bluuebunny/crossref_metadata_2025_split huggingface dataset:
Doxycycline is a viable alternative to tetracycline for use in insect Tet-Off transgenic sexing systems, as assessed in the blowflies Cochliomyia hominivorax and Lucilia cuprina (Diptera: Calliphoridae)
Authors: Arp Alex P , Williamson Megan E , Vasquez Mario , Quintero Gladys , Vargas Lowman Aidamalia , Sagel Agustin , Scott Maxwell J 
Published: February 2024

Abstract
Transgenic insect strains with tetracycline repressible (Tet-Off) female-lethal genes provide significant advantages over traditional sterile insect techniques for insect population control, such as reduced diet and labor costs and more efficient population suppression. Tet-Off systems are suppressed by tetracycline-class antibiotics, most commonly tetracycline (Tc) or doxycycline (Dox), allowing for equal sex ratio colonies of transgenic insects when reared with Tc or Dox and male-only generations in their absence. Dox is a more stable molecule and has increased uptake than Tc, which could be advantageous in some insect mass-rearing systems. Here, we evaluated the suitability of Dox for rearing Tet-Off female-lethal strains of Australian sheep blowfly, Lucilia cuprina (Wiedemann, 1830) (Diptera: Calliphoridae), and New World screwworm, Cochliomyia hominivorax (Coquerel, 1858) (Diptera: Calliphoridae), and the effects of dosage on strain performance. For both species, colonies were able to be maintained with mixed-sex ratios at much lower dosages of Dox than Tc. Biological yields of C. hominivorax on either antibiotic were not significantly different. Reduction of Dox dosages in C. hominivorax diet did not affect biological performance, though rearing with 10 or 25 μg/mL was more productive than 50 μg/mL. Additionally, C. hominivorax mating performance and longevity were equal on all Dox dosages. Overall, Dox was a suitable antibiotic for mass-rearing Tet-Off female-lethal L. cuprina and C. hominivorax and was functional at much lower dosages than Tc.
A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia)
Authors: Tsai Whitney L E , Escalona Merly , Garrett Kimball L , Terrill Ryan S , Sahasrabudhe Ruta , Nguyen Oanh , Beraut Eric , Seligmann William , Fairbairn Colin W , Harrigan Ryan J , McCormack John E , Alfaro Michael E , Smith Thomas B , Bay Rachael A 
Published: February 2024

Abstract
The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California’s riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.
Multi-tissue transcriptome-wide association studies identified 235 genes for intrinsic subtypes of breast cancer
Authors: Li James L , McClellan Julian C , Zhang Haoyu , Gao Guimin , Huo Dezheng 
Published: February 2024

Abstract

Background
Although genome-wide association studies (GWAS) of breast cancer (BC) identified common variants which differ between intrinsic subtypes, genes through which these variants act to impact BC risk have not been fully established. Transcriptome-wide association studies (TWAS) have identified genes associated with overall BC risk, but subtype-specific differences are largely unknown.

Methods
We performed two multi-tissue TWAS for each BC intrinsic subtype, including an expression-based approach that collated TWAS signals from expression quantitative trait loci (eQTLs) across multiple tissues and a novel splicing-based approach that collated signals from splicing QTLs (sQTLs) across intron clusters and subsequently across tissues. We used summary statistics for five intrinsic subtypes including Luminal A-like, Luminal B-like, Luminal B/HER2-negative-like, HER2-enriched-like, and triple-negative BC, generated from 106 278 BC cases and 91 477 controls in the Breast Cancer Association Consortium.

Results
Overall, we identified 235 genes in 88 loci that were associated with at least one of the five intrinsic subtypes. Most genes were subtype-specific, and many have not been reported in previous TWAS. We discovered common variants that modulate expression of CHEK2 confer increased risk to Luminal A-like BC, in contrast to the viewpoint that CHEK2 primarily harbors rare, penetrant mutations. Additionally, our splicing-based TWAS provided population-level support for MDM4 splice variants that increased the risk of triple-negative BC.

Conclusion
Our comprehensive, multi-tissue TWAS corroborated previous GWAS loci for overall BC risk and intrinsic subtypes, while underscoring how common variation that impacts expression and splicing of genes in multiple tissue types can be used to further elucidate the etiology of BC.
(Mal)adaptive sibling self and other communicative resilience in the context of parental substance use
Authors: Nolan-Cody Haley , Scharp Kristina M 
Published: February 2024

Abstract
Managing parental substance use disorder (SUD) within the family context is a collaborative effort. For families with multiple children, the sibling relationship might be one source of support for dealing with this stressor. Findings from a sample of adult siblings with parents with SUD highlighted that they (a) experience five resilience triggers, (b) utilize self and other communicative resilience (CR) processes, and (c) experience a tensional process in which CR can be both adaptive, maladaptive, and simultaneously both. Overall, we advance the communication theory of resilience by (a) being the first to apply the other-resilience heuristic, (b) exploring relationships between self-resilience and other-resilience, (c) introducing a new CR tension, and (d) discussing the potential benefit of engaging in what we call strategic resilience. By analyzing the resilience processes of adult siblings experiencing parental SUD, we also recommend practical applications for social workers, providers, and counselors.
Non-foliar photosynthesis and nitrogen assimilation influence grain yield in durum wheat regardless of water conditions
Authors: Vicente Rubén , Vergara-Díaz Omar , Uberegui Estefanía , Martínez-Peña Raquel , Morcuende Rosa , Kefauver Shawn C , López-Cristoffanini Camilo , Aparicio Nieves , Serret María Dolores , Araus José Luis 
Published: February 2024

Abstract
There is a need to generate improved crop varieties adapted to the ongoing changes in the climate. We studied durum wheat canopy and central metabolism of six different photosynthetic organs in two yield-contrasting varieties. The aim was to understand the mechanisms associated with the water stress response and yield performance. Water stress strongly reduced grain yield, plant biomass, and leaf photosynthesis, and down-regulated C/N-metabolism genes and key protein levels, which occurred mainly in leaf blades. By contrast, higher yield was associated with high ear dry weight and lower biomass and ears per area, highlighting the advantage of reduced tillering and the consequent improvement in sink strength, which promoted C/N metabolism at the whole plant level. An improved C metabolism in blades and ear bracts and N assimilation in all photosynthetic organs facilitated C/N remobilization to the grain and promoted yield. Therefore, we propose that further yield gains in Mediterranean conditions could be achieved by considering the source–sink dynamics and the contribution of non-foliar organs, and particularly N assimilation and remobilization during the late growth stages. We highlight the power of linking phenotyping with plant metabolism to identify novel traits at the whole plant level to support breeding programmes.
The maternal embrace: the protection of plant embryos
Authors: Woudenberg Sjoerd , Hadid Feras , Weijers Dolf , Borassi Cecilia 
Published: February 2024

Abstract
All land plants—the embryophytes—produce multicellular embryos, as do other multicellular organisms, such as brown algae and animals. A unique characteristic of plant embryos is their immobile and confined nature. Their embedding in maternal tissues may offer protection from the environment, but also physically constrains development. Across the different land plants, a huge discrepancy is present between their reproductive structures whilst leading to similarly complex embryos. Therefore, we review the roles that maternal tissues play in the control of embryogenesis across land plants. These nurturing, constraining, and protective roles include both direct and indirect effects. In this review, we explore how the maternal surroundings affect embryogenesis and which chemical and mechanical barriers are in place. We regard these questions through the lens of evolution, and identify key questions for future research.
Excessive iron deposition in root apoplast is involved in growth arrest of roots in response to low pH
Authors: Fang Xian Zhi , Xu Xiao Lan , Ye Zheng Qian , Liu Dan , Zhao Ke Li , Li Dong Ming , Liu Xing Xing , Jin Chong Wei 
Published: February 2024

Abstract
The rhizotoxicity of protons (H+) in acidic soils is a fundamental constraint that results in serious yield losses. However, the mechanisms underlying H+-mediated inhibition of root growth are poorly understood. In this study, we revealed that H+-induced root growth inhibition in Arabidopsis depends considerably on excessive iron deposition in the root apoplast. Reducing such aberrant iron deposition by decreasing the iron supply or disrupting the ferroxidases LOW PHOSPHATE ROOT 1 (LPR) and LPR2 attenuates the inhibitory effect of H+ on primary root growth efficiently. Further analysis showed that excessive iron deposition triggers a burst of highly reactive oxygen species, consequently impairing normal root development. Our study uncovered a valuable strategy for improving the ability of plants to tolerate H+ toxicity by manipulating iron availability.
Rapid polarization variations in the O4 supergiant ζ Puppis
Authors: Bailey Jeremy , Howarth Ian D , Cotton Daniel V , Kedziora-Chudczer Lucyna , De Horta Ain , Martell Sarah L , Eldridge Colin , Luckas Paul 
Published: February 2024

ABSTRACT
We present time-series linear-polarization observations of the bright O4 supergiant ζ Puppis. The star is found to show polarization variation on time-scales of around an hour and longer. Many of the observations were obtained contemporaneously with Transiting Exoplanet Survey Satellite (TESS) photometry. We find that the polarization varies on similar time-scales to those seen in the TESS light curve. The previously reported 1.78-d photometric periodicity is seen in both the TESS and polarization data. The amplitude ratio of photometry to polarization is ∼9 for the periodic component and the polarization variation is oriented along position angle ∼70°–160°. Higher frequency stochastic variability is also seen in both data sets with an amplitude ratio of ∼19 and no preferred direction. We model the polarization expected for a rotating star with bright photospheric spots and find that models that fit the photometric variation produce too little polarization variation to explain the observations. We suggest that the variable polarization is more likely the result of scattering from the wind, with corotating interaction regions producing the periodic variation and a clumpy outflow producing the stochastic component. The Hα emission line strength was seen to increase by 10 per cent in 2021 with subsequent observations showing a return to the pre-2018 level.
An extreme ultra-compact X-ray binary in a globular cluster: multiwavelength observations of RZ 2109 explored in a triple system framework
Authors: Dage Kristen C , Bahramian Arash , Naoz Smadar , Bobrick Alexey , Athukoralalage Wasundara , Brumback McKinley C , Haggard Daryl , Kundu Arunav , Zepf Stephen E 
Published: February 2024

ABSTRACT
The globular cluster ultraluminous X-ray source, RZ 2109, is a complex and unique system that has been detected at X-ray, ultraviolet, and optical wavelengths. Based on almost 20 yr of Chandra and XMM–Newton observations, the X-ray luminosity exhibits order of magnitude variability, with the peak flux lasting on the order of a few hours. We perform robust time series analysis on the archival X-ray observations and find that this variability is periodic on a time-scale of 1.3 ± 0.04 d. The source also demonstrates broad [O iii] λ5007 emission, which has been observed since 2004, suggesting a white dwarf donor and therefore an ultra-compact X-ray binary. We present new spectra from 2020 and 2022, marking 18 yr of observed [O iii] emission from this source. Meanwhile, we find that the globular cluster counterpart is unusually bright in the NUV/UVW2 band. Finally, we discuss RZ 2109 in the context of the eccentric Kozai–Lidov mechanism and show that the observed 1.3 d periodicity can be used to place constraints on the tertiary configuration, ranging from 20 min (for a 0.1 M⊙ companion) to approximately 95 min (for a 1 M⊙ companion), if the eccentric Kozai–Lidov mechanism is at the origin of the periodic variability.
Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect
Authors: Ma Li-Jun , Cao Li-Jun , Chen Jin-Cui , Tang Meng-Qing , Song Wei , Yang Fang-Yuan , Shen Xiu-Jing , Ren Ya-Jing , Yang Qiong , Li Hu , Hoffmann Ary Anthony , Wei Shu-Jun 
Published: February 2024

Abstract
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.
How snoRNAs can contribute to cancer at multiple levels
Authors: Zacchini Federico , Barozzi Chiara , Venturi Giulia , Montanaro Lorenzo 
Published: February 2024

Abstract
snoRNAs are a class of non-coding RNAs known to guide site specifically RNA modifications such as 2′-O-methylation and pseudouridylation. Recent results regarding snoRNA alterations in cancer has been made available and suggest their potential evaluation as diagnostic and prognostic biomarkers. A large part of these data, however, was not consistently confirmed and failed to provide mechanistic insights on the contribution of altered snoRNA expression to the neoplastic process. Here, we aim to critically review the available literature on snoRNA in cancer focusing on the studies elucidating the functional consequences of their deregulation. Beyond the canonical guide function in RNA processing and modification we also considered additional roles in which snoRNA, in various forms and through different modalities, are involved and that have been recently reported.
SAMHD1 expression contributes to doxorubicin resistance and predicts survival outcomes in diffuse large B-cell lymphoma patients
Authors: Daddacha Waaqo , Monroe Dominique , Schlafstein Ashley J , Withers Allison E , Thompson Elizabeth B , Danelia Diana , Luong Nho C , Sesay Fatmata , Rath Sandip K , Usoro Edidiong R , Essien Mark E , Jung Andrew T , Jiang Jinmeng G , Hu Jiaxuan , Mahboubi Bijan , Williams Arilyn , Steinbeck Julia E , Yang Xiaofeng , Buchwald Zachary S , Dynan William S , Switchenko Jeffrey M , Kim Baek , Khan Mohammad K , Jaye David L , Yu David S 
Published: February 2024

Abstract
Diffuse large B-cell lymphoma (DLBCL) is a commonly diagnosed, aggressive non-Hodgkin's lymphoma. While R-CHOP chemoimmunotherapy is potentially curative, about 40% of DLBCL patients will fail, highlighting the need to identify biomarkers to optimize management. SAMHD1 has a dNTPase-independent role in promoting resection to facilitate DNA double-strand break (DSB) repair by homologous recombination. We evaluated the relationship of SAMHD1 levels with sensitivity to DSB-sensitizing agents in DLBCL cells and the association of SAMHD1 expression with clinical outcomes in 79 DLBCL patients treated with definitive therapy and an independent cohort dataset of 234 DLBCL patients. Low SAMHD1 expression, Vpx-mediated, or siRNA-mediated degradation/depletion in DLBCL cells was associated with greater sensitivity to doxorubicin and PARP inhibitors. On Kaplan–Meier log-rank survival analysis, low SAMHD1 expression was associated with improved overall survival (OS), which on subset analysis remained significant only in patients with advanced stage (III-IV) and moderate to high risk (2–5 International Prognostic Index (IPI)). The association of low SAMHD1 expression with improved OS remained significant on multivariate analysis independent of other adverse factors, including IPI, and was validated in an independent cohort. Our findings suggest that SAMHD1 expression mediates doxorubicin resistance and may be an important prognostic biomarker in advanced, higher-risk DLBCL patients.
Real-World Clinical Performance of a DNA-Based Comprehensive Genomic Profiling Assay for Detecting Targetable Fusions in Nonsquamous NSCLC
Authors: Mack Philip C , Keller-Evans Rachel B , Li Gerald , Lofgren Katherine T , Schrock Alexa B , Trabucco Sally E , Allen Justin M , Tolba Khaled , Oxnard Geoffrey R , Huang Richard S P 
Published: February 2024

Abstract

Background
Genomic fusions are potent oncogenic drivers across cancer types and many are targetable. We demonstrate the clinical performance of DNA-based comprehensive genomic profiling (CGP) for detecting targetable fusions.

Materials and Methods
We analyzed targetable fusion genes in &gt;450 000 tissue specimens profiled using DNA CGP (FoundationOne CDx, FoundationOne). Using a de-identified nationwide (US-based) non–small cell lung cancer (NSCLC) clinico-genomic database, we assessed outcomes in patients with nonsquamous NSCLC (NonSqNSCLC) who received matched therapy based on a fusion identified using DNA CGP. Lastly, we modeled the added value of RNA CGP for fusion detection in NonSqNSCLC.

Results
We observed a broad diversity of fusion partners detected with DNA CGP in conjunction with targetable fusion genes (ALK, BRAF, FGFR2, FGFR3, NTRK1/2/3, RET, and ROS1). In NonSqNSCLC with oncogenic ALK, NTRK, RET, and ROS1 fusions detected by DNA CGP, patients treated with a matched tyrosine kinase inhibitor had better real-world progression-free survival than those receiving alternative treatment regimens and benefit was observed regardless of the results of orthogonal fusion testing. An estimated 1.3% of patients with NonSqNSCLC were predicted to have an oncogenic driver fusion identified by RNA, but not DNA CGP, according to a model that accounts for multiple real-world factors.

Conclusion
A well-designed DNA CGP assay is capable of robust fusion detection and these fusion calls are reliable for informing clinical decision-making. While DNA CGP detects most driver fusions, the clinical impact of fusion detection is substantial for individual patients and exhaustive efforts, inclusive of additional RNA-based testing, should be considered when an oncogenic driver is not clearly identified.
Barometric geolocators can reveal unprecedented details about the migratory ecology of small birds
Authors: Rhyne Garrett S , Stouffer Philip C , Briedis Martins , Nussbaumer Raphaël 
Published: February 2024

ABSTRACT
Knowing the location of migratory birds throughout their annual cycle is fundamental for many questions in ornithology. Technological advances have provided several approaches, with increasing miniaturization allowing deployment on smaller and smaller birds. Here, we examine the strengths and limitations of barometric pressure geolocators (pressure tags), which have recently been shown to be extremely effective in tracking small birds (&lt;25 g). The newly developed geolocation by pressure workflow (GeoPressureR) uses a global weather analysis dataset and hidden Markov movement model to reveal locations more accurately or continuously than can be achieved by other available light-weight devices (e.g., light-level geolocators, automated radio telemetry, and archival GPS tags). Additionally, pressure data can provide altitude information and document generally intractable flight behavior, as well as exact migratory phenologies. This new technology can be applied to important unresolved problems such as altitudinal migration, stopover site use, molt migration, vertical airspace use, and drivers of migratory flight initiation, duration, and direction. We provide an example of a pressure tag on a Swainson’s Warbler (Limnothlypis swainsonii) deployed on its breeding territory in Virginia, USA, revealing the complete story of its migration to and from Cuba, including its refined wintering site, stopover sites, and migration routes, all with precise timing. Studies relying on pressure tags are still subject to biases related to recovery of the devices for data extraction, and application to birds that exhibit extensive aerial movements (e.g., swallows and swifts) remains challenging. Widespread deployment of pressure tags could show unprecedented details of bird migration and other aspects of aerial behavior, which could benefit conservation and greatly enrich our understanding of avian movement ecology.