bluuebunny/crossref_metadata_2025_split huggingface dataset:
Telomere-to-telomere genome assembly of melon (Cucumis melo L. var. inodorus) provides a high-quality reference for meta-QTL analysis of important traits
Authors: Wei Minghua , Huang Ying , Mo Changjuan , Wang Haiyan , Zeng Qingguo , Yang Wenli , Chen Jihao , Zhang Xuejun , Kong Qiusheng 
Published: September 2023

Abstract
Melon is an important horticultural crop with extensive diversity in many horticultural groups. To explore its genomic diversity, it is necessary to assemble more high-quality complete genomes from different melon accessions. Meanwhile, a large number of QTLs have been mapped in several studies. Integration of the published QTLs onto a complete genome can provide more accurate information for candidate gene cloning. To address these problems, a telomere-to-telomere (T2T) genome of the elite melon landrace Kuizilikjiz (Cucumis melo L. var. inodorus) was de novo assembled and all the published QTLs were projected onto it in this study. The results showed that a high-quality Kuizilikjiz genome with the size of 379.2 Mb and N50 of 31.7 Mb was de novo assembled using the combination of short reads, PacBio high-fidelity long reads, Hi-C data, and a high-density genetic map. Each chromosome contained the centromere and telomeres at both ends. A large number of structural variations were observed between Kuizilikjiz and the other published genomes. A total of 1294 QTLs published in 67 studies were collected and projected onto the T2T genome. Several clustered, co-localized, and overlapped QTLs were determined. Furthermore, 20 stable meta-QTLs were identified, which significantly reduced the mapping intervals of the initial QTLs and greatly facilitated identification of the candidate genes. Collectively, the T2T genome assembly together with the numerous projected QTLs will not only broaden the high-quality genome resources but also provide valuable and abundant QTL information for cloning the genes controlling important traits in melon.
Designing of future ornamental crops: a biotechnological driven perspective
Authors: Partap Mahinder , Verma Vipasha , Thakur Meenakshi , Bhargava Bhavya 
Published: September 2023

Abstract
With a basis in human appreciation of beauty and aesthetic values, the new era of ornamental crops is based on implementing innovative technologies and transforming symbols into tangible assets. Recent advances in plant biotechnology have attracted considerable scientific and industrial interest, particularly in terms of modifying desired plant traits and developing future ornamental crops. By utilizing omics approaches, genomic data, genetic engineering, and gene editing tools, scientists have successively explored the underlying molecular mechanism and potential gene(s) behind trait regulation such as floral induction, plant architecture, stress resistance, plasticity, adaptation, and phytoremediation in ornamental crop species. These signs of progress lay a theoretical and practical foundation for designing and enhancing the efficiency of ornamental plants for a wide range of applications. In this review, we briefly summarized the existing literature and advances in biotechnological approaches for the improvement of vital traits in ornamental plants. The future ornamental plants, such as light-emitting plants, biotic/abiotic stress detectors, and pollution abatement, and the introduction of new ornamental varieties via domestication of wild species are also discussed.
Some Unipotent Arthur Packets for Reductive p-adic Groups
Authors: Ciubotaru Dan , Mason-Brown Lucas , Okada Emile 
Published: September 2023

Abstract
Let ${\textsf k}$ be a $p$-adic field, and let $\textbf {G}({\textsf k})$ be the ${\textsf k}$-points of a connected reductive group, inner to split. The set of Aubert–Zelevinsky duals of the constituents of a tempered L-packet forms an Arthur packet for $\textbf {G}({\textsf k})$. In this paper, we give an alternative characterization of such Arthur packets in terms of the wavefront set, proving in some instances a conjecture of Jiang–Liu and Shahidi. Pursuing an analogy with real and complex groups, we define some special unions of Arthur packets, which we call weak Arthur packets and describe their constituents in terms of their Langlands parameters.
Understanding Organisms Using Ecological Observatory Networks
Authors: Dantzer B , Mabry K E , Bernhardt J R , Cox R M , Francis C D , Ghalambor C K , Hoke K L , Jha S , Ketterson E , Levis N A , McCain K M , Patricelli G L , Paull S H , Pinter-Wollman N , Safran R J , Schwartz T S , Throop H L , Zaman L , Martin L B 
Published: September 2023

Synopsis
Human activities are rapidly changing ecosystems around the world. These changes have widespread implications for the preservation of biodiversity, agricultural productivity, prevalence of zoonotic diseases, and sociopolitical conflict. To understand and improve the predictive capacity for these and other biological phenomena, some scientists are now relying on observatory networks, which are often composed of systems of sensors, teams of field researchers, and databases of abiotic and biotic measurements across multiple temporal and spatial scales. One well-known example is NEON, the US-based National Ecological Observatory Network. Although NEON and similar networks have informed studies of population, community, and ecosystem ecology for years, they have been minimally used by organismal biologists. NEON provides organismal biologists, in particular those interested in NEON's focal taxa, with an unprecedented opportunity to study phenomena such as range expansions, disease epidemics, invasive species colonization, macrophysiology, and other biological processes that fundamentally involve organismal variation. Here, we use NEON as an exemplar of the promise of observatory networks for understanding the causes and consequences of morphological, behavioral, molecular, and physiological variation among individual organisms.
Gravitation search-based hybrid algorithm for solving inverse kinematics of an n-link redundant manipulator
Authors: S A R Sheik Masthan , Kanagaraj G , Yu Vincent F 
Published: September 2023

Abstract
Inverse kinematics is one of the most complicated problems in robotics. The inverse kinematics calculation is the basis for any industrial robot’s ability to plan and follow a trajectory. This paper proposes a hybrid algorithm, e3GSA, based on the gravitational search algorithm (GSA) for solving the inverse kinematics problem of an n-link redundant robot manipulator. The algorithm’s efficiency was evaluated using a fitness function comprising of position error, orientation error, and collision error, and it was found to perform better than the conventional GSA in simulations. A generalized framework was proposed and tested by simulating a 6-, 8-, and 12-link robot manipulators. Experimental validation is carried out using a 6-link robot manipulator, which shows that the simulation data are on par with the experimental data. The proposed algorithm was also found to perform adaptively with faster convergence rates and lesser computation time, making it a better choice for other engineering problems that can be transformed into optimization problems.
Reference genome of the bicolored carpenter ant, Camponotus vicinus
Authors: Ward Philip S , Cash Elizabeth I , Ferger Kailey , Escalona Merly , Sahasrabudhe Ruta , Miller Courtney , Toffelmier Erin , Fairbairn Colin , Seligmann William , Shaffer H Bradley , Tsutsui Neil D 
Published: September 2023

Abstract
Carpenter ants in the genus Camponotus are large, conspicuous ants that are abundant and ecologically influential in many terrestrial ecosystems. The bicolored carpenter ant, Camponotus vicinus Mayr, is distributed across a wide range of elevations and latitudes in western North America, where it is a prominent scavenger and predator. Here, we present a high-quality genome assembly of C. vicinus from a sample collected in Sonoma County, California, near the type locality of the species. This genome assembly consists of 38 scaffolds spanning 302.74 Mb, with contig N50 of 15.9 Mb, scaffold N50 of 19.9 Mb, and BUSCO completeness of 99.2%. This genome sequence will be a valuable resource for exploring the evolutionary ecology of C. vicinus and carpenter ants generally. It also provides an important tool for clarifying cryptic diversity within the C. vicinus species complex, a genetically diverse set of populations, some of which are quite localized and of conservation interest.
Agenesis of flexor pollicis longus without thenar hypoplasia: a case report and literature review
Authors: Alwatari Mohammed , Khalaf Ahmed , Alghannami Mohammed , Alwattary Maryam 
Published: September 2023

Abstract
We present a case of congenital of flexor pollicis longus agenesis without thenar hypoplasia in a 12-year-old girl with no history of trauma. Two-staged corrective surgery was planned. In the first stage, the flexor pulley was reconstructed using silicone followed by the second stage 3 months later when flexor pollicis longus reconstruction was performed using tendon transfer of the flexor digitorum superficialis. The patient completed post-operative physiotherapy and the result of the surgical treatment in both functional and cosmetic aspects was, in the authors’ opinion, excellent.
Evolution of the Mutation Spectrum Across a Mammalian Phylogeny
Authors: Beichman Annabel C , Robinson Jacqueline , Lin Meixi , Moreno-Estrada Andrés , Nigenda-Morales Sergio , Harris Kelley 
Published: September 2023

Abstract
Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species’ 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
Solar eclipses observed worldwide in the first half of the 15th century and ΔT determined from multiply observed eclipses
Authors: Tanikawa Kiyotaka , Sôma Mitsuru , Simmonds Ockie , Iwahashi Kiyomi 
Published: September 2023

Abstract
The main purpose of the present paper is to list all the solar eclipses which took place in the first half of the 15th century, to list all the available records of observation of these eclipses, and, by using the multiply observed or contemporaneously observed solar eclipses, to determine ΔT for a few periods of the first half of the 15th century. We make the table using solar eclipse records from East Asia (China, Korea, and Japan), India, West Asia, and Europe, though the table is not perfect because the compilation of records is not complete in some of the relevant areas. We evaluate the reliability of the Chinese records of solar eclipses. The Chinese official history book, the Mingshi, records visible eclipses, while it does not record invisible eclipses. A simple analysis shows that the reliability of the book is $97\%$. The marginally observable eclipses in China are useful for us to determine ΔT. We briefly consider the Māori eclipse observed in 1409. We extract the multiply observed eclipses and check whether these are useful for determining the value of ΔT. Finally, with newly added records of solar eclipses, we re-determine the value range of ΔT during the years 1431–1433 (see Tanikawa et al. 2019, in Proc. 5th Symposium on Historical Astronomical Records and Modern Science), and add a new ΔT in the year 1445.
Reproducible Quantitative Trait Loci for Resistance to Soft Rot Caused by Dickeya dianthicola Derived from the Wild Potato Solanum microdontum (PI 458355) Are Located on Chromosomes 1, 3, and 5
Authors: Fenstemaker Sean , Ma Xing , Bamberg John , Swingle Bryan 
Published: September 2023

The potato wild relative Solanum microdontum is a breeder-friendly source of genetic resistance to soft rot. Our objectives were to (i) identify loci associated with soft rot resistance in S. microdontum germplasm and (ii) develop bi-parental populations in a self-compatible S. tuberosum genetic background to recover segregating F2 progenies, construct a linkage map, and identify quantitative trait loci (QTLs). Under objective (i), tubers from 103 S. microdontum genotypes from the United States Potato Genebank were inoculated with a high virulence strain of Dickeya dianthicola, and lesion size was measured after a 24-h incubation period at 30°C. Association analysis using 3,490 polymorphic Infinium array SNP markers identified soft rot resistance loci on chromosomes 1, 2, 3, 5, 7, 8, 11, and 12. Under objective (ii), a resistant S. microdontum accession PI 458355 was crossed with a highly fertile, self-compatible, diploid S. tuberosum pollen parent (PI 654351) to generate segregating F2 populations. Composite interval mapping was conducted using a genetic linkage map with 970 GBS-based SNP markers. Reproducible QTLs were detected on chromosomes 1, 3, and 5, explaining 11, 13, and 23% of the phenotypic variation, respectively. Homozygous S. microdontum alleles at the QTL on chromosome 5 and heterozygous or homozygous S. microdontum alleles at QTLs on chromosomes 1 and 3 significantly decrease lesion size compared with the homozygous S. tuberosum parent. The germplasm created in these studies provides a resource for studying traits from S. microdontum, and we can use the advanced F2 selections for future potato improvement. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato
Authors: Adhikari Tika B. , Olukolu Bode A. , Paudel Rajan , Pandey Anju , Halterman Dennis , Louws Frank J. 
Published: September 2023

Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. ( A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.
Dead or Alive, that Is the Question: Development and Assessment of Molecular Synchytrium endobioticum Viability Tests
Authors: van de Vossenberg Bart T. L. H. , Smith Donna S. , van Gent-Pelzer Marga P. E. , van den Berg Marlies , Govaert Marcel , Helderman Carin M. , van der Lee Theo A. J. 
Published: September 2023

Potato wart disease caused by the obligate biotrophic fungus Synchytrium endobioticum is a devastating disease that can result in significant crop losses. Resting spores of this pathogen can remain viable and infectious in soil for decades. The detection of viable resting spores using conventional methods such as bioassays and direct microscopic examination are challenging and time-consuming and require specific expertise and facilities. Molecular methods, such as real-time PCR, have been shown to be effective in detecting the presence of S. endobioticum DNA in soil samples but cannot differentiate between viable and nonviable spores. In this paper, we present three novel mRNA-based molecular tests to potentially detect viable S. endobioticum resting spores. The tests are specific to the transcribed mRNA and do not detect the genomic DNA of the target genes. We demonstrate the analytical sensitivity using synthetic constructs of the target mRNAs. The tests were found to be able to repeatedly detect 10 target copies per reaction. Soils and waste of potato processing industries free from S. endobioticum were used to assess the exclusivity of the tests. The biological relevance of mRNA detection was determined in the context of replicated bioassays. Applications of the tests to facilitate collection management, assessment of the effects of treatments on presumed viability of S. endobioticum resting spores, and the potential use in descheduling of previously infested plots are discussed. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Achilles tendon disorders
Authors: Patch David A. , Andrews Nicholas A. , Scheinberg Mila , Jacobs Roshan A. , Harrelson Whitt M. , Rallapalle Vyshnavi , Sinha Tanvee , Shah Ashish 
Published: September 2023

ABSTRACT
Achilles tendon-related pain affects up to 6% of the US population during their lifetime and is commonly encountered by primary care providers. An accurate diagnosis and early conservative management can improve patient quality of life and reduce unnecessary surgical consultations, saving healthcare dollars. Achilles tendon pathologies can be categorized into acute (pain lasting less than 6 weeks), chronic (pain lasting more than 6 weeks), and acute on chronic (worsening of pain with preexisting chronic Achilles tendon pathology). This article describes the diagnosis, conservative management, indications for imaging, and indications for surgical referral for acute and chronic Achilles tendon rupture, Achilles tendinitis, gastrocnemius strain, plantaris rupture, insertional Achilles tendinopathy, Haglund deformity, and noninsertional Achilles tendinopathy.
Eye of the Carpenter: How Well do Orthopaedic Surgeons Estimate Angular Measurements in Derotational Osteotomies?
Authors: Chaclas Nathan , Dyer Olivia , Mayers Alexander , Wheatley Benjamin , Grandizio Louis C. , Seeley Mark 
Published: September 2023

Background:
Femoral derotational osteotomies are used by orthopaedic surgeons to decrease version in a variety of pathologies. Intraoperatively, the goal of the surgery is to decrease the rotation of the femur to within physiological range. Surgeons generally visually estimate the angle of correction based on bone markers at the rotating cylindrical portion of the femur. This study sought first to assess the accuracy and inter-rater reliability of surgeons with respect to angle creation, and then to implement a training intervention.

Methods:
A rotational femur model was constructed and tested among surgeons and nonsurgeons. Surgeons were then randomized into an experimental and control cohort with training on the model as the intervention. Subjects were asked to create target angles of 15, 30, 45, and 60 degrees using only Kirschner wires and then only bone marks for reference. Independent and paired t-tests were performed to determine variability between cohorts.

Results:
The mean angle creation error and range of the surgeon cohort were significantly lower than those of the nonsurgeon cohort. Within the nonsurgeon cohort, the mean angle creation error and range of the wire modality were significantly lower than that of the mark modality. The mean angle creation error and range of the trained cohort were significantly lower than the untrained cohort.

Conclusions:
The considerable inter-subject range within the surgeon cohort highlights a need for the reinforcement of basic geometric principles within orthopaedic instruction. This model allows for immediate, accurate feedback on angle creation, and training appears to be both time and cost-effective. The physiological range allows for a level of variability between surgical outcomes without consequence. However, the more than 20 degree range determined by this study does not fall within those bounds and should be addressed.

Clinical Relevance:
Moving forward, rotational estimation as a surgical skill should increase in prominence within orthopaedic instruction to maximize future joint health, and additional emphasis should be placed on fundamental spatial orientation during training.