bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct analysis of the broad-line SN 2019ein: connection with the core-normal SN 2011fe
Authors: Yarbrough Zach , Baron E , DerKacy James M , Washington I , Hoeflich P , Burrow Anthony 
Published: March 2023

ABSTRACT
Type Ia supernovae (SNe Ia) are important cosmological probes and contributors to galactic nucleosynthesis, particularly of the iron group elements. To improve both their reliability as cosmological probes and to understand galactic chemical evolution, it is vital to understand the binary progenitor system and explosion mechanism. The classification of SNe Ia into Branch groups has led to some understanding of the similarities and differences among the varieties of observed SNe Ia. Branch groups are defined by the pseudo-equivalent widths of the two prominent Si ii lines, leading to four distinct groups: core-normal (CN), shallow-silicon, cool, and broad-line (BL). However, partly due to small sample size, little work has been done on the BL group. We perform direct spectral analysis on the pre-maximum spectra of the BL SN 2019ein, comparing and contrasting to the CN SN 2011fe. Both SN 2019ein and SN 2011fe were first observed spectroscopically within 2 d of discovery, allowing us to follow the spectroscopic evolution of both SNe in detail. We find that the optical depths of the primary features of both the CN and BL SNe are very similar, except that there is a Doppler shift between them. We further examine the BL group and show that for nine objects with pre-maximum spectra in the range (−6)–(−2) d with respect to B-maximum all the emission peaks of the Si ii λ6355 line of BL are blueshifted pre-maximum, suggesting a possible classification criterion.
Scattering of light in thin magnetized envelopes – II
Authors: Silant’ev N A , Alekseeva G A , Ananjevskaja Yu K 
Published: March 2023

ABSTRACTWe consider optically thin spherical stellar envelopes with dipole magnetic field. The source of magnetic dipole field is assumed point like and emits the non-polarized monochromatic radiation. This paper carry on the previous paper of authors, where the general theory is presented and the circular polarization of scattered radiation is calculated for small values of magnetic fields corresponding to parameter x ≪ 1 (x = ωB/ω ≃ 0.933 × 10−8λ(μm)B(G)). The Stokes parameters of scattered radiation mutually transform into each other due to interference. Here we obtained the explicit formulas describing the transformation of all Stokes parameters for any value of parameter x. The qualitative discussion of these formulas is presented. These formulas show that for x ∼ 1 the transformation leads to large variations of all Stokes parameters. The linear and circular polarizations acquire oscillating dependence on the propagation path. For x ≫ 1 the single scattered radiation has very small circular polarization of the order ∼1/x ≪ 1 and large linear polarization. In this case the transformation gives rise to additional value of observed circular polarization, which is proportional to initial single scattered value. The observed linear polarization acquires small inclination angle relative to the plane ‘line of sight–direction of magnetic dipole’ due to existence of small circular polarization. The Stokes parameters of single scattered radiation from all envelope without taking into account the interference effects are given for x ≫ 1.
Evolutionary Trajectories are Contingent on Mitonuclear Interactions
Authors: Biot-Pelletier Damien , Bettinazzi Stefano , Gagnon-Arsenault Isabelle , Dubé Alexandre K , Bédard Camille , Nguyen Tuc H M , Fiumera Heather L , Breton Sophie , Landry Christian R 
Published: March 2023

AbstractCritical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that the maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths toward higher fitness. To test this prediction, we submitted 1,344 populations derived from 7 mitonuclear genotypes of Saccharomyces cerevisiae to &gt;300 generations of experimental evolution in conditions that either select for a mitochondrial function or do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.
Diversified Mammalian Visual Adaptations to Bright- or Dim-Light Environments
Authors: Gai Yulin , Tian Ran , Liu Fangnan , Mu Yuan , Shan Lei , Irwin David M , Liu Yang , Xu Shixia , Yang Guang 
Published: March 2023

AbstractPhotic niche shifts of mammals are associated with changing visual capabilities, primarily mediated by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin (RH1) for dim-light vision. To further elucidate molecular mechanisms of mammalian visual adaptations to different light environments, a systematic study incorporating evolutionary analyses across diverse groups and in vitro assays have been carried out. Here, we collected gene sequences for the three opsins from 220 species covering all major mammalian clades. After screening for cone opsin gene losses, we estimated selective pressures on each of the three genes and compared the levels of selection experienced by species living in bright- and dim-light environments. SWS1 pigment is shown to experience accelerated evolution in species living in bright-light environments as has RH1 in aquatic cetaceans, indicating potential shifts for ecological adaptations. To further elucidate the functional mechanisms for these two pigments, we then carried out site-directed mutagenesis in representative taxa. For SWS1, violet and ultraviolet sensitivities in the pika and mouse are mainly affected by substitutions at the critical sites 86 and 93, which have strong epistatic interaction. For RH1, the phenotypic difference between the sperm whale and bovine sequences is largely contributed by a substitution at site 195, which could be critical for dim-light sensation for deep-diving species. Different evolutionary patterns for the visual pigments have been identified in mammals, which correspond to photic niches, although additional phenotypic assays are still required to fully explain the functional mechanisms.
The novel GATA1-interacting protein HES6 is an essential transcriptional cofactor for human erythropoiesis
Authors: Wang Zi , Wang Pan , Zhang Jieying , Gong Han , Zhang Xuchao , Song Jianhui , Nie Ling , Peng Yuanliang , Li Yanan , Peng Hongling , Cui Yajuan , Li Heng , Hu Bin , Mi Jun , Liang Long , Liu Hong , Zhang Ji , Ye Mao , Yazdanbakhsh Karina , Mohandas Narla , An Xiuli , Han Xu , Liu Jing 
Published: March 2023

Abstract
Normal erythropoiesis requires the precise regulation of gene expression patterns, and transcription cofactors play a vital role in this process. Deregulation of cofactors has emerged as a key mechanism contributing to erythroid disorders. Through gene expression profiling, we found HES6 as an abundant cofactor expressed at gene level during human erythropoiesis. HES6 physically interacted with GATA1 and influenced the interaction of GATA1 with FOG1. Knockdown of HES6 impaired human erythropoiesis by decreasing GATA1 expression. Chromatin immunoprecipitation and RNA sequencing revealed a rich set of HES6- and GATA1-co-regulated genes involved in erythroid-related pathways. We also discovered a positive feedback loop composed of HES6, GATA1 and STAT1 in the regulation of erythropoiesis. Notably, erythropoietin (EPO) stimulation led to up-regulation of these loop components. Increased expression levels of loop components were observed in CD34+ cells of polycythemia vera patients. Interference by either HES6 knockdown or inhibition of STAT1 activity suppressed proliferation of erythroid cells with the JAK2V617F mutation. We further explored the impact of HES6 on polycythemia vera phenotypes in mice. The identification of the HES6–GATA1 regulatory loop and its regulation by EPO provides novel insights into human erythropoiesis regulated by EPO/EPOR and a potential therapeutic target for the management of polycythemia vera.
Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae
Authors: Ellison Mitchell A , Namjilsuren Sanchirmaa , Shirra Margaret K , Blacksmith Matthew S , Schusteff Rachel A , Kerr Eleanor M , Fang Fei , Xiang Yufei , Shi Yi , Arndt Karen M 
Published: March 2023

Abstract
The Paf1 complex (Paf1C) is a conserved transcription elongation factor that regulates transcription elongation efficiency, facilitates co-transcriptional histone modifications, and impacts molecular processes linked to RNA synthesis, such as polyA site selection. Coupling of the activities of Paf1C to transcription elongation requires its association with RNA polymerase II (Pol II). Mutational studies in yeast identified Paf1C subunits Cdc73 and Rtf1 as important mediators of Paf1C association with Pol II on active genes. While the interaction between Rtf1 and the general elongation factor Spt5 is relatively well-understood, the interactions involving Cdc73 have not been fully elucidated. Using a site-specific protein cross-linking strategy in yeast cells, we identified direct interactions between Cdc73 and two components of the Pol II elongation complex, the elongation factor Spt6 and the largest subunit of Pol II. Both of these interactions require the tandem SH2 domain of Spt6. We also show that Cdc73 and Spt6 can interact in vitro and that rapid depletion of Spt6 dissociates Paf1 from chromatin, altering patterns of Paf1C-dependent histone modifications genome-wide. These results reveal interactions between Cdc73 and the Pol II elongation complex and identify Spt6 as a key factor contributing to the occupancy of Paf1C at active genes in Saccharomyces cerevisiae.
Structural basis for the tRNA-dependent activation of the terminal complex of selenocysteine synthesis in humans
Authors: Puppala Anupama K , Castillo Suchkou Jennifer , French Rachel L , Kiernan Kaitlyn A , Simonović Miljan 
Published: March 2023

Abstract
O-Phosphoseryl-tRNASec selenium transferase (SepSecS) catalyzes the terminal step of selenocysteine (Sec) synthesis in archaea and eukaryotes. How the Sec synthetic machinery recognizes and discriminates tRNASec from the tRNA pool is essential to the integrity of the selenoproteome. Previously, we suggested that SepSecS adopts a competent conformation that is pre-ordered for catalysis. Herein, using high-resolution X-ray crystallography, we visualized tRNA-dependent conformational changes in human SepSecS that may be a prerequisite for achieving catalytic competency. We show that tRNASec binding organizes the active sites of the catalytic protomer, while stabilizing the N- and C-termini of the non-catalytic protomer. Binding of large anions to the catalytic groove may further optimize the catalytic site for substrate binding and catalysis. Our biochemical and mutational analyses demonstrate that productive SepSecS•tRNASec complex formation is enthalpically driven and primarily governed by electrostatic interactions between the acceptor-, TΨC-, and variable arms of tRNASec and helices α1 and α14 of SepSecS. The detailed visualization of the tRNA-dependent activation of SepSecS provides a structural basis for a revised model of the terminal reaction of Sec formation in archaea and eukaryotes.
Survival After Sentinel Lymph Node Biopsy Compared with Axillary Lymph Node Dissection for Female Patients with T3-4c Breast Cancer
Authors: Li Peiyong , Yang Ciqiu , Zhang Junsheng , Chen Yitian , Zhang Xiaoqi , Liang Minting , Huang Na , Chen Yilin , Wang Kun 
Published: March 2023

Abstract

Background
For patients with cN0 and T1-2 breast cancer, sentinel lymph node biopsy (SLNB) can provide survival results equivalent to axillary lymph node dissection (ALND). However, whether it can be performed on T3-4c patients is still controversial.

Materials and Methods
Female patients diagnosed with cN0, T3-4c, and M0 breast cancer from 2004 to 2019 were identified using the surveillance, epidemiology and end results (SEER) database and divided into 2 groups, the SLNB group (1-5 regional lymph nodes examined) and the ALND group (≥10 regional lymph nodes examined). Finally, only those with pN0 disease were included in the SLNB group. The baseline differences in clinicopathological characteristics between groups were eliminated by propensity score matching (PSM). We also conducted subgroup analyses according to age, overall TNM stage, breast cancer subtypes, surgical approaches, radiation therapy, and chemotherapy. The primary endpoint was survival.

Results
With a mean follow-up of 75 months, a total of 186 deaths were reported among 864 patients. The overall survival (OS) and breast cancer-specific survival (BCSS) in the SLNB group were 78.2% and 87.5%, respectively, and that in the ALND group were 78.7% and 87.3%, respectively. The unadjusted hazard ratio (HR) for OS and BCSS in the SLNB group (vs. the ALND group) was 0.922 (95% CI, 0.691-1.230, P = .580) and 0.874 (95% CI, 0.600-1.273, P = .481), respectively. Besides, the OS and BCSS between the 2 groups were also similar in all subgroup analyses.

Conclusions
SLNB may be performed on female patients with cN0, T3-4c, and M0 breast cancer.
The functional evolution of architecturally different plant geranyl diphosphate synthases from geranylgeranyl diphosphate synthase
Authors: Song Shuyan , Jin Ruitao , Chen Yufan , He Sitong , Li Kui , Tang Qian , Wang Qi , Wang Linjuan , Kong Mengjuan , Dudareva Natalia , Smith Brian J , Zhou Fei , Lu Shan 
Published: March 2023

Abstract
Terpenoids constitute the largest class of plant primary and secondary metabolites with a broad range of biological and ecological functions. They are synthesized from isopentenyl diphosphate and dimethylallyl diphosphate, which in plastids are condensed by geranylgeranyl diphosphate synthases (GGPPSs) to produce GGPP (C20) for diterpene biosynthesis and by geranyl diphosphate synthases (GPPSs) to form GPP (C10) for monoterpene production. Depending on the plant species, unlike homomeric GGPPSs, GPPSs exist as homo- and heteromers, the latter of which contain catalytically inactive GGPPS-homologous small subunits (SSUs) that can interact with GGPPSs. By combining phylogenetic analysis with functional characterization of GGPPS homologs from a wide range of photosynthetic organisms, we investigated how different GPPS architectures have evolved within the GGPPS protein family. Our results reveal that GGPPS gene family expansion and functional divergence began early in nonvascular plants, and that independent parallel evolutionary processes gave rise to homomeric and heteromeric GPPSs. By site-directed mutagenesis and molecular dynamics simulations, we also discovered that Leu-Val/Val-Ala pairs of amino acid residues were pivotal in the functional divergence of homomeric GPPSs and GGPPSs. Overall, our study elucidated an evolutionary path for the formation of GPPSs with different architectures from GGPPSs and uncovered the molecular mechanisms involved in this differentiation.
Two B-box proteins, PavBBX6/9, positively regulate light-induced anthocyanin accumulation in sweet cherry
Authors: Wang Yanyan , Xiao Yuqin , Sun Yueting , Zhang Xiang , Du Bingyang , Turupu Maihemuti , Yao Qisheng , Gai Shilin , Tong Shi , Huang Jing , Li Tianhong 
Published: March 2023

Abstract
Anthocyanin production in bicolored sweet cherry (Prunus avium cv. Rainier) fruit is induced by light exposure, leading to red coloration. The phytohormone abscisic acid (ABA) is essential for this process, but the regulatory relationships that link light and ABA with anthocyanin-associated coloration are currently unclear. In this study, we determined that light treatment of bicolored sweet cherry fruit increased anthocyanin accumulation and induced ABA production and that ABA participates in light-modulated anthocyanin accumulation in bicolored sweet cherry. Two B-box (BBX) genes, PavBBX6/9, were highly induced by light and ABA treatments, as was anthocyanin accumulation. The ectopic expression of PavBBX6 or PavBBX9 in Arabidopsis (Arabidopsis thaliana) increased anthocyanin biosynthesis and ABA accumulation. Overexpressing PavBBX6 or PavBBX9 in sweet cherry calli also enhanced light-induced anthocyanin biosynthesis and ABA accumulation. Additionally, transient overexpression of PavBBX6 or PavBBX9 in sweet cherry peel increased anthocyanin and ABA contents, whereas silencing either gene had the opposite effects. PavBBX6 and PavBBX9 directly bound to the G-box elements in the promoter of UDP glucose-flavonoid-3-O-glycosyltransferase (PavUFGT), a key gene for anthocyanin biosynthesis, and 9-cis-epoxycarotenoid dioxygenase 1 (PavNCED1), a key gene for ABA biosynthesis, and enhanced their activities. These results suggest that PavBBX6 and PavBBX9 positively regulate light-induced anthocyanin and ABA biosynthesis by promoting PavUFGT and PavNCED1 expression, respectively. Our study provides insights into the relationship between the light-induced ABA biosynthetic pathway and anthocyanin accumulation in bicolored sweet cherry fruit.
Riboflavin mediates m6A modification targeted by miR408, promoting early somatic embryogenesis in longan
Authors: Xu Xiaoping , Zhang Chunyu , Xu Xiaoqiong , Cai Roudi , Guan Qingxu , Chen Xiaohui , Chen Yukun , Zhang Zihao , XuHan Xu , Lin Yuling , Lai Zhongxiong 
Published: March 2023

Abstract
Plant somatic embryogenesis (SE) is an in vitro biological process wherein bipolar structures are induced to form somatic cells and regenerate into whole plants. MicroRNA (miRNA) is an essential player in plant SE. However, the mechanism of microRNA408 (miR408) in SE remains elusive. Here, we used stable transgenic technology in longan (Dimocarpus longan) embryogenic calli to verify the mechanism by which miR408 promotes cell division and differentiation of longan early SE. dlo-miR408-3p regulated riboflavin biosynthesis by targeting nudix hydrolase 23 (DlNUDT23), a previously unidentified gene mediating N6-methyladenosine (m6A) modification and influencing RNA homeostasis and cell cycle gene expression during longan early SE. We showed that DlMIR408 overexpression (DlMIR408-OE) promoted 21-nt miRNA biosynthesis. In DlMIR408-OE cell lines, dlo-miR408-3p targeted and downregulated DlNUDT23, promoted riboflavin biosynthesis, decreased flavin mononucleotide (FMN) accumulation, promoted m6A level, and influenced miRNA homeostasis. DNA replication, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, the pentose phosphate pathway, and taurine and hypotaurine metabolism were also closely associated with riboflavin metabolism. In a riboflavin feeding assay, dlo-miR408-3p and pre-miR408 were upregulated and DlNUDT23 was downregulated, increasing the m6A level and cell division and differentiation in longan globular embryos. When riboflavin biosynthesis was inhibited, dlo-miR408-3p was downregulated and DlNUDT23 was upregulated, which decreased m6A modification and inhibited cell division but did not inhibit cell differentiation. FMN artificial demethylated m6A modification affected the homeostasis of precursor miRNA and miRNA. Our results revealed a mechanism underlying dlo-miR408-3p-activated riboflavin biosynthesis in which DlNUDT23 is targeted, m6A modification is dynamically mediated, and cell division is affected, promoting early SE in plants.
How the Other Half Died: Immigration and Mortality in U.S. Cities
Authors: Ager Philipp , Feigenbaum James J , Hansen Casper W , Tan Hui Ren 
Published: March 2023

Abstract
Fears of immigrants as a threat to public health have a long and sordid history. At the turn of the 20th century, when immigrants made up one-third of the population in crowded American cities, contemporaries blamed high urban mortality rates on the newest arrivals. We evaluate how the implementation of country-specific immigration quotas in the 1920s affected urban health. Cities with larger quota-induced reductions in immigration experienced a persistent decline in mortality rates, driven by a reduction in deaths from infectious diseases. The unfavourable living conditions immigrants endured explains the majority of the effect as quotas reduced residential crowding and mortality declines were largest in cities where immigrants resided in more crowded conditions and where public health resources were stretched thinnest.
Prevalence and clinical associations of ultrasound-confirmed enthesitis in systemic lupus erythematosus
Authors: Fagni Filippo , Bettiol Alessandra , Silvestri Elena , Fedi Roberto , Palermo Adalgisa , Urban Maria Letizia , Mazzotta Ruggero , Malandrino Danilo , Bello Federica , Mattioli Irene , Simon David , Di Scala Gerardo , Schett Georg , Prisco Domenico , Emmi Giacomo 
Published: March 2023

Abstract

Objectives
To assess the prevalence of US-confirmed enthesitis in a cohort of patients with SLE and to analyse the clinical associations to enthesitis during the course of SLE.

Methods
In a retrospective analysis of the SLE cohort of the Lupus Unit of the Careggi University Hospital, US examinations of SLE patients presenting with tender and/or swollen joints were retrieved to assess the presence of enthesitis. Patients with US-proven enthesitis were compared with SLE controls with tender and/or swollen joints who showed no US evidence of enthesitis. Clinical and laboratory features were compared at disease onset and during follow-up.

Results
A total of 400 patients fulfilling EULAR/ACR classification criteria for SLE were assessed. Of these, 106 underwent articular US examination. Evidence of enthesitis was found in 31/106 (29.2%) patients. Seventy-one patients without US-enthesitis were included as controls; four were excluded due to lack of follow-up data. Laboratory and clinical features were comparable between cases and controls at disease onset. Throughout a median follow-up of 10.0 (interquartile range [IQR] 8.3–23.3) years for cases and 12.4 (IQR 7.2–13.3) years for controls, patients with enthesitis were less likely to develop renal involvement (22.6% vs 46.5%, P = 0.028) and failed B cell depletion more frequently (75.0% vs 0%).

Conclusion
In SLE patients with clinically active joints, US-proven enthesitis is a fairly common finding. Enthesitis in SLE could be the hallmark of a distinct disease phenotype with less renal involvement, more arthritis and low response to anti-CD 20 therapy, potentially requiring a tailored treatment.