bluuebunny/crossref_metadata_2025_split huggingface dataset:
Practical galaxy morphology tools from deep supervised representation learning
Authors: Walmsley Mike , Scaife Anna M M , Lintott Chris , Lochner Michelle , Etsebeth Verlon , Géron Tobias , Dickinson Hugh , Fortson Lucy , Kruk Sandor , Masters Karen L , Mantha Kameswara Bharadwaj , Simmons Brooke D 
Published: February 2022

ABSTRACT
Astronomers have typically set out to solve supervised machine learning problems by creating their own representations from scratch. We show that deep learning models trained to answer every Galaxy Zoo DECaLS question learn meaningful semantic representations of galaxies that are useful for new tasks on which the models were never trained. We exploit these representations to outperform several recent approaches at practical tasks crucial for investigating large galaxy samples. The first task is identifying galaxies of similar morphology to a query galaxy. Given a single galaxy assigned a free text tag by humans (e.g. ‘#diffuse’), we can find galaxies matching that tag for most tags. The second task is identifying the most interesting anomalies to a particular researcher. Our approach is 100 per cent accurate at identifying the most interesting 100 anomalies (as judged by Galaxy Zoo 2 volunteers). The third task is adapting a model to solve a new task using only a small number of newly labelled galaxies. Models fine-tuned from our representation are better able to identify ring galaxies than models fine-tuned from terrestrial images (ImageNet) or trained from scratch. We solve each task with very few new labels; either one (for the similarity search) or several hundred (for anomaly detection or fine-tuning). This challenges the longstanding view that deep supervised methods require new large labelled data sets for practical use in astronomy. To help the community benefit from our pretrained models, we release our fine-tuning code zoobot. Zoobot is accessible to researchers with no prior experience in deep learning.
The impact of AGN outflows on the surface habitability of terrestrial planets in the Milky Way
Authors: Ambrifi A , Balbi A , Lingam M , Tombesi F , Perlman E 
Published: February 2022

ABSTRACTIt is well known that active galactic nuclei (AGNs) are accompanied by winds and outflows, some of which may reach weakly relativistic speeds of about 10 per cent the speed of light. Yet, in spite of their ubiquity, the impact of AGN outflows in modulating surface habitability of terrestrial planets on galactic scales, using the Milky Way as the basis for comparison, is poorly investigated and inadequately understood. In this work, we address this issue by focusing on two key mechanisms: AGN winds can heat atmospheres and drive the atmospheric escape, as well as stimulate the formation of nitrogen oxides and thence cause ozone depletion. By developing simple models, we estimate the maximal distance up to which these deleterious effects are rendered significant for Earth-like planets in the Milky Way, and thereby demonstrate that this value may extend to ≲ 1 kpc. In the case of quasars hosting larger supermassive black holes, such effects could actually influence the AGN host galaxy as a whole.
Cosmic ray production in superbubbles
Authors: Vieu T , Gabici S , Tatischeff V , Ravikularaman S 
Published: February 2022

ABSTRACT
We compute the production of cosmic rays (CRs) in the dynamical superbubble (SB) produced by a cluster of massive stars. Stellar winds, supernova remnants, and turbulence are found to accelerate particles so efficiently that the non-linear feedback of the particles must be taken into account in order to ensure that the energy balance is not violated. High-energy particles do not scatter efficiently on the turbulence and escape quickly after each supernova explosion, which makes both their intensity inside the bubble and injection in the interstellar medium intermittent. On the other hand, the stochastic acceleration of low-energy particles hardens the spectra at GeV energies. Because CRs damp the turbulence cascade, this hardening is less pronounced when non-linearities are taken into account. Nevertheless, spectra with hard components extending up to 1–10 GeV and normalized to an energy density of 1–100 eV cm−3 are found to be typical signatures of CRs produced in SBs. Efficient shock reacceleration within compact clusters is further shown to produce hard, slightly concave spectra, while the presence of a magnetized shell is shown to enhance the confinement of CRs in the bubble and therefore the collective plasma effects acting on them. We eventually estimate the overall contribution of SBs to the Galactic CR content and show typical gamma-ray spectra expected from hadronic interactions in SB shells. In both cases, a qualitative agreement with observations is obtained.
Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes
Authors: Morgado Leonor , Salgueiro Carlos A 
Published: February 2022

Abstract
Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.
TRIM65 determines the fate of a novel subtype of pituitary neuroendocrine tumors via ubiquitination and degradation of TPIT
Authors: Yao Hong , Xie Wanqun , Dai Yuting , Liu Yanting , Gu Weiting , Li Jianfeng , Wu Liang , Xie Jing , Rui Weiwei , Ren Bohan , Xue Li , Cheng Yijun , Lin Shaojian , Li Changsheng , Tang Hao , Wang Yu , Lou Meiqing , Zhang Xiaobiao , Hu Ronggui , Shang Hanbing , Huang Jinyan , Wu Zhe Bao 
Published: February 2022

AbstractBackgroundPituitary neuroendocrine tumors (PitNETs) are common intracranial tumors that are classified into seven histological subtypes, including lactotroph, somatotroph, corticotroph, thyrotroph, gonadotroph, null cell, and plurihormonal PitNETs. However, the molecular characteristics of these types of PitNETs are not completely clear.MethodsA total of 180 consecutive cases of PitNETs were collected to perform RNA sequencing. All subtypes of PitNETs were distinguished by unsupervised clustering analysis. We investigated the regulation of TPIT by TRIM65 and its effects on ACTH production and secretion in ACTH-secreting pituitary cell lines, as well as in murine models using biochemical analyses, confocal microscopy, and luciferase reporter assays.ResultsA novel subtype of PitNETs derived from TPIT lineage cells was identified as with normal TPIT transcription but with lowered protein expression. Furthermore, for the first time, TRIM65 was identified as the E3 ubiquitin ligase of TPIT. Depending on the RING domain, TRIM65 ubiquitinated and degraded the TPIT protein at multiple Lys sites. In addition, TRIM65-mediated ubiquitination of TPIT inhibited POMC transcription and ACTH production to determine the fate of the novel subtype of PitNETs in vitro and in vivo.ConclusionOur studies provided a novel classification of PitNETs and revealed that the TRIM65-TPIT complex controlled the fate of the novel subtype of PitNETs, which provides a potential therapy target for Cushing’s disease.
Prevalence of Menthol and Menthol Capsule Cigarette Use Among 11–16 Year Olds in Wales Prior to a Ban on Characterizing Flavors in Cigarettes: Findings From the 2019 Student Health and Wellbeing Survey
Authors: Moodie Crawford , Page Nicholas , Moore Graham 
Published: February 2022

Abstract

Introduction
The use of flavored cigarettes has increased in many countries because of the inclusion of one or more frangible flavor-changing capsules in the filter. Research suggests that these “capsule” cigarettes appeal most to youth, but little is known about how prevalent their use is among children.

Methods
A cross-sectional school survey was conducted between September and December 2019 with 11–16 year-olds (N = 119 388) from 198 secondary schools across Wales; the sample represented approximately two-thirds of all 11–16 year-olds in the country. The sample was asked about smoking behavior, with a quarter (N = 26 950) also asked about awareness of menthol cigarettes, and use of menthol and menthol capsule cigarettes if a current smoker (N = 1447).

Results
Current smoking prevalence was 5.7% among the entire sample and 5.9% among the analytical sample (those also asked about menthol and menthol capsule cigarettes). For the analytical sample, almost all current smokers (93.2%) were aware of menthol cigarettes, with three-fifths (60.5%) reporting having used menthol cigarettes in the past 30 days (42.3% capsule cigarettes, 18.2% noncapsule cigarettes). In comparison to nonmenthol smokers, those using menthol cigarettes (capsule and noncapsule) were more likely to be frequent smokers, with those using menthol capsule cigarettes more likely to have smoked for longer.

Conclusions
While past research suggests that flavored cigarettes appeal to youth, this study shows just how popular these products, and capsule cigarettes, in particular, were among young smokers in Wales. It also raises questions about why capsule cigarettes have received such limited public health attention.

Implications
That three in five 11–16 year-old smokers reported using menthol cigarettes in the past 30 days highlights how appealing these products are to young people, particularly capsule cigarettes, used by seventy percent of menthol smokers. Capsule cigarettes are one of the most successful tobacco product innovations in decades, even in countries with comprehensive bans on tobacco marketing and standardized packaging. The dearth of research on capsule cigarettes is a failure of global public health. Evaluation of the ban on characterizing flavors in the United Kingdom and across the European Union is critical.
Multicenter Real-World Study on Effectiveness and Early Discontinuation Predictors in Patients With Non-small Cell Lung Cancer Receiving Nivolumab
Authors: Pasello Giulia , Lorenzi Martina , Calvetti Lorenzo , Oliani Cristina , Pavan Alberto , Favaretto Adolfo , Palazzolo Giovanni , Giovanis Petros , Zustovich Fable , Bonetti Andrea , Bernardi Daniele , Mandarà Marta , Aprile Giuseppe , Crivellaro Giovanna , Sinigaglia Giusy , Tognazzo Sandro , Morandi Paolo , Bortolami Alberto , Marino Valentina , Bonanno Laura , Guarneri Valentina , Conte PierFranco 
Published: February 2022

Abstract

Background
Real-world (RW) evidence on nivolumab in pretreated patients with non-small cell lung cancer (NSCLC) by matching data from administrative health flows (AHFs) and clinical records (CRs) may close the gap between pivotal trials and clinical practice.

Methods
This multicenter RW study aims at investigating median time to treatment discontinuation (mTTD), overall survival (mOS) of nivolumab in pretreated patients with NSCLC both from AHF and CR; clinical-pathological features predictive of early treatment discontinuation (etd), budget impact (BI), and cost-effectiveness analysis were investigated; mOS in patients receiving nivolumab and docetaxel was assessed.

Results
Overall, 237 patients with NSCLC treated with nivolumab were identified from AHFs; mTTD and mOS were 4.2 and 9.8 months, respectively; 141 (59%) received at least 6 treatment cycles, 96 (41%) received &lt; 6 (etd). Median overall survival in patients with and without etd were 3.3 and 19.6 months, respectively (P &lt; .0001). Higher number, longer duration, and higher cost of hospitalizations were observed in etd cases. Clinical records were available for 162 patients treated with nivolumab (cohort 1) and 83 with docetaxel (cohort 2). Median time to treatment discontinuation was 4.8 and 2.6 months, respectively (P &lt; .0001); risk of death was significantly higher in cohort 2 or cohort 1 with etd compared with cohort 1 without etd (P &lt; .0001). Predictors of etd were body mass index &lt;25, Eastern Cooperative Oncology Group performance status &gt;1, neutrophile-to-lymphocyte ratio &gt;2.91, and concomitant treatment with antibiotics and glucocorticoids. The incremental cost-effectiveness ratio of nivolumab was 3323.64 euros ($3757.37) in all patients and 2805.75 euros ($3171.47) for patients without etd. Finally, the BI gap (real-theoretical) was 857 188 euros ($969 050.18).

Conclusion
We defined predictors and prognostic-economic impact of nivolumab in etd patients.
Vulnerable Neotropical migratory songbird demonstrates flexibility in space use in response to rainfall change
Authors: Brunner Alicia R , Marra Peter P , Tonra Christopher M 
Published: February 2022

AbstractBehavioral flexibility of individuals is essential if organisms are to ultimately adapt to climate change. As environmental conditions, such as precipitation patterns become increasingly variable, fine-scale spatiotemporal flexibility in space use may allow for individuals to track resources during periods of adverse or atypical conditions. Individual behavioral flexibility is observable over short timeframes and can therefore be used to assess resilience of a species to projected shifts in climate. The goal of our study was to determine if and how individuals modified their space and habitat use in response to rainfall-driven changes in resources throughout a period of atypical seasonal rainfall patterns. We used radio telemetry to estimate home ranges of nonbreeding Swainson’s Warblers (Limnothlypis swainsonii) in 2 time frames (bi-seasonally and bi-weekly) in Jamaica during dry and wet periods. We measured habitat structure and food (leaf litter arthropod) availability within each home range to determine possible predictors of space use change. Individuals modified the area and/or location of their home ranges with changes in precipitation, and those occupying more open habitats had greater changes in home range area as seasonal rainfall increased. As food increased following rain, individuals constricted their home ranges (bi-weekly) or shifted spatially (bi-seasonally) to a novel area with greater food availability. This suggests individuals are able to rapidly respond to how their environment changes, presumably adjusting to trade-offs between home range size and resource availability. This flexibility may be a key behavioral component in enduring long-term increasingly unpredictable environmental variability and may have population-level consequences. These responses are, however, mediated by habitat, suggesting the ability to respond to variable or poor conditions is not homogeneous across a population.
CamelliA-based simultaneous imaging of Ca2+ dynamics in subcellular compartments
Authors: Guo Jingzhe , He Jiangman , Dehesh Katayoon , Cui Xinping , Yang Zhenbiao 
Published: February 2022

Abstract
As a universal second messenger, calcium (Ca2+) transmits specific cellular signals via a spatiotemporal signature generated from its extracellular source and internal stores. Our knowledge of the mechanisms underlying the generation of a Ca2+ signature is hampered by limited tools for simultaneously monitoring dynamic Ca2+ levels in multiple subcellular compartments. To overcome the limitation and to further improve spatiotemporal resolutions, we have assembled a molecular toolset (CamelliA lines) in Arabidopsis (Arabidopsis thaliana) that enables simultaneous and high-resolution monitoring of Ca2+ dynamics in multiple subcellular compartments through imaging different single-colored genetically encoded calcium indicators. We uncovered several Ca2+ signatures in three types of Arabidopsis cells in response to internal and external cues, including rapid oscillations of cytosolic Ca2+ and apical plasma membrane Ca2+ influx in fast-growing Arabidopsis pollen tubes, the spatiotemporal relationship of Ca2+ dynamics in four subcellular compartments of root epidermal cells challenged with salt, and a shockwave-like Ca2+ wave propagating in laser-wounded leaf epidermis. These observations serve as a testimony to the wide applicability of the CamelliA lines for elucidating the subcellular sources contributing to the Ca2+ signatures in plants.
Overexpression of Arabidopsis nucleolar GTP-binding 1 (NOG1) proteins confers drought tolerance in rice
Authors: Pant Bikram D , Lee Seonghee , Lee Hee-Kyung , Krom Nick , Pant Pooja , Jang YoonJeong , Mysore Kirankumar S 
Published: February 2022

Abstract
As a major adverse environmental factor in most parts of the world, drought causes substantial crop yield losses. Rice (Oryza sativa) is one of the staple foods for more than one-half of the world’s population. Rice plants are sensitive to even mild drought stress and need almost twice the amount of water compared to wheat (Triticum aestivum) or maize (Zea mays). Arabidopsis (Arabidopsis thaliana) small GTPase Nucleolar GTP-binding protein 1 (AtNOG1) plays a role in biotic stress tolerance. Here, we created transgenic rice lines constitutively overexpressing AtNOG1-1 or AtNOG1-2. We also developed rice RNA interference (RNAi) lines that show downregulation of OsNOG1. AtNOG1-1 and AtNOG1-2 overexpressors showed enhanced drought tolerance without compromising grain yield, whereas OsNOG1-RNAi was more susceptible to drought when compared to wild-type plants. Analysis of physiological parameters showed increased cell sap osmolality, relative water content, and abscisic acid (ABA) level, but decreased leaf water loss in AtNOG1-1 or AtNOG1-2 overexpressor lines compared to the control. We found upregulation of several genes involved in ABA and jasmonic acid (JA) signaling, stomata regulation, osmotic potential maintenance, stress protection, and disease resistance in AtNOG1-1 and AtNOG1-2 overexpressor lines compared to the control. We elucidated the role of NOG1-2 and NOG1-1 in regulation of silica body formation around stomata to prevent transpirational water loss. These results provide an avenue to confer drought tolerance in rice.
GLYCINE-RICH RNA-BINDING PROTEIN 7 potentiates effector-triggered immunity through an RNA recognition motif
Authors: Sukarta Octavina C A , Zheng Qi , Slootweg Erik J , Mekken Mark , Mendel Melanie , Putker Vera , Bertran André , Brand Anouk , Overmars Hein , Pomp Rikus , Roosien Jan , Boeren Sjef , Smant Geert , Goverse Aska 
Published: February 2022

AbstractThe activity of intracellular plant nucleotide-binding leucine-rich repeat (NB-LRR) immune receptors is fine-tuned by interactions between the receptors and their partners. Identifying NB-LRR interacting proteins is therefore crucial to advance our understanding of how these receptors function. A co-immunoprecipitation/mass spectrometry screening was performed in Nicotiana benthamiana to identify host proteins associated with the resistance protein Gpa2, a CC-NB-LRR immune receptor conferring resistance against the potato cyst nematode Globodera pallida. A combination of biochemical, cellular, and functional assays was used to assess the role of a candidate interactor in defense. A N. benthamiana homolog of the GLYCINE-RICH RNA-BINDING PROTEIN7 (NbGRP7) protein was prioritized as a Gpa2-interacting protein for further investigations. NbGRP7 also associates in planta with the homologous Rx1 receptor, which confers immunity to Potato Virus X. We show that NbGRP7 positively regulates extreme resistance by Rx1 and cell death by Gpa2. Mutating the NbGRP7 RNA recognition motif (RRM) compromises its role in Rx1-mediated defense. Strikingly, ectopic NbGRP7 expression is likely to impact the steady-state levels of Rx1, which relies on an intact RRM. Our findings illustrate that NbGRP7 is a pro-immune component in effector-triggered immunity by regulating Gpa2/Rx1 function at a posttranscriptional level.
The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple
Authors: Ji Xing-Long , Li Hong-Liang , Qiao Zhi-Wen , Zhang Jiu-Cheng , Sun Wei-Jian , You Chun-Xiang , Hao Yu-Jin , Wang Xiao-Fei 
Published: February 2022

Abstract
Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.
THE EFFECT OF OUT-OF-PLANE PATIENT SHIELDING ON CT RADIATION EXPOSURE AND TUBE CURRENT MODULATIONS: A PHANTOM STUDY ACROSS THREE VENDORS
Authors: Rautiainen Jari , Juntunen Mikael A K , Kotiaho Antti O 
Published: February 2022

AbstractThe aim of this study was to evaluate how out-of-plane patient shielding affects radiation exposure parameters and tube current modulation on different vendors’ computed tomography (CT) scanners. Helical CT scans were performed using two homogenous phantoms to mimic patient attenuation. Four CT scanners from three vendors were investigated by varying the distance of the patient shield from the border of the imaging volume. Scans were performed with a shield placed before and after the localizer. Changes in volume computed tomography dose index (CTDIvol), dose-length product (DLP) and tube current-time products were studied. Out-of-field lead shield increased the CTDIvol and DLP values for each scanner at least for one scan setting when the shield was present in the localizer. The most notable changes were recorded with &gt;1.3 pitch values when the shield was closest to the scanned volume (2.5 cm), and the scan direction was towards the shield. The usage of patient shields in the localizer CT scans can disturb TCM even when placed 7.5 cm away from the edge of the scan.