bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

ABSTRACT
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

ABSTRACT
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

AbstractThe 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

Abstract
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)’.
An overview of elastic waveguides with dynamic sub-structures
Authors: Slepyan Leonid , Movchan Alexander B. 
Published: October 2022

The dynamic response of elastic waveguides is important for a wide range of applications that involve dispersive waves as well as wave localization. In particular, a case of special interest relates to waveguides subjected to moving loads. In the case where the elongated structure includes a sequence of built-in resonators, the range of resonance regimes may be extended accordingly. The present paper gives an overview of several mathematical formulations that connect Floquet theory to the dynamic response of multi-scale waveguides, which include inertial sub-structures subjected to external forces.This article is part of the theme issue ‘Wave generation and transmission in multi-scale complex media and structured metamaterials (part 2)’.
Asymptotics of the meta-atom: plane wave scattering by a single Helmholtz resonator
Authors: Smith M. J. A. , Cotterill P. A. , Nigro D. , Parnell W. J. , Abrahams I. D. 
Published: October 2022

Using a combination of multipole methods and the method of matched asymptotic expansions, we present a solution procedure for acoustic plane wave scattering by a single Helmholtz resonator in two dimensions. Closed-form representations for the multipole scattering coefficients of the resonator are derived, valid at low frequencies, with three fundamental configurations examined in detail: the thin-walled, moderately thick-walled and extremely thick-walled limits. Additionally, we examine the impact of dissipation for extremely thick-walled resonators, and also numerically evaluate the scattering, absorption and extinction cross-sections (efficiencies) for representative resonators in all three wall thickness regimes. In general, we observe strong enhancement in both the scattered fields and cross-sections at the Helmholtz resonance frequencies. As expected, dissipation is shown to shift the resonance frequency, reduce the amplitude of the field, and reduce the extinction efficiency at the fundamental Helmholtz resonance. Finally, we confirm results in the literature on Willis-like coupling effects for this resonator design, and connect these findings to earlier works by several of the authors on two-dimensional arrays of resonators, deducing that depolarizability effects (off-diagonal terms) for a single resonator do not ensure the existence of Willis coupling effects (bianisotropy) in bulk.
This article is part of the theme issue ‘Wave generation and transmission in multi-scale complex media and structured metamaterials (part 2)’.
Asymptotic analysis of in-plane dynamic problems for elastic media with rigid clusters of small inclusions
Authors: Nieves Michael J. , Movchan Alexander B. 
Published: October 2022

We present formal asymptotic approximations of fields representing the in-plane dynamic response of elastic solids containing clusters of closely interacting small rigid inclusions. For finite densely perforated bodies, the asymptotic scheme is developed to approximate the eigenfrequencies and the associated eigenmodes of the elastic medium with clamped boundaries. The asymptotic algorithm is also adapted to address the scattering of in-plane waves in infinite elastic media containing dense clusters. The results are accompanied by numerical simulations that illustrate the accuracy of the asymptotic approach.
This article is part of the theme issue ‘Wave generation and transmission in multi-scale complex media and structured metamaterials (part 2)’.