: Casal Moura Marta , Crowson Cynthia S , Specks Ulrich , Warrington Kenneth J , Zand Ladan , Sethi Sanjeev , Fervenza Fernando C
Published: October 2022

The risk of progression to end-stage kidney disease (ESKD) in patients with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) and glomerulonephritis (AAV-GN) remains high. At 5 years of follow-up, 14–25% of patients will evolve to ESKD, suggesting that kidney survival is not optimized in patients with AAV. The addition of plasma exchange (PLEX) to standard remission induction has been the standard of care, particularly in patients with severe renal disease. However, there is still some debate regarding which patients benefit from PLEX.

A recently published meta-analysis concluded that the addition of PLEX to standard remission induction in AAV probably reduced the risk of ESKD at 12 months and that PLEX was associated with an estimated absolute risk reduction for ESKD at 12 months of 16.0% for those at high risk or with a serum creatinine >5.7 mg/dl (high certainty of important effects). These findings were interpreted as supportive of offering PLEX to patients with AAV and a high risk of progression to ESKD or requiring dialysis and are making their way into societies recommendations.

However, the results of the analysis can be debated. We provide an overview on the meta-analysis as an attempt to guide the audience through how the data were generated, to comment on our interpretation of the results and to explain why we feel uncertainty remains. In addition, we would like to provide insights in two questions that we believe are very relevant to consider when addressing the role of PLEX: the role of kidney biopsy findings in the decision making of whom might benefit from PLEX and the impact of novel treatments (i.e. complement factor 5a inhibitors) in avoiding progression to ESKD at 12 months. The treatment of patients with severe AAV-GN is complex and further studies that include only patients at high risk of progression to ESKD are needed.
Antithrombotic therapy following revascularization for chronic limb-threatening ischaemia: a European survey from the ESC Working Group on Aorta and Peripheral Vascular Diseases
Authors: De Carlo Marco , Schlager Oliver , Mazzolai Lucia , Brodmann Marianne , Espinola-Klein Christine , Staub Daniel , Aboyans Victor , Sillesen Henrik , Debus Sebastian , Venermo Maarit , Belch Jill , Ferrari Mauro , De Caterina Raffaele
Published: October 2022

Aims

Chronic limb-threatening ischaemia (CLTI) entails dismal outcomes and is an absolute indication to lower extremity revascularization (LER) whenever possible. Antithrombotic therapy is here crucial, but available evidence on best strategies (choice of drugs, combinations, duration) is scarce. We conducted a European internet-based survey on physicians’ use of antithrombotic therapy after revascularization for CLTI, under the aegis of the ESC Working Group on Aorta and Peripheral Vascular Disease in collaboration with other European scientific societies involved in CLTI management and agreeing to send the survey to their affiliates.

Methods and results

225 respondents completed the questionnaire. Antithrombotic therapy following surgical/endovascular LER varies widely across countries and specialties, with dedicated protocols reported only by a minority (36%) of respondents. Dual antiplatelet therapy with aspirin and clopidogrel is the preferred choice for surgical (37%) and endovascular (79%) LER. Dual pathway inhibition (DPI) with aspirin and low-dose rivaroxaban is prescribed by 16% of respondents and is tightly related to the availability of reimbursement (OR 6.88; 95% CI 2.60–18.25) and to the choice of clinicians rather than of physicians performing revascularization (OR 2.69; 95% CI 1.10–6.58). A ≥ 6 months-duration of an intense (two-drug) postprocedural antithrombotic regimen is more common among surgeons than among medical specialists (OR 2.08; 95% CI 1.10–3.94). Bleeding risk assessment is not standardised and likely underestimated.

Conclusion

Current antithrombotic therapy of CLTI patients undergoing LER remains largely discretional, and prescription of DPI is related to reimbursement policies. An individualised assessment of thrombotic and bleeding risks is largely missing.
A big (male) fish in a small pond? The gendered effect of relative ability on STEM aspirations under stereotype threat
Authors: Kim Jinho , Liu Ran , Zhao Xiaohang
Published: October 2022

Despite gender similarity in math ability, studies show persistent gender differences in STEM aspirations among adolescents. Extending previous literature on student math ability, biased self-assessment, and gender stereotypes, this paper emphasizes on the important process of social comparison in producing gender disparities in STEM aspirations. In particular, we examine the crucial role of relative ability, or a student’s ordinal ability rank within their peer group, and its interaction with the gender-math stereotypical environment. Using unique information on random classroom assignments from the China Educational Panel Survey (CEPS), we are able to exploit idiosyncratic variation in classmate composition to identify the effect of ability rank on student STEM aspirations and the moderating role of student exposure to gender-math stereotype. We show that after controlling for absolute cognitive ability, the effect of a student’s ability rank on STEM aspirations differs by gender, with girls benefiting less relative to boys from a higher ability rank in class. Moreover, this gender difference in the effect of ability rank on STEM aspirations is larger among students who are exposed to a higher level of gender-math stereotype from classmates. We discuss the theoretical and empirical implications of our findings.
Who benefits from school-to-work linkages in the labour market? A comparison between natives, migrants educated abroad, and those educated domestically
Authors: Geven Sara , Spörlein Christoph
Published: October 2022

Recent research suggests that people with more occupation-specific qualifications (i.e. qualifications that link to a smaller set of occupations) experience greater benefits in the labour market. Based on human capital, signalling and credentialing theory, we argue that these benefits may vary between the native majority population, individuals with a migration background who hold a foreign qualification, and individuals with a migration background with a domestic qualification. Using data from the German Microcensus, we find that for both the native majority and immigrants with a domestic qualification, holding a more occupation-specific qualification relates to a higher chance of working in a position the individual is educated for in terms of both level and field. Holding a more occupation-specific qualification also relates to higher labour market returns (i.e. income and occupational status) for those who work in a job for which they are educated, yet is mostly negatively related to the labour market returns for those who do not work in a job for which they are educated. Migrants with a foreign qualification profit less from holding occupation-specific qualifications and suffer more from their associated disadvantages.
Double standards? Co-authorship and gender bias in early-stage academic evaluations
Authors: Gërxhani Klarita , Kulic Nevena , Liechti Fabienne
Published: October 2022

This article studies gender bias in early-stage academic evaluations in Italy and investigates whether this bias depends on various types of authorship in collaborative work across three academic fields: humanities, economics, and social sciences. We test our hypotheses via a factorial survey (vignette) experiment on a sample from the entire population of associate and full professors employed at Italian public universities in 2019. This is one of the few experiments conducted with university professors to consider hiring propensities in academia. Contrary to our general expectations, we do not find gender bias in relation to co-authorship in our general population of interest. However, the results provide some evidence that when the evaluator is a man, highly collaborative women academics in Italy receive less favourable evaluations of their qualifications compared to male colleagues with identical credentials. This gender bias is found in economics, a field where the conventions of co-authorship allow for greater uncertainty about individual contributions to a joint publication.
Evaluation of student engagement through knowledge elaboration and the use of comics in Microbiology education
Authors: da Silva Vincent Rosa , Vieira Mônica Larucci
Published: October 2022

Despite the many challenges faced by the sudden adaptation of the teaching–learning processes during the emergency remote teaching (ERT) imposed by the COVID-19 pandemic, this period allowed the exploration of innovative educational methods. Here, we report the description and evaluation of a didactic activity designed to foster an active learning environment among Veterinary Medicine undergraduate students enrolling in Microbiology classes during the ERT period at the University of Minas Gerais. The activity consisted of initial expositive classes, followed by students’ active search for information, and the execution of a report and short comics covering the topic. The activity was evaluated by a voluntary postquestionnaire. The results suggest that the students had good emotional and educational perception toward the task, and that they noticed the elaboration of the comics as the most valuable tool aiding in the retention of microbiological concepts. We conclude that the proposed strategy, specially by the incorporation of the comics, helped the meaningful learning of microbiology.
Inflammatory bowel disease-associated adherent-invasive Escherichia coli have elevated host-defense peptide resistance
Authors: Cho Youn Hee , Renouf Michael J , Omotoso Oluwafikemi , McPhee Joseph B
Published: October 2022

Adherent-invasive Escherichia coli (AIEC) are isolated from inflammatory bowel disease (IBD) patients at a higher rate than from control patients. Using a collection of E. coli strains collected from Crohn's disease (CD), ulcerative colitis (UC), or non-IBD control patients, antibiotic and resistance to the antimicrobial peptides HBD-3 and LL-37 was assessed. Carriage of bacterial-encoded omptin protease genes was assessed by PCR and omptin protease activity was measured using a whole-cell based fluorescence assay. Elevated resistance to antibiotics and host defense peptides in IBD-associated AIEC were observed. IBD-associated strains showed increased (but statistically non-significant) antibiotic resistance. CD-associated strains showed greater (but statistically non-significant) resistance to HBD3-mediated killing while UC-associated strains showed statistically greater resistance to LL-37 mediated killing. High-level resistance to LL-37 was associated with carriage of omptin protease genes and with increased omptin protease activity. Antimicrobial host defense peptide resistance may be an adaptive feature of AIEC leading to enhanced pathogenesis during the initiation or progression of IBD.
Geriatric Frailty Is Associated With Oxidative Stress, Accumulation, and Defective Repair of DNA Double-Strand Breaks Independently of Age and Comorbidities
Authors: Kravvariti Evrydiki , Ntouros Panagiotis A , Vlachogiannis Nikolaos I , Pappa Maria , Souliotis Vassilis L , Sfikakis Petros P
Published: October 2022

Defects in the DNA damage response and repair (DDR/R) network accumulate during the aging process. Physical frailty, a state of reduced physiological function and decreased resilience to biological stressors, is also exacerbated by aging, but its link with DDR/R aberrations beyond the effect of age and comorbidities is unclear. Fifty-three community-dwelling older adults, aged 65–102 years, who underwent frailty classification according to the Rockwood Clinical Frailty Scale (CFS), and 51 healthy adults younger than 45 years were examined in parallel. The following DDR/R parameters were determined in their peripheral blood mononuclear cells (PBMCs): (a) oxidative stress and abasic (apurinic/apyrimidinic; AP) sites, (b) endogenous DNA damage (alkaline comet assay olive tail moment [OTM] indicative of DNA single-strand breaks [SSBs] and double-strand breaks [DSBs] and γH2AX levels by immunofluorescence [DSBs only]), (c) capacity of the 2 main DNA repair mechanisms (DSB repair and nucleotide excision repair). Older individual-derived PBMCs displayed reduced-to-oxidized glutathione ratios indicative of increased levels of oxidative stress and increased AP sites, as well as increased accumulation of endogenous DNA damage (OTM and γH2AX) and defective DSB-repair capacity, compared with younger controls. These DDR/R aberrations were more pronounced in frail versus nonfrail older adults. Notably, oxidative stress, AP sites, DSBs, and DSB-repair capacity were associated with individual CFS levels after adjusting for chronological age, sex, Charlson Comorbidity Index, and polypharmacy. Geriatric frailty is independently associated with increased DNA damage formation and reduced DSB-R capacity, supporting further research into these measures as potential frailty biomarkers.
Crustal and uppermost mantle structure beneath Tristan da Cunha using surface wave phase velocity from horizontal components OBS ambient seismic noise
Authors: Zhang Hao , Geissler Wolfram H , Schmidt-Aursch Mechita C , Bonadio Raffaele
Published: October 2022

We applied ambient noise tomography on data from an ocean bottom seismometer (OBS) experiment around Tristan da Cunha in the South Atlantic, in order to determine the crust and uppermost mantle shear velocity structure beneath this region. The determination of the orientation of the horizontal seismometer components allowed to perform ambient noise cross-correlation with all three components of 19 broad-band OBSs and two land stations. We extracted the phase velocity dispersion curves from the first higher mode Rayleigh waves and fundamental mode Love waves at periods of 3–8 s, which were only observed in the radial and transverse components, respectively. Following the two-steps inversion of surface wave tomography, we finally obtained a 3-D shear velocity model around Tristan da Cunha. Our results concur with previous studies in this region. The 3-D shear velocity model documents that there is a shallow conduit of low shear velocity underneath the volcanic archipelago, extending to at least ∼25 km depth. This conduit in the lithosphere may represent the magmatic plumbing system. We also observe indications for low shear velocities in the uppermost mantle beneath the seamounts in the southwest of the island, in an area where the deeper Tristan mantle plume is assumed.
Breaking with convention? Zeitenwende and the traditional pillars of German foreign policy
Authors: Blumenau Bernhard
Published: October 2022

On 27 February 2022, German Chancellor Olaf Scholz addressed the Bundestag and announced a watershed moment (Zeitenwende) for Germany's conduct of foreign affairs. Against the backdrop of the historical pillars of German foreign policy, this article reviews the core implications of the Zeitenwende doctrine. It analyses how the new policy continued or transformed traditional notions underpinning Germany's external relations: Westbindung (integration into the West) and European integration, multilateralism, the pursuit of a rules-based international order and NATO membership, hesitant leadership, Ostpolitik and Wandel durch Handel (transformation through trade), as well as a foreign policy not relying on military means. It argues that Zeitenwende represented a break with some traditional notions, such as Ostpolitik and Wandel durch Handel, and to some extent the non-military foreign policy. However, Zeitenwende also reconfirmed other traditions: Westbindung, a commitment to multilateralism and the rules-based order, as well as the reluctance to assert German leadership. With Zeitenwende, Germany remained firmly committed to the EU and NATO as the country acknowledged that it must do more for its own, and for Europe's, security. Zeitenwende represented Germany's coming to terms with, and final acceptance of, the realities of the post-Cold War European order.
Offensive ideas: structural realism, classical realism and Putin's war on Ukraine
Authors: Edinger Harald
Published: October 2022

Controversy has surrounded realist explanations of the causes of Russia's war against Ukraine, particularly John Mearsheimer's charge of western responsibility. This article seeks to clarify and contextualize his argument, situating it within the broader paradigm. Realism, and even its narrower offensive sub-school, offers a wide range of contrasting interpretations, depending on which major actors are studied and what characteristics they are endowed with. Like its classical predecessor, structural realism is premised on implicit views of human nature. In an effort to explicate some of these assumptions about the behavioural micro-foundations of states and their leaders, the article investigates main components of structural theory—including power differentials, ‘rational’ interests and states as unitary actors—and connects these concepts to base emotions like fear and anger. It argues that realists do well to differentiate between the aspirations of states and individual leaders' quest for power and status. In the same vein, reference to Russian security concerns may be emblematic of elites' perceived challenges of cultural subordination, and Putin's personal fears for the stability of his regime. Engagement with realist thought is essential, in part because of its continuing influence on policy-making (particularly in Russia) and in order to forestall improper co-option of caricaturized versions of realist arguments.
From revolution and terrorism to revolutionary terrorism: the case of militant Salafism
Authors: Dixon Matthew , Lawson George
Published: October 2022

What is the relationship between revolution and terrorism? Much of the time, terrorism and revolution are taken to be distinct forms of political contention. This article argues that, to the contrary, their relationship is much closer than is often imagined. We show that a range of contemporary terrorist groups contain revolutionary elements: they seek to capture and hold territory, and see themselves as part of movements where the goal is to transform international as well as domestic orders. This provides two points of distinction: first, between ‘order-maintaining’ and ‘order-transforming’ goals; and second, between ‘minimalist’ and ‘maximalist’ tactics. The result is a taxonomy of different types of ‘revolutionary terrorism’. This analytic is used to dig deeper into the parameters of revolutionary terrorism, using militant Salafism as an example of a maximalist, order-transforming movement. A focus on transnational, order-transforming revolutionary terrorism generates a range of insights into the violent strategies, international dynamics and organizational forms used by Islamic State, al-Qaeda and related groups. The resulting research agenda, the article concludes, is rich in possibilities.
Twisted-fin parametric study to enhance the solidification performance of phase-change material in a shell-and-tube latent heat thermal energy storage system
Authors: Bo Liu , Mahdi Jasim M , Rahbari Alireza , Majdi Hasan Sh , Xin Yi , Yaïci Wahiba , Talebizadehsardari Pouyan
Published: October 2022

Phase change material (PCM) is considered as one of the most effective thermal energy storage (TES) systems to balance energy supply and demand. A key challenge in designing efficient PCM-based TES systems lies in the enhancement of heat transmission during phase transition. This study numerically examines the privilege of employing twisted-fin arrays inside a shell-and-tube latent heat storage unit to improve the solidification performance. The presence of twisted fins contributes to the dominating role of heat conduction by their curved shapes, which restricts the role of natural convection but largely aids the overall heat-transfer process during solidification. The heat-discharge rate of twisted-fin configuration is increased by ∼14 and ∼55% compared to straight fin and no fin configurations—leading to a reduction in the solidification duration by ∼13 and ∼35%, respectively. The solidification front at various times has also been assessed through a detailed parametric study over the fin height, fin pitch number, and fin thickness. Over the range of values assumed, the fin height is the most dominant parameter – increasing the heat-retrieval rate from 10.0 to 11.4 W and decreasing the discharge time from above 3600 to 2880 s by varying the fin height from 2.5 to 7.5 mm.
Using Red Panel Traps to Detect Spotted-Wing Drosophila and its Infestation in US Berry and Cherry Crops
Authors: Panthi Babu , Cloonan Kevin R , Rodriguez-Saona Cesar , Short Brent D , Kirkpatrick Danielle M , Loeb Gregory M , Aflitto Nicholas C , Wiman Nik , Andrews Heather , Drummond Frank A , Fanning Philip D , Ballman Elissa , Johnson Benjamin , Beal Dylan J , Beers Elizabeth H , Burrack Hannah J , Isaacs Rufus , Perkins Jacquelyn , Liburd Oscar E , Lambert Arden R , Walton Vaughn M , Harris Edwin T , Mermer Serhan , Polk Dean , Wallingford Anna K , Adhikari Rosan , Sial Ashfaq A
Published: October 2022

Spotted-wing drosophila (SWD), Drosophila suzukii Matsumura (Diptera: Drosophilidae), is an invasive pest of thin-skinned fruits in the United States. Monitoring traps are an integral part of SWD integrated pest management, allowing early detection and timely management of this pest. An ideal monitoring trap should be easy to use, effective in capturing SWD, sensitive and selective to male SWD which are easy to identify due to their spotted wings, and able to predict fruit infestation from trap captures. Deli-cup-based liquid traps (grower standard), which make in-situ observations difficult, were compared with red-panel sticky traps, both baited with commercial lures (Scentry, Trécé Broad-Spectrum (BS), and Trécé High-Specificity (HS)), across several US states in blueberries (lowbush and highbush), blackberry, raspberry, and cherry crops during 2018 and 2021. Results showed that red-panel traps effectively captured SWD, were able to detect male SWD early in the season while also being selective to male SWD all season-long, and in some cases linearly related male SWD trap captures with fruit infestation. Scentry and Trécé BS lures captured similar numbers of SWD, though Trécé BS and Trécé HS were more selective for male SWD in red panel traps than liquid traps in some cases. In conclusion, due to its ease of use with less processing time, red-panel traps are promising tools for detecting and identifying male SWD in-situ and for predicting fruit infestation. However, further research is needed to refine the trap captures and fruit infestation relationship and elucidate the trap-lure interactions in berry and cherry crops.
Characterization and Phylogenetic Implication of Complete Mitochondrial Genome of the Medicinal Ant Formica sinae (Hymenoptera: Formicidae): Genomic Comparisons in Formicidae
Authors: Zhang Xin-Min , Li Ting , Liu Xia , Xu Zheng-Hui
Published: October 2022

Ants (Hymenoptera: Formicidae) are among the largest and most widespread families of terrestrial insects and are valuable to medical and ecological investigations. The mitochondrial genome has been widely used as a reliable genetic marker for species identification and phylogenetic analyses. To further understand the mitogenome-level characteristics of the congeneric Formicidae species, the complete mitogenome of Formica sinae (Hymenoptera: Formicidae) was sequenced, annotated, and compared with other 48 Formicidae species. The results showed that gene composition, content, and codon usage were conserved. The complete mitochondrial genome of F. sinae was 17,432 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region located between rrnS and trnM, which was 1,256 bp long, the longest of all sequenced species. Gene rearrangement was not detected in Formica species (Hymenoptera: Formicidae). All PCGs of F. sinae were initiated with ATN codons and terminated with the TAA codon. The overall nucleotide composition of F. sinae was AT-biased (83.51%), being 80.58% in PCGs, 86.68% in tRNAs, 87.10% in rRNAs, and 88.70% in the control region. Phylogenetic analyses indicated that each subfamily formed a strongly monophyletic group. Furthermore, F. sinae clustered with Formica fusca (Hymenoptera: Formicidae) and Formica selysi (Hymenoptera: Formicidae). This work enhances the genetic data of Formicidae and contributes to our understanding of their phylogenic relationship, evolution, and utilization.
sconce: a cosmic web finder for spherical and conic geometries
Authors: Zhang Yikun , de Souza Rafael S , Chen Yen-Chi
Published: October 2022

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called sconce (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (scms) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard scms method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as sconce-scms and has been made publicly available.
Ocean dynamics and tracer transport over the south pole geysers of Enceladus
Authors: Kang Wanying , Marshall John , Mittal Tushar , Bire Suyash
Published: October 2022

Over the south pole of Enceladus, an icy moon of Saturn, geysers eject water into space in a striped pattern, making Enceladus one of the most attractive destinations in the search for extraterrestrial life. We explore the ocean dynamics and tracer/heat transport associated with geysers as a function of the assumed salinity of the ocean and various core-shell heat partitions and bottom heating patterns. We find that, even if heating is concentrated into a narrow band on the seafloor directly beneath the south pole, the warm fluid becomes quickly mixed with its surroundings due to baroclinic instability. The warming signal beneath the ice is diffuse and insufficient to prevent the geyser from freezing over. Instead, if heating is assumed to be local to the geyser (either generated in the ice due to tidal dissipation or friction or generated in the ocean as water flushes in/out of the geyser slot under tidal forcing), geyser can be sustained. In this case, the upper ocean beneath the ice becomes stably stratified creating a barrier to vertical communication, leading to transit time-scales from the core to the ice shell of hundreds of years in contrast to purported transit time-scales of weeks to months.
A Comparison of Granite Genesis in the Adelaide Fold Belt and Glenelg River Complex Using U–Pb, Hf and O Isotopes in Zircon
Authors: Turner Simon , Ireland Trevor , Foden John , Belousova Elena , Wörner Gerhard , Keeman Jelte
Published: October 2022

We present new U–Pb ages and Hf and O isotope data for zircon from I-, S- and A-type granites from both the western and eastern edges of the Delamerian Orogen in southeastern Australia. The I-type Tanunda Creek Gneiss contains zircon populations of 507 ± 4 and 492 ± 6 Ma inferred to reflect igneous and metamorphic ages, respectively. The I-type Palmer Granite yielded an age of 509 ± 3 Ma, and the Port Elliot S-type Granite has a magmatic age of 508 ± 7 Ma. Inherited zircon in these granites range from 1092 to 3343 Ma, probably derived from assimilation of Adelaide Group sediments. The Murray Bridge A-type Granite is 490 ± 2 Ma in age and lacks inherited zircon. In the Glenelg River Complex, an S-type migmatite from near Harrow contains a complex zircon population. It is most likely ~500 Ma in age and has inherited zircon of 550–700, 1000–1100 and 2437 Ma, hence matching those from the Kanmantoo Group. From this and detrital zircon ages, we infer that only the Kanmantoo Group extends across the Murray Basin into the Glenelg River Complex. The Wando Tonalite and Loftus Creek I-type granites yielded ages of 501 ± 2 and 486 ± 3 Ma, respectively. Zircon from the Dergholm Granite has suffered Pb loss, and the best age estimate for this granite is 488 ± 5 Ma. Combining all the granite data together, εHft and δ18O in the magmatic zircon range from 5.6 to −10.3 and from 5.8 to 8.1, respectively, and are well correlated. The zircon indicates the same temporal and compositional evolution of granitic petrogenesis across ~300 km of strike, reaffirming the notion that these terranes form part of the same orogen. Westward-directed subduction caused orogenic thickening, heating and increasing amounts of crustal contribution. This was followed by convective thinning of the thickened mantle lithosphere and a return to more primitive magmas lacking significant crustal contributions. It contrasts significantly with inferred granite petrogenesis and tectonic style in the younger Lachlan and New England Fold Belts further east that were not built upon extended cratonic lithosphere.
Leaf habit determines the hydraulic and resource-use strategies in tree saplings from the Sonoran Desert
Authors: González-Rebeles Georgina , Méndez-Alonzo Rodrigo , Paz Horacio , Terrazas Teresa , Tinoco-Ojanguren Clara
Published: October 2022

The drought susceptibility of woody saplings may explain their low survival in arid environments. Therefore, it is critical to determine which morphological and physiological traits are more responsive to drought among young plants. This study tested whether plant responses to experimental drought differ between two plant functional groups: the deciduous and evergreen species. We predicted that deciduous species would present a tighter stomatal control under drought, coupled with fast carbon fixation under no stress, tending toward isohydry and faster growth rates than the evergreen species. Using 1-year-old saplings from three evergreen and four deciduous Sonoran Desert tree species, we evaluated their hydraulic and gas exchange traits under three experimental irrigation conditions: high, intermediate and low water availability. We measured CO2 assimilation rates (A), stomatal conductance (gs), the level of iso-anisohydry (as the plant’s ability to maintain constant their water potential) and seven morphological and growth-related traits throughout 2 months. Under high water availability, saplings reached their maximum values of A and gs, which were significantly higher for deciduous than evergreen species. Correlations among hydroscape area (HA) and leaf traits positioned species along the iso/anisohydric continuum. Deciduous species presented isohydric characteristics, including low HA, high gs, A and Huber values (HVs), and traits indicative of a faster use of resources, such as low stem-specific density (SSD) and low leaf mass per area (LMA). By contrast, evergreen species showed traits that indicate slow resource use and anisohydric behavior, such as high HA, SSD and LMA, and low gs, A and HVs. Deciduous species drastically reduced gas exchange rates in response to drought, while evergreen maintained low rates independently of drought intensity. Overall, desert saplings showed strategies concordant with the iso-anisohydric continuum and the fast–slow use of resources.
Host root exudates initiate a foraging preference by the root parasite Santalum album
Authors: Li Zhenshuang , Meng Sen , Qin Fangcuo , Wang Shengkun , Liang Junfeng , He Xinhua , Lu Junkun
Published: October 2022

Haustoria of root-parasitic plants draw nutrients from the roots of host species. While recent studies have assessed host preferences of parasitic plants, how root-exuded chemicals can mediate host tropism and selection by root-parasitic plants is poorly understood. Under greenhouse conditions, we performed two pot experiments to determine whether the root parasite Santalum album selectively forages for superior hosts (N2-fixing Acacia confusa Merr. or Dalbergia odorifera T. Chen) rather than for inferior hosts (non-N2-fixing Bischofia polycarpa (levl.) Airy Shaw or Dracontomelon duperreranum Pierre), and whether S. album uses host root exudates and/or specific chemicals in these root exudates to locate and trigger haustorium formation. Lateral roots and haustoria of S. album seedlings exhibited greater growth in the direction of D. odorifera roots than toward roots from the other three hosts. Comparative metabolic analysis revealed that D. odorifera root exudates were enriched in isoflavonoid, flavonoid and flavone/flavonol biosynthesis pathways, and that the relative contents of flavonoids were significantly greater in the root exudates of D. odorifera than in those of the other three hosts. Root exudates from D. odorifera significantly promoted S. album root growth, haustorium formation and reactive oxygen species accumulation in haustoria. Our results demonstrate that the key step in plant parasitism by S. album is based on root exudation by a host plant; the exudates function as a metabolite signal that activate lateral root growth and haustorium formation. Our results also indicate that flavonoids in the root exudates could play an important role in S. album foraging activity. Information on the responses of root parasites to host root exudates and/or haustorium-inducing chemicals may be useful for selecting superior host species to plant with valuable species of root parasites.
Novel insights on genes and pathways involved in Pinus elliottii response to resinosis
Authors: Zhang Guoyun , Zhang Xu , Yu Sujun , Sun Honggang
Published: October 2022

Pinus elliottii, an important coniferous timber species, has recently become one of the most popular sources of resin in China. Resinosis is a common disease that may negatively affect pine tree growth and production. In this study, we used single-molecule real-time sequencing and Illumina RNA sequencing to generate an accurate transcriptome for P. elliottii. The transcriptome included 90,026 transcripts, 5160 long non-coding RNAs and 7710 transcription factors. We then analyzed RNA-sequencing, small RNA-sequencing and degradome data to identify genes, miRNAs and key miRNA–target pairs involved in response to resinosis in P. elliottii. We identified 1305 genes and 1151 miRNAs exhibiting significant differential expression in response to resinosis. According to the degradome sequencing analysis, 318 differentially expressed transcripts were targets of 14 differentially expressed miRNAs. Our study has provided resources for further functional characterization of genes and miRNAs involved in resinosis in P. elliottii, which should aid the future disease-resistance breeding of this species.
Stem hydraulic conductivity and embolism resistance ofQuercusspecies are associated with their climatic niche
Authors: Guan Xinyi , Wen Yin , Zhang Ya , Chen Zhao , Cao Kun-Fang
Published: October 2022

The hydraulic traits of a plant species may reflect its climate adaptations. Southwest China is considered as a biodiversity hotpot of the genus Quercus (oak). However, the hydraulic adaptations of Asian oaks to their climate niches remain unclear.

Ten common garden-grown oak species with distinct natural distributions in eastern Asia were used to determine their stem xylem embolism resistance (water potential at 50% loss of hydraulic conductivity, P50), stem hydraulic efficiency (vessel anatomy and sapwood specific hydraulic conductivity (Ks)) and leaf anatomical traits. We also compiled four key functional traits: wood density, hydraulic-weighted vessel diameter, Ks and P50 data for 31 oak species from previous literature. We analyzed the relationship between hydraulic traits and climatic factors over the native ranges of 41 oak species.

Our results revealed that the 10 Asian oak species, which are mainly distributed in humid subtropical habitats, possessed a stem xylem with low embolism resistance and moderate hydraulic efficiency. The deciduous and evergreen species of the 10 Asian oaks differed in the stem and leaf traits related to hydraulic efficiency. Ks differed significantly between the two phenological groups (deciduous and evergreens) in the 41-oak dataset. No significant difference in P50 between the two groups was found for the 10 Asian oaks or the 41-oak dataset. The oak species that can distribute in arid habitats possessed a stem xylem with high embolism resistance. Ks negatively related to the humidity of the native range of the 10 Asian oaks, but showed no trend when assessing the entire global oak dataset.

Our study suggests that stem hydraulic conductivity and embolism resistance in Quercus species are shaped by their climate niche. Our findings assist predictions of oak drought resistance with future climate changes for oak forest management.
Application of synthetic biology in bladder cancer
Authors: Ding Mengting , Lin Jiaxing , Qin Caipeng , Wei Ping , Tian Jiahe , Lin Tianxin , Xu Tao
Published: October 2022

Bladder cancer (BC) is the most common malignant tumor of the genitourinary system. The age of individuals diagnosed with BC tends to decrease in recent years. A variety of standard therapeutic options are available for the clinical management of BC, but limitations exist. It is difficult to surgically eliminate small lesions, while radiation and chemotherapy damage normal tissues, leading to severe side effects. Therefore, new approaches are required to improve the efficacy and specificity of BC treatment. Synthetic biology is a field emerging in the last decade that refers to biological elements, devices, and materials that are artificially synthesized according to users’ needs. In this review, we discuss how to utilize genetic elements to regulate BC-related gene expression periodically and quantitatively to inhibit the initiation and progression of BC. In addition, the design and construction of gene circuits to distinguish cancer cells from normal cells to kill the former but spare the latter are elaborated. Then, we introduce the development of genetically modified T cells for targeted attacks on BC. Finally, synthetic nanomaterials specializing in detecting and killing BC cells are detailed. This review aims to describe the innovative details of the clinical diagnosis and treatment of BC from the perspective of synthetic biology.
Enlargement of main corneal incision: clinical intraindividual comparison of two preloaded intraocular lens injectors
Authors: Khoramnia Ramin , Baur Isabella D. , Łabuz Grzegorz , Chychko Lizaveta , Köppe Maximilian K. , Hallak Mustafa K. , Auffarth Gerd U.
Published: October 2022

Purpose:

To compare the enlargement of the clear corneal incision from IOL implantation with 2 different intraocular lens (IOL) injectors: the AutonoMe preloaded with the Clareon IOL and the Multisert preloaded with the Vivinex IOL.

Setting:

The David J. Apple Center for Vision Research, Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany.

Design:

Prospective randomized clinical comparative study.

Methods:

96 eyes of 48 patients with cataract were intraindividually randomized to treatment with 1 of the 2 injectors. For Multisert eyes, the insert shield (IS) was used in the advanced position in 23 eyes. The initial incision was 2.2 mm, and intraoperative measurements of the incision size were made before and after IOL injection. 3 months postoperatively, keratometry and uncorrected (UDVA) and corrected (CDVA) distance visual acuities were assessed.

Results:

Results are reported for 96 eyes of 48 patients. The mean incision enlargement was 0.213 ± 0.068 mm in the Multisert with the IS group, 0.265 ± 0.055 mm in the fellow eyes (AutonoMe) (P < .05), 0.272 ± 0.060 mm in Multisert eyes treated without the IS, and 0.296 ± 0.066 mm for the fellow eyes (AutonoMe) (P > .05). The mean absolute surgically induced astigmatism was 0.42 ± 0.23 diopters (D), 0.50 ± 0.25 D, and 0.44 ± 0.18 D in the Multisert with the IS, Multisert without the IS, and AutonoMe group, respectively (P > .05). The UDVA and CDVA were comparable in all groups.

Conclusions:

The Multisert was associated with less wound enlargement than the AutonoMe. All groups had comparable functional outcomes. Therefore, the observed difference in incision enlargement may be of limited clinical relevance.
Negative refraction and mode trapping of flexural–torsional waves in elastic lattices
Authors: Madine K. H. , Colquitt D. J.
Published: October 2022

We consider the propagation of flexural and torsional waves in a square lattice of Euler–Bernoulli beams. The refraction and reflection of waves across interfaces between two dissimilar lattices is investigated. By carefully controlling the inertial and elastic properties of the lattice elements, we demonstrate that it is possible to induce negative refraction and other associated phenomena. These effects are shown to be broadband and are facilitated by the unprecedented control over wave propagation afforded by the interaction between torsional and flexural waves and the additional freedom associated with the applied forcing. Closed-form analytical findings are accompanied by numerical simulations, which demonstrate negative refraction, unidirectional reflection and mode trapping.

This article is part of the theme issue ‘Wave generation and transmission in multi-scale complex media and structured metamaterials (part 2)’.