bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate dust temperature determination in a z = 7.13 galaxy
Authors: Bakx Tom J L C , Sommovigo Laura , Carniani Stefano , Ferrara Andrea , Akins Hollis B , Fujimoto Seiji , Hagimoto Masato , Knudsen Kirsten K , Pallottini Andrea , Tamura Yoichi , Watson Darach 
Published: September 2021

ABSTRACT
We report ALMA Band 9 continuum observations of the normal, dusty star-forming galaxy A1689-zD1 at z = 7.13, resulting in a ∼4.6 σ detection at 702 GHz. For the first time, these observations probe the far-infrared spectrum shortward of the emission peak of a galaxy in the Epoch of Reionization (EoR). Together with ancillary data from earlier works, we derive the dust temperature, Td, and mass, Md, of A1689-zD1 using both traditional modified blackbody spectral energy density fitting, and a new method that relies only on the [C ii] 158 μm line and underlying continuum data. The two methods give $T_{\rm d} = (42^{+13}_{-7}, 40^{+13}_{-7}$) K, and $M_{\rm d} = (1.7^{+1.3}_{-0.7}, 2.0^{+1.8}_{-1.0})\, \times {}\, 10^{7} \, \mathrm{ M}_{\odot }$. Band 9 observations improve the accuracy of the dust temperature (mass) estimate by ∼50 per cent (6 times). The derived temperatures confirm the reported increasing Td-redshift trend between z = 0 and 8; the dust mass is consistent with a supernova origin. Although A1689-zD1 is a normal UV-selected galaxy, our results, implying that ∼85 per cent of its star-formation rate is obscured, underline the non-negligible effects of dust in EoR galaxies.
Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses
Authors: Mei Han , Kosakovsky Pond Sergei , Nekrutenko Anton 
Published: September 2021

Abstract
The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE—the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements—places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.
Light and shade of citizen science for less charismatic invertebrate groups: quality assessment of iNaturalist nonmarine mollusc observations in central Italy
Authors: Barbato Debora , Benocci Andrea , Guasconi Mirko , Manganelli Giuseppe 
Published: September 2021

ABSTRACT
Citizen science has grown in importance in recent years: many projects have been launched and records are being collected on an unprecedented scale. However, certain less charismatic invertebrate groups are still underreported and the accuracy and quality of their records in crowd-sourced citizen-science projects have rarely been investigated. Here, we used expert review to conduct quality control of nonmarine mollusc observations from central Italy on the online citizen-science platform iNaturalist (https://www.inaturalist.org/). As of December 2019, c. 400 observations of nonmarine molluscs had been reported from Tuscany on iNaturalist. Most records (59.4%) were identified to species level by the iNaturalist community and included a total of 90 taxa, providing interesting new chorological data of certain entities. Although identification of more than half the observations uploaded by the community was confirmed by expert malacologists, some major issues emerged: low quality of photographic vouchers; bias in favour of a few large common species; poor taxonomic knowledge producing incorrect identifications; and difficulty of identifying many taxa without anatomical study. Expert review remains an essential tool for verification and improvement of data quality in citizen-science projects. In this regard, information on the main diagnostic characters of the more common species (e.g. certain medium–large-sized snails and slugs) as well as tips on how to take good quality photographic images could be provided to volunteers in the form of simple guides and tutorials. High-quality training resources to support recorders and regular feedback and teamwork between scientists and citizens could prevent unverified or inaccurate records from impairing the accuracy of citizen-science datasets and offer a real opportunity to discover and conserve less charismatic taxa.
Becoming and Beyond: Applying Goethe’s Progressive and Retrogressive Metamorphosis to Fanny Hensel’s Piano Sonatas
Authors: Osborne Tyler 
Published: September 2021

AbstractOver the last decade, Janet Schmalfeldt’s concept of “becoming” has provided groundwork to evaluate how ambiguous formal moments gradually come into focus through the practice of retrospective reinterpretation. I supplement Schmalfeldt’s Hegelian perspective with concepts drawn from Goethe’s botanical studies to propose a type of becoming that is not limited to retrospective reinterpretation but instead embraces gradual thematic transformations that can function either progressively or retrogressively. Using Fanny Hensel’s piano sonatas as case studies, I explain how the two categories of progressive and retrogressive metamorphosis are fitting metaphors to describe gradual thematic transformations within Romantic-era composers’ works that resist formal prototypes.
The Times are A-Changin’: Metric Flexibility and Text Expression in 1960s and 1970s Singer-Songwriter Music
Authors: Murphy Nancy 
Published: September 2021

AbstractIn 1960s and 1970s singer-songwriter music, some artists used a malleable approach to meter in performance that resulted in songs with extremes of self-expressive timing flexibility that cannot be accounted for by using a single conception of meter. As a solution, this article draws together theories of metric hierarchy, metrical reinterpretation, and metric process to develop the theory of flexible meter. This approach recasts meter as able to encompass the variety of metric scenarios presented by these singer-songwriters, from metric regularity to metric ambiguity and vacillations between these two possibilities. Performances by Bob Dylan, Joni Mitchell, Buffy Sainte-Marie, Paul Simon, and Cat Stevens are discussed to investigate their levels of engagement with meter—the degree to which their performances are regular or ambiguous—and how the individual metric style of each artist contributes to the self-expressive singer-songwriter performance practice.
Two coexisting pseudo-mirror heteromolecular telomeric G-quadruplexes in opposite loop progressions differentially recognized by a low equivalent of Thioflavin T
Authors: Fu Wenqiang , Jing Haitao , Xu Xiaojuan , Xu Suping , Wang Tao , Hu Wenxuan , Li Huihui , Zhang Na 
Published: September 2021

Abstract
The final 3′-terminal residue of the telomeric DNA G-overhang is inherently less precise. Here, we describe how alteration of the last 3′-terminal base affects the mutual recognition between two different G-rich oligomers of human telomeric DNA in the formation of heteromolecular G-quadruplexes (hetero-GQs). Associations between three- and single-repeat fragments of human telomeric DNA, target d(GGGTTAGGGTTAGGG) and probe d(TAGGGT), in Na+ solution yield two coexisting forms of (3 + 1) hybrid hetero-GQs: the kinetically favourable LLP-form (left loop progression) and the thermodynamically controlled RLP-form (right loop progression). However, only the adoption of a single LLP-form has been previously reported between the same probe d(TAGGGT) and a target variant d(GGGTTAGGGTTAGGGT) having one extra 3′-end thymine. Moreover, the flanking base alterations of short G-rich probe variants also significantly affect the loop progressions of hetero-GQs. Although seemingly two pseudo-mirror counter partners, the RLP-form exhibits a preference over the LLP-form to be recognized by a low equivalent of fluorescence dye thioflavin T (ThT). To a greater extent, ThT preferentially binds to RLP hetero-GQ than with the corresponding telomeric DNA duplex context or several other representative unimolecular GQs.
A rapid method to visualize human mitochondrial DNA replication through rotary shadowing and transmission electron microscopy
Authors: Kosar Martin , Piccini Daniele , Foiani Marco , Giannattasio Michele 
Published: September 2021

Abstract
We report a rapid experimental procedure based on high-density in vivo psoralen inter-strand DNA cross-linking coupled to spreading of naked purified DNA, positive staining, low-angle rotary shadowing, and transmission electron microscopy (TEM) that allows quick visualization of the dynamic of heavy strand (HS) and light strand (LS) human mitochondrial DNA replication. Replication maps built on linearized mitochondrial genomes and optimized rotary shadowing conditions enable clear visualization of the progression of the mitochondrial DNA synthesis and visualization of replication intermediates carrying long single-strand DNA stretches. One variant of this technique, called denaturing spreading, allowed the inspection of the fine chromatin structure of the mitochondrial genome and was applied to visualize the in vivo three-strand DNA structure of the human mitochondrial D-loop intermediate with unprecedented clarity.
ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation
Authors: Wang Yimin , Fan Jing , Wang Jianshu , Zhu Yi , Xu Lin , Tong Deng , Cheng Hong 
Published: September 2021

Abstract
Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.
Structural basis of transcription activation by the global regulator Spx
Authors: Shi Jing , Li Fangfang , Wen Aijia , Yu Libing , Wang Lu , Wang Fulin , Jin Yuanling , Jin Sha , Feng Yu , Lin Wei 
Published: September 2021

AbstractSpx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter DNA. However, the precise mechanism by which it interacts with RNAP and promoter DNA to initiate transcription remains obscure. Here, we report the cryo-EM structure of an intact Spx-dependent transcription activation complex (Spx–TAC) from Bacillus subtilis at 4.2 Å resolution. The structure traps Spx in an active conformation and defines key interactions accounting for Spx-dependent transcription activation. Strikingly, an oxidized Spx monomer engages RNAP by simultaneously interacting with the C-terminal domain of RNAP alpha subunit (αCTD) and σA. The interface between Spx and αCTD is distinct from those previously reported activators, indicating αCTD as a multiple target for the interaction between RNAP and various transcription activators. Notably, Spx specifically wraps the conserved –44 element of promoter DNA, thereby stabilizing Spx–TAC. Besides, Spx interacts extensively with σA through three different interfaces and promotes Spx-dependent transcription activation. Together, our structural and biochemical results provide a novel mechanistic framework for the regulation of bacterial transcription activation and shed new light on the physiological roles of the global Spx-family transcription factors.
Combinatorial assembly platform enabling engineering of genetically stable metabolic pathways in cyanobacteria
Authors: Taylor George M , Hitchcock Andrew , Heap John T 
Published: September 2021

Abstract
Cyanobacteria are simple, efficient, genetically-tractable photosynthetic microorganisms which in principle represent ideal biocatalysts for CO2 capture and conversion. However, in practice, genetic instability and low productivity are key, linked problems in engineered cyanobacteria. We took a massively parallel approach, generating and characterising libraries of synthetic promoters and RBSs for the cyanobacterium Synechocystis sp. PCC 6803, and assembling a sparse combinatorial library of millions of metabolic pathway-encoding construct variants. Genetic instability was observed for some variants, which is expected when variants cause metabolic burden. Surprisingly however, in a single combinatorial round without iterative optimisation, 80% of variants chosen at random and cultured photoautotrophically over many generations accumulated the target terpenoid lycopene from atmospheric CO2, apparently overcoming genetic instability. This large-scale parallel metabolic engineering of cyanobacteria provides a new platform for development of genetically stable cyanobacterial biocatalysts for sustainable light-driven production of valuable products directly from CO2, avoiding fossil carbon or competition with food production.
Integrative analysis of epigenetics data identifies gene-specific regulatory elements
Authors: Schmidt Florian , Marx Alexander , Baumgarten Nina , Hebel Marie , Wegner Martin , Kaulich Manuel , Leisegang Matthias S , Brandes Ralf P , Göke Jonathan , Vreeken Jilles , Schulz Marcel H 
Published: September 2021

Abstract
Understanding how epigenetic variation in non-coding regions is involved in distal gene-expression regulation is an important problem. Regulatory regions can be associated to genes using large-scale datasets of epigenetic and expression data. However, for regions of complex epigenomic signals and enhancers that regulate many genes, it is difficult to understand these associations. We present StitchIt, an approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples. StitchIt segments epigenetic signal tracks over many samples to generate the location and the target genes of a REM simultaneously. We show that this approach leads to a more accurate and refined REM detection compared to standard methods even on heterogeneous datasets, which are challenging to model. Also, StitchIt REMs are highly enriched in experimentally determined chromatin interactions and expression quantitative trait loci. We validated several newly predicted REMs using CRISPR-Cas9 experiments, thereby demonstrating the reliability of StitchIt. StitchIt is able to dissect regulation in superenhancers and predicts thousands of putative REMs that go unnoticed using peak-based approaches suggesting that a large part of the regulome might be uncharted water.
The fate of notch-1 transcript is linked to cell cycle dynamics by activity of a natural antisense transcript
Authors: Vujovic Filip , Rezaei-Lotfi Saba , Hunter Neil , Farahani Ramin M 
Published: September 2021

Abstract
A core imprint of metazoan life is that perturbations of cell cycle are offset by compensatory changes in successive cellular generations. This trait enhances robustness of multicellular growth and requires transmission of signaling cues within a cell lineage. Notably, the identity and mode of activity of transgenerational signals remain largely unknown. Here we report the discovery of a natural antisense transcript encoded in exon 25 of notch-1 locus (nAS25) by which mother cells control the fate of notch-1 transcript in daughter cells to buffer against perturbations of cell cycle. The antisense transcript is transcribed at G1 phase of cell cycle from a bi-directional E2F1-dependent promoter in the mother cell where the titer of nAS25 is calibrated to the length of G1. Transmission of the antisense transcript from mother to daughter cells stabilizes notch-1 sense transcript in G0 phase of daughter cells by masking it from RNA editing and resultant nonsense-mediated degradation. In consequence, nAS25-mediated amplification of notch-1 signaling reprograms G1 phase in daughter cells to compensate for the altered dynamics of the mother cell. The function of nAS25/notch-1 in integrating G1 phase history of the mother cell into that of daughter cells is compatible with the predicted activity of a molecular oscillator, slower than cyclins, that coordinates cell cycle within cell lineage.
Toward a mechanistic understanding of DNA binding by forkhead transcription factors and its perturbation by pathogenic mutations
Authors: Dai Shuyan , Qu Linzhi , Li Jun , Chen Yongheng 
Published: September 2021

Abstract
Forkhead box (FOX) proteins are an evolutionarily conserved family of transcription factors that play numerous regulatory roles in eukaryotes during developmental and adult life. Dysfunction of FOX proteins has been implicated in a variety of human diseases, including cancer, neurodevelopment disorders and genetic diseases. The FOX family members share a highly conserved DNA-binding domain (DBD), which is essential for DNA recognition, binding and function. Since the first FOX structure was resolved in 1993, &gt;30 FOX structures have been reported to date. It is clear now that the structure and DNA recognition mechanisms vary among FOX members; however, a systematic review on this aspect is lacking. In this manuscript, we present an overview of the mechanisms by which FOX transcription factors bind DNA, including protein structures, DNA binding properties and disease-causing mutations. This review should enable a better understanding of FOX family transcription factors for basic researchers and clinicians.
Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment
Authors: Tang Kaihao , Wang Weiquan , Sun Yamin , Zhou Yiqing , Wang Pengxia , Guo Yunxue , Wang Xiaoxue 
Published: September 2021

Abstract
The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of prophages that are highly divergent from known phages remains challenging. In this study, by taking advantage of the lysis-lysogeny switch of temperate phages, we designed Prophage Tracer, a tool for recognizing active prophages in prokaryotic genomes using short-read sequencing data, independent of phage gene similarity searching. Prophage Tracer uses the criterion of overlapping split-read alignment to recognize discriminative reads that contain bacterial (attB) and phage (attP) att sites representing prophage excision signals. Performance testing showed that Prophage Tracer could predict known prophages with precise boundaries, as well as novel prophages. Two novel prophages, dsDNA and ssDNA, encoding highly divergent major capsid proteins, were identified in coral-associated bacteria. Prophage Tracer is a reliable data mining tool for the identification of novel temperate phages and mobile genetic elements. The code for the Prophage Tracer is publicly available at https://github.com/WangLab-SCSIO/Prophage_Tracer.
Focal segmental glomerulosclerosis histologic variants and renal outcomes based on nephrotic syndrome, immunosuppression and proteinuria remission
Authors: Kawaguchi Takehiko , Imasawa Toshiyuki , Kadomura Moritoshi , Kitamura Hiroshi , Maruyama Shoichi , Ozeki Takaya , Katafuchi Ritsuko , Oka Kazumasa , Isaka Yoshitaka , Yokoyama Hitoshi , Sugiyama Hitoshi , Sato Hiroshi 
Published: September 2021

Abstract

Background
The associations of focal segmental glomerulosclerosis (FSGS) histological variants with renal outcomes have rarely been investigated comprehensively by clinically relevant subgroups in this modern age.

Methods
Data on 304 (173 nephrotic and 131 non-nephrotic) patients with biopsy-confirmed FSGS from 2010 to 2013 were analyzed using the Japanese nationwide renal biopsy registry. The primary outcome was a composite of a 30% decline in estimated glomerular filtration rate or progression to end-stage kidney disease 5 years from the biopsy. We compared outcomes of FSGS variants according to the Columbia classification using survival analyses. Subgroup analyses were performed based on nephrotic syndrome (NS), immunosuppression and proteinuria remission (PR; proteinuria &lt;0.3 g/day) during follow-up. Additionally, associations of NS, immunosuppression and PR with outcomes were examined for each variant.

Results
The distribution of variants was 48% (n = 145) FSGS not otherwise specified, 19% (n = 57) tip, 15% (n = 47) perihilar, 13% (n = 40) cellular and 5% (n = 15) collapsing. The outcome event occurred in 87 patients (29%). No significant differences in the outcome were found among the variants. Subgroup analyses yielded similar results. However, there was a trend toward improved outcome in patients with PR irrespective of variants [hazard ratio adjusted for histological variant and potential confounders (adjusted HR) 0.19 (95% confidence interval 0.10–0.34)]. NS was marginally associated with better outcome compared with non-NS [adjusted HR 0.50 (95% confidence interval 0.25–1.01)].

Conclusions
FSGS variants alone might not have significant impacts on the renal outcome after 5 years, while PR could be predictive of improved renal prognosis for any variant. Specific strategies and interventions to achieve PR for each variant should be implemented for better renal outcomes.