bluuebunny/crossref_metadata_2025_split huggingface dataset:
WISE-PS1-STRM: neural network source classification and photometric redshifts for WISE×PS1
Authors: Beck Róbert , Dodds S Curt , Szapudi István 
Published: June 2022

ABSTRACT
We cross-match between the WISE All-Sky and PS1 3π DR2 source catalogues. The resulting catalogue has 354 590 570 objects, significantly fewer than the parent PS1 catalogue, but its combination of optical and infrared colours facilitate both better source classification and photometric redshift estimation. We perform a neural network-based classification of the objects into galaxies, quasars, and stars, then run neural network-based photometric redshift estimation for the galaxies. The star sample purity and quasar sample completeness measures improve substantially, and the resulting photo-z’s are significantly more accurate in terms of statistical scatter and bias than those calculated from PS1 properties alone. The catalogue will be a basis for future large-scale structure studies, and will be made available as a high-level science product via the Mikulski Archive for Space Telescopes.
Deep forest: neural network reconstruction of intergalactic medium temperature
Authors: Wang Runxuan , Croft Rupert A C , Shaw Patrick 
Published: June 2022

ABSTRACT
We explore the use of deep learning to infer the temperature of the intergalactic medium from the transmitted flux in the high-redshift Ly α forest. We train neural networks on sets of simulated spectra from redshift z = 2–3 outputs of cosmological hydrodynamic simulations, including high-temperature regions added in post-processing to approximate bubbles heated by He ii reionization. We evaluate how well the trained networks are able to reconstruct the temperature from the effect of Doppler broadening in the simulated input Ly α forest absorption spectra. We find that for spectra with high resolution (10 $\, {\rm km}\, {\rm s}^{-1}$ pixel) and moderate signal-to-noise ratio (20–50), the neural network is able to reconstruct the intergalactic medium temperature smoothed on scales of $\sim 6 \, h^{-1}\, {\rm Mpc}$ quite well. Concentrating on discontinuities, we find that high-temperature regions of width $25 \, h^{-1}\, {\rm Mpc}$ and temperature $20\, 000$ K can be fairly easily detected and characterized. We show an example where multiple sightlines are combined to yield tomographic images of hot bubbles. Deep learning techniques may be useful in this way to help us understand the complex temperature structure of the intergalactic medium around the time of helium reionization.
Towards an understanding of long gamma-ray burst environments through circumstellar medium population synthesis predictions
Authors: Chrimes A A , Gompertz B P , Kann D A , van Marle A J , Eldridge J J , Groot P J , Laskar T , Levan A J , Nicholl M , Stanway E R , Wiersema K 
Published: June 2022

ABSTRACT
The temporal and spectral evolution of gamma-ray burst (GRB) afterglows can be used to infer the density and density profile of the medium through which the shock is propagating. In long-duration (core-collapse) GRBs, the circumstellar medium (CSM) is expected to resemble a wind-blown bubble, with a termination shock, separating the stellar wind and the interstellar medium (ISM). A long standing problem is that flat density profiles, indicative of the ISM, are often found at lower radii than expected for a massive star progenitor. Furthermore, the presence of both wind-like environments at high radii and ISM-like environments at low radii remains a mystery. In this paper, we perform a ‘CSM population synthesis’ with long GRB progenitor stellar evolution models. Analytic results for the evolution of wind blown bubbles are adjusted through comparison with a grid of 2D hydrodynamical simulations. Predictions for the emission radii, ratio of ISM to wind-like environments, wind, and ISM densities are compared with the largest sample of afterglow derived parameters yet compiled, which we make available for the community. We find that high ISM densities of n ∼ 1000 cm−3 best reproduce observations. If long GRBs instead occur in typical ISM densities of n ∼ 1 cm−3, then the discrepancy between theory and observations is shown to persist at a population level. We discuss possible explanations for the origin of variety in long GRB afterglows, and for the overall trend of CSM modelling to over-predict the termination shock radius.
Orbital parameters and activity of ZZ Tau – a low-mass young binary with circumbinary disc
Authors: Belinski A , Burlak M , Dodin A , Emelyanov N , Ikonnikova N , Lamzin S , Safonov B , Tatarnikov A 
Published: June 2022

ABSTRACT
We present the results of our new observations of the young binary ZZ Tau with a circumbinary disc. The system was found to consist of two coeval (age &lt; 2 Myr) classical T Tauri stars with the total mass 0.86 ± 0.09 M⊙, orbital period 46.8 ± 0.8 yr, semimajor axis 88.2 ± 2.1 mas, eccentricity 0.58 ± 0.02, and the orbital inclination 123${_{.}^{\circ}}$8 ± 1${_{.}^{\circ}}$0. The accretion rate of ZZ Tau A and ZZ Tau B is approximately 7 × 10−10 and 2 × 10−10 M⊙ yr−1, respectively. No correlation was found between the long-term photometric variability of ZZ Tau and orbital position of its components. The periodic light variations with P = 4.171 ± 0.002 d were observed in the BVRI bands presumably connected with an accretion (hot) spot on the surface of the primary (ZZ Tau A). At the same time, no periodicity was observed in the U band nor in the emission line profile variations probably, due to the significant contribution of ZZ Tau B’s emission, which dominates shortward of λ ≈ 0.4 $\mu$m. We argue that the extinction in the direction to the primary is noticeably larger than that to the secondary. It appeared that the rotation axis of the primary is inclined to the line of sight by ≈31° ± 4°. We also concluded that ZZ Tau is the source of a CO molecular outflow; however, ZZ Tau IRS rather than ZZ Tau is the source of the Herbig–Haro object HH393.
Comparing NED and SIMBAD classifications across the contents of nearby galaxies
Authors: Kuhn L , Shubat M , Barmby P 
Published: June 2022

ABSTRACT
Cataloguing and classifying celestial objects is one of the fundamental activities of observational astrophysics. In this work, we compare the contents of two comprehensive data bases, the NASA Extragalactic Database (NED) and Set of Identifications, Measurements and Bibliography for Astronomical Data (SIMBAD) in the vicinity of nearby galaxies. These two data bases employ different classification schemes – one flat and one hierarchical – and our goal was to determine the compatibility of classifications for objects in common. Searching both data bases for objects within the respective isophotal radius of each of the ∼1300 individual galaxies in the Local Volume Galaxy sample, we found that, on average, NED contains about 10 times as many entries as SIMBAD and about two-thirds of SIMBAD objects are matched by position to a NED object, at 5 arcsec tolerance. These quantities do not depend strongly on the properties of the parent galaxies. We developed an algorithm to compare individual object classifications between the two data bases and found that 88 per cent of the classifications agree; we conclude that NED and SIMBAD contain consistent information for sources in common in the vicinity of nearby galaxies. Because many galaxies have numerous sources contained only in one of NED or SIMBAD, researchers seeking the most complete picture of an individual galaxy’s contents are best served by using both data bases.
Mergers prompted by dynamics in compact, multiple-star systems: a stellar-reduction case for the massive triple TIC 470710327
Authors: Vigna-Gómez Alejandro , Liu Bin , Aguilera-Dena David R , Grishin Evgeni , Ramirez-Ruiz Enrico , Soares-Furtado Melinda 
Published: June 2022

ABSTRACT
TIC 470710327, a massive compact hierarchical triple-star system, was recently identified by NASA’s Transiting Exoplanet Survey Satellite. TIC 470710327 is comprised of a compact (1.10 d) circular eclipsing binary, with total mass $\approx 10.9\!-\!13.2\, \rm {M_{\odot }}$, and a more massive $\approx 14\!-\!17\, \rm {M_{\odot }}$ eccentric non-eclipsing tertiary in a 52.04 d orbit. Here, we present a progenitor scenario for TIC 470710327 in which ‘2 + 2’ quadruple dynamics result in Zeipel–Lidov–Kozai oscillations that lead to a contact phase of the more massive binary. In this scenario, the two binary systems should form in a very similar manner, and dynamics trigger the merger of the more massive binary either during late phases of star formation or several Myr after the zero-age main sequence, when the stars begin to expand. Any evidence that the tertiary is a highly magnetized (∼1–10 kG), slowly rotating blue main-sequence star would hint towards a quadruple origin. Finally, our scenario suggests that the population of inclined compact multiple-stellar systems is reduced into coplanar systems, via mergers, late during star formation or early in the main sequence. The elucidation of the origin of TIC 470710327 is crucial in our understanding of multiple massive star formation and evolution.
A multiplexed, three-dimensional pooling and next-generation sequencing strategy for creating barcoded mutant arrays: construction of a Schizosaccharomyces pombe transposon insertion library
Authors: Li Yanhui , Molyneaux Neil , Zhang Haitao , Zhou Gang , Kerr Carly , Adams Mark D , Berkner Kathleen L , Runge Kurt W 
Published: June 2022

Abstract
Arrayed libraries of defined mutants have been used to elucidate gene function in the post-genomic era. Yeast haploid gene deletion libraries have pioneered this effort, but are costly to construct, do not reveal phenotypes that may occur with partial gene function and lack essential genes required for growth. We therefore devised an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes that can be generalized to other organisms or collections of DNA samples. We developed a novel but simple three-dimensional pooling and multiplexed sequencing approach that leveraged sequence information to reduce the number of required sequencing reactions by orders of magnitude, and were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations. The insertion mutations are in the genes and untranslated regions of nonessential, essential and noncoding RNA genes, and produced a wider range of phenotypes compared to the cognate deletion mutants, including novel phenotypes. This mutant library represents both a proof of principle for an efficient method to produce novel mutant libraries and a valuable resource for the S. pombe research community.
Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine
Authors: Syroegin Egor A , Aleksandrova Elena V , Polikanov Yury S 
Published: June 2022

Abstract
Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.
Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity
Authors: Zheng Lirong , Lu Hui , Zan Bing , Li Song , Liu Hao , Liu Zhuo , Huang Juan , Liu Yongjia , Jiang Fan , Liu Qian , Feng Yan , Hong Liang 
Published: June 2022

Abstract
Prokaryotic Argonaute proteins (pAgos) widely participate in hosts to defend against the invasion of nucleic acids. Compared with the CRISPR-Cas system, which requires a specific motif on the target and can only use RNA as guide, pAgos exhibit precise endonuclease activity on any arbitrary target sequence and can use both RNA and DNA as guide, thus rendering great potential for genome editing applications. Hitherto, most in-depth studies on the structure-function relationship of pAgos were conducted on thermophilic ones, functioning at ∼60 to 100°C, whose structures were, however, determined experimentally at much lower temperatures (20–33°C). It remains unclear whether these low-temperature structures can represent the true conformations of the thermophilic pAgos under their physiological conditions. The present work studied three pAgos, PfAgo, TtAgo and CbAgo, whose physiological temperatures differ significantly (95, 75 and 37°C). By conducting thorough experimental and simulation studies, we found that thermophilic pAgos (PfAgo and TtAgo) adopt a loosely-packed structure with a partially-melted surface at the physiological temperatures, largely different from the compact crystalline structures determined at moderate temperatures. In contrast, the mesophilic pAgo (CbAgo) assumes a compact crystalline structure at its optimal function temperature. Such a partially-disrupted structure endows thermophilic pAgos with great flexibility both globally and locally at the catalytic sites, which is crucial for them to achieve high DNA-cleavage activity. To further prove this, we incubated thermophilic pAgos with urea to purposely disrupt their structures, and the resulting cleavage activity was significantly enhanced below the physiological temperature, even at human body temperature. Further testing of many thermophilic Agos present in various thermophilic prokaryotes demonstrated that their structures are generally disrupted under physiological conditions. Therefore, our findings suggest that the highly dynamical structure with a partially-melted surface, distinct from the low-temperature crystalline structure, could be a general strategy assumed by thermophilic pAgos to achieve the high DNA-cleavage activity.
Definition, diagnosis and clinical management of non-obstructive kidney dysplasia: a consensus statement by the ERKNet Working Group on Kidney Malformations
Authors: Kohl Stefan , Avni Fred E , Boor Peter , Capone Valentina , Clapp William L , De Palma Diego , Harris Tess , Heidet Laurence , Hilger Alina C , Liapis Helen , Lilien Marc , Manzoni Gianantonio , Montini Giovanni , Negrisolo Susanna , Pierrat Marie-Jeanne , Raes Ann , Reutter Heiko , Schreuder Michiel F , Weber Stefanie , Winyard Paul J D , Woolf Adrian S , Schaefer Franz , Liebau Max C 
Published: June 2022

ABSTRACT
Kidney dysplasia is one of the most frequent causes of chronic kidney failure in children. While dysplasia is a histological diagnosis, the term ‘kidney dysplasia’ is frequently used in daily clinical life without histopathological confirmation. Clinical parameters of kidney dysplasia have not been clearly defined, leading to imprecise communication amongst healthcare professionals and patients. This lack of consensus hampers precise disease understanding and the development of specific therapies. Based on a structured literature search, we here suggest a common basis for clinical, imaging, genetic, pathological and basic science aspects of non-obstructive kidney dysplasia associated with functional kidney impairment. We propose to accept hallmark sonographic findings as surrogate parameters defining a clinical diagnosis of dysplastic kidneys. We suggest differentiated clinical follow-up plans for children with kidney dysplasia and summarize established monogenic causes for non-obstructive kidney dysplasia. Finally, we point out and discuss research gaps in the field.
Outcome and effect of vaccination in SARS-CoV-2 Omicron infection in hemodialysis patients: a cohort study
Authors: Ashby Damien R , Caplin Ben , Corbett Richard W , Asgari Elham , Kumar Nicola , Sarnowski Alexander , Hull Richard , Makanjuola David , Cole Nicholas , Chen Jian , Nyberg Sofia , Forbes Suzanne , McCafferty Kieran , Zaman Faryal , Cairns Hugh , Sharpe Claire , Bramham Kate , Motallebzadeh Reza , Anwari Kashif , Roper Tayeba , Salama Alan D , Banerjee Debasish ,   The pan-London Covid-19 renal audit groups, Ali Omer , Antonelou Marilina , Bennet-Richards Katy , Blunden Mark , Booth John , Charif Rawya , Chaudhury Saurabh , Cove-Smith Andrea , Dobbie Hamish , Dodd Phillippa , Dreyer Gavin , Duncan Neill , Goodlad Catriona , Griffith Megan , Hassan Sevda , Hemmilla Ulla , Hendra Heidy , Hill Peter , James Ajith , Jones Daniel , Laurence Anila , Loucaidou Marina , Lucisano Gaetano , Mahalingasivam Viyaasan , Manson Bethia , McGuiness Daniel , McLean Adam , Montero Rosa , Muthuppalaniappan Vasantha , Oates Tom , Palmer Andrew , Rajakariar Ravi , Salisbury Emma , Samad Nasreen , Sandhu Eleanor , Stern Edward , Tandaric Damir , Tomlinson James , Vajgel Gisele , Webster Phil , White William , Wiles Kate , Wright David , Yousef Sajeda 
Published: June 2022

ABSTRACT

Background
Hemodialysis patients are at high risk of Covid-19, though vaccination has significant efficacy in preventing and reducing the severity of infection. Little information is available on disease severity and vaccine efficacy since the dissemination of the Omicron variant.

Methods
In a multi-center study, during a period of the epidemic driven by the Omicron variant, all hemodialysis patients positive for SARS-CoV-2 were identified. Outcomes were analyzed according to predictor variables including vaccination status. Risk of infection was analyzed using a Cox proportional hazards model.

Results
SARS-CoV-2 infection was identified in 1126 patients including 200 (18%) unvaccinated, 56 (5%) post first dose, 433 (38%) post second dose, and 437 (39%) at least 7 days beyond their third dose. The majority of patients had a mild course but 160 (14%) were hospitalized and 28 (2%) died. In regression models adjusted for age and comorbidity, two-dose vaccination was associated with a 39% (95%CI: 2%–62%) reduction in admissions, but third doses provided additional protection, with a 51% (95%CI: 25%–69%) further reduction in admissions. Among 1265 patients at risk at the start of the observation period, SARS-CoV-2 infection was observed in 211 (17%). Two-dose vaccination was associated with a 41% (95%CI: 3%–64%) reduction in the incidence of infection, with no clear additional effect provided by third doses.

Conclusions
These data demonstrate lower incidence of SARS-CoV-2 infection after vaccination in dialysis patients during an Omicron dominant period of the epidemic. Among those developing infection, severe illness was less common with prior vaccination, particularly after third vaccine doses.
Structural Characterization of L-Galactose Dehydrogenase: An Essential Enzyme for Vitamin C Biosynthesis
Authors: Vargas Jhon A , Leonardo Diego A , D’Muniz Pereira Humberto , Lopes Adriana R , Rodriguez Hicler N , Cobos Marianela , Marapara Jorge L , Castro Juan C , Garratt Richard C 
Published: June 2022

Abstract
In plants, it is well-known that ascorbic acid (vitamin C) can be synthesized via multiple metabolic pathways but there is still much to be learned concerning their integration and control mechanisms. Furthermore, the structural biology of the component enzymes has been poorly exploited. Here we describe the first crystal structure for an L-galactose dehydrogenase [Spinacia oleracea GDH (SoGDH) from spinach], from the D-mannose/L-galactose (Smirnoff–Wheeler) pathway which converts L-galactose into L-galactono-1,4-lactone. The kinetic parameters for the enzyme are similar to those from its homolog from camu camu, a super-accumulator of vitamin C found in the Peruvian Amazon. Both enzymes are monomers in solution and have a pH optimum of 7, and their activity is largely unaffected by high concentrations of ascorbic acid, suggesting the absence of a feedback mechanism acting via GDH. Previous reports may have been influenced by changes of the pH of the reaction medium as a function of ascorbic acid concentration. The structure of SoGDH is dominated by a (β/α)8 barrel closely related to aldehyde-keto reductases (AKRs). The structure bound to NAD+ shows that the lack of Arg279 justifies its preference for NAD+ over NADP+, as employed by many AKRs. This favors the oxidation reaction that ultimately leads to ascorbic acid accumulation. When compared with other AKRs, residue substitutions at the C-terminal end of the barrel (Tyr185, Tyr61, Ser59 and Asp128) can be identified to be likely determinants of substrate specificity. The present work contributes toward a more comprehensive understanding of structure–function relationships in the enzymes involved in vitamin C synthesis.
WOX family transcriptional regulators modulate cytokinin homeostasis during leaf blade development in Medicago truncatula and Nicotiana sylvestris
Authors: Wang Hui , Li Xue , Wolabu Tezera , Wang Ziyao , Liu Ye , Tadesse Dimiru , Chen Naichong , Xu Aijiao , Bi Xiaojing , Zhang Yunwei , Chen Jianghua , Tadege Million 
Published: June 2022

Abstract
The plant-specific family of WUSCHEL (WUS)-related homeobox (WOX) transcription factors is key regulators of embryogenesis, meristem maintenance, and lateral organ development in flowering plants. The modern/WUS clade transcriptional repressor STENOFOLIA/LAMINA1(LAM1), and the intermediate/WOX9 clade transcriptional activator MtWOX9/NsWOX9 antagonistically regulate leaf blade expansion, but the molecular mechanism is unknown. Using transcriptome profiling and biochemical methods, we determined that NsCKX3 is the common target of LAM1 and NsWOX9 in Nicotiana sylvestris. LAM1 and NsWOX9 directly recognize and bind to the same cis-elements in the NsCKX3 promoter to repress and activate its expression, respectively, thus controlling the levels of active cytokinins in vivo. Disruption of NsCKX3 in the lam1 background yielded a phenotype similar to the knockdown of NsWOX9 in lam1, while overexpressing NsCKX3 resulted in narrower and shorter lam1 leaf blades reminiscent of NsWOX9 overexpression in the lam1 mutant. Moreover, we established that LAM1 physically interacts with NsWOX9, and this interaction is required to regulate NsCKX3 transcription. Taken together, our results indicate that repressor and activator WOX members oppositely regulate a common downstream target to function in leaf blade outgrowth, offering a novel insight into the role of local cytokinins in balancing cell proliferation and differentiation during lateral organ development.