bluuebunny/crossref_metadata_2025_split huggingface dataset:
The super-enhancer repertoire in porcine liver
Authors: Zhang Yi , Zhang Jinbi , Wang Caixia , Dai Hongjian , Du Xing , Li Qifa , Pan Zengxiang 
Published: February 2023

AbstractThe transcriptional initiation of genes is inextricably bound with the functions of cis-regulatory sequences. The pig is one of the most important livestock species and an ideal animal model for biomedical studies. At the same time, the liver is a critical organ with diverse and complex metabolic functions. Here, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with high-throughput sequencing to profile the chromatin landscape of histone H3 lysine 27 acetylation (H3K27ac), histone H3 lysine 4 monomethylation (H3K4me1), and CCAAT enhancer-binding protein β (C-EBPβ) in the 70-d-old porcine liver, compared the different profiles among the three markers and their associated stitched-enhancers by stitching and sorting the peaks within 12.5 kb (Pott and Lieb, 2015) and generated the porcine liver-specific super-enhancers (SEs) by the combination of three markers. Compared to typical enhancers (TEs) and other stitched-enhancers, liver-specific SEs showed a higher density of cis-motifs and SNPs, which may recruit more tissue-specific vital TFs. The expression profiles in fetal and 70-d-old pigs proved that a large proportion of SE-associated genes were up-regulated and were more related to hepatic metabolisms and detoxification pathways. Our results illustrated the difference and connection among promoter and enhancer markers, identified the features of liver SEs and their associated genes, and provided novel insight into cis-element identification, function, and liver transcriptional regulation.
Inner nuclear membrane proteins Lem2 and Bqt4 interact with different lipid synthesis enzymes in fission yeast
Authors: Hirano Yasuhiro , Kinugasa Yasuha , Kubota Yoshino , Obuse Chikashi , Haraguchi Tokuko , Hiraoka Yasushi 
Published: February 2023

AbstractThe nuclear envelope (NE) is a double-membrane structure consisting of inner and outer membranes that spatially separate the nucleus from the cytoplasm, and its function is critical for cellular functions such as genome maintenance. In the fission yeast, Schizosaccharomyces pombe, the inner nuclear membrane proteins, Lem2 and Bqt4, play pivotal roles in maintaining the NE structure. We previously found that the double deletion of lem2+ and bqt4+ causes a synthetic lethal defect associated with severe NE rupture, and overexpression of Elo2, a solo very-long-chain fatty acid elongase, suppresses this defect by restoring the NE. However, the molecular basis of this restoration remains elusive. To address this, we identified Lem2- and Bqt4-binding proteins via immunoprecipitation and mass spectrometry in this study. Forty-five and 23 proteins were identified as Lem2- and Bqt4-binding proteins, respectively. Although these binding proteins partially overlapped, Lem2 and Bqt4 interacted with different types of lipid metabolic enzymes: Cho2, Ole1 and Erg11 for Lem2 and Cwh43 for Bqt4. These enzymes are known to be involved in various lipid synthesis processes, suggesting that Lem2 and Bqt4 may contribute to the regulation of lipid synthesis by binding to these enzymes.
Three Layers of Uncertainty
Authors: Aydogan Ilke , Berger Loïc , Bosetti Valentina , Liu Ning 
Published: February 2023

Abstract
We explore decision-making under uncertainty using a framework that decomposes uncertainty into three distinct layers: (1) risk, which entails inherent randomness within a given probability model; (2) model ambiguity, which entails uncertainty about the probability model to be used; and (3) model misspecification, which entails uncertainty about the presence of the correct probability model among the set of models considered. Using a new experimental design, we isolate and measure attitudes toward each layer separately. We conduct our experiment on three different subject pools and document the existence of a behavioral distinction between the three layers. In addition to providing new insights into the underlying processes behind ambiguity aversion, we provide the first empirical evidence of the role of model misspecification in decision-making under uncertainty.
The Role of Age at Migration in Socio-Cultural Integration: Testing Mediating Mechanisms among Recent Refugees
Authors: Klok Jolien , van der Linden Meta 
Published: February 2023

AbstractAlthough age (at migration) is an important factor to influence the socio-cultural integration process of refugees, we know fairly little about exactly how ageing does so. We consider intergroup contact and identification as member of the host city as socio-cultural integration and take the case of recent refugees in the Netherlands to propose and test two mechanisms; language comprehension and health. Using data from 764 recent refugees from the Bridge survey we employ structural equation modelling to test these mechanisms simultaneously for the two measures of socio-cultural integration. Language comprehension mediates the relationship between age and intergroup contact, while health mediates between age and identification. We conclude that a more careful consideration of age in integration literature is necessary, as up till now it has too often been used as a proxy for an array of (social) phenomena. The findings add to better understanding older refugees’ challenges in socio-cultural integration.
Satisfaction with current hormone therapy and goals of additional gender-affirming care in transgender adults
Authors: Siira Meron , Getahun Darios , Silverberg Michael J , Tangpricha Vin , Goodman Michael , Yeung Howa 
Published: February 2023

AbstractBackgroundMany transgender persons seek hormone therapy to reduce gender dysphoria and improve quality of life, but little is known about patient satisfaction with current gender-affirming hormone therapy.AimTo examine patient satisfaction with current gender-affirming hormone therapy and patients’ goals of additional hormone therapy.MethodsTransgender adults in the validated multicenter STRONG cohort (Study of Transition, Outcomes, and Gender) were asked to complete a cross-sectional survey about current and planned hormone therapy and the effects that they experienced or hoped to gain. The proportion of respondents reporting overall satisfaction with hormone therapy were compared with χ2 or Fisher exact test. Cochran-Mantel-Haenszel analysis was used to compare the covariates of interest while controlling for age at the time of survey completion.OutcomesPatient satisfaction across hormone therapies, each measured with a 5-point scale, was averaged and dichotomized.ResultsOut of 2136 eligible transgender adults, 696 (33%) completed the survey: 350 transfeminine (TF) and 346 transmasculine (TM) respondents. Most participants (80%) were satisfied or very satisfied with their current hormone therapies. TF participants and older participants were less likely to report being satisfied with their current hormone therapies than TM participants and younger participants, respectively. However, TM and TF categories were not associated with patient satisfaction after controlling for age at the time of survey completion. More TF persons planned to take additional treatment. The most frequent goals for additional hormone therapy for TF persons included breast size growth, feminine body fat distribution, and facial feature softening; for TM persons, goals included diminishing dysphoria, greater muscle mass, and masculine body fat distribution.Clinical ImplicationsMultidisciplinary care beyond provision of hormone therapy—such as involvement of surgical, dermatologic, reproductive health, mental health, and/or gender expression care—may be important to help achieve unmet gender-affirming care goals.Strengths and LimitationsThis study had a modest response rate and included only respondents with private insurance, limiting generalizability.ConclusionUnderstanding patient satisfaction and goals of care will assist shared decision making and counseling in patient-centered gender-affirming therapy.
Elevated [CO2] negatively impacts C4 photosynthesis under heat and water stress without penalizing biomass
Authors: Al-Salman Yazen , Ghannoum Oula , Cano Francisco Javier 
Published: February 2023

Abstract
Elevated [CO2] (eCO2) and water stress reduce leaf stomatal conductance (gs), which may affect leaf thermoregulation during heat waves (heat stress). Two sorghum lines, with different leaf width were grown in a glasshouse at a mean day temperature of 30 °C, under different [CO2] and watering levels, and subjected to heat stress (43 °C) for 6 d at the start of the reproductive stage. We measured leaf photosynthetic and stomatal responses to light transients before harvesting the plants. Photosynthesis at growth conditions (Agrowth) and biomass accumulation were enhanced by eCO2 under control conditions. Heat stress increased gs, especially in wider leaves, and reduced the time constant of stomatal opening (kopen) at ambient [CO2] but not eCO2. However, heat stress reduced photosynthesis under water stress and eCO2 due to increased leaf temperature and reduced evaporative cooling. eCO2 prevented the reduction of biomass under both water and heat stress, possibly due to improved plant and soil water status as a result of reduced gs. Our results suggest that the response of the C4 crop sorghum to future climate conditions depends on the trade-off between low gs needed for high water use efficiency and drought tolerance, and the high gs needed for improved thermoregulation and heat tolerance under an eCO2 future.
Evaluation of loop-mediated isothermal amplification assay for visual detection ofAcinetobacter baumanniidirectly from soil and water sample from Mangalore
Authors: Nayak Srajana , Do Carmo Lobo Nia , Anupama Karanth Padyana , Nayak Ashwath , Akshay Sadanand Dangari , Maiti Biswajit 
Published: February 2023

AbstractAcinetobacter baumannii is a well-known nosocomial pathogen that commonly inhabits soil and water and has been implicated in numerous hospital-acquired infections. The existing methods for detecting A. baumannii have several drawbacks, such as being time-consuming, expensive, labor-intensive, and unable to distinguish between closely related Acinetobacter species. Thus, it is important to have a simple, rapid, sensitive, and specific method for its detection. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay using hydroxynaphthol blue dye to visualize A. baumannii by targeting its pgaD gene. The LAMP assay was performed using a simple dry bath and was shown to be specific and highly sensitive, as it could detect up to 10 pg/μl of A. baumannii DNA. Further, the optimized assay was used to detect A. baumannii in soil and water samples by culture-medium enrichment. Out of 27 samples tested, 14 (51.85%) samples were positive for A. baumannii through LAMP assay, while only 5 (18.51%) samples were found to be positive through conventional methods. Thus, the LAMP assay has been found to be a simple, rapid, sensitive, and specific method that can be used as a point-of-care diagnostic tool for detecting A. baumannii.
Normal functions and maximal order types
Authors: Freund Anton , Manca Davide 
Published: February 2023

Abstract
Transformations of well partial orders induce functions on the ordinals, via the notion of maximal order type. In most examples from the literature, these functions are not normal, in marked contrast with the central role that normal functions play in ordinal analysis and related work from computability theory. The present paper aims to explain this phenomenon. In order to do so, we investigate a rich class of order transformations that are known as $\textsf {WPO}$-dilators. According to a first main result of this paper, $\textsf {WPO}$-dilators induce normal functions when they satisfy a rather restrictive condition, which we call strong normality. Moreover, the reverse implication holds as well, for reasonably well-behaved $\textsf {WPO}$-dilators. Strong normality also allows us to explain another phenomenon: by previous work of Freund, Rathjen and Weiermann, a uniform Kruskal theorem for $\textsf {WPO}$-dilators is as strong as $\varPi ^1_1$-comprehension, while the corresponding result for normal dilators on linear orders is equivalent to the much weaker principle of $\varPi ^1_1$-induction. As our second main result, we show that $\varPi ^1_1$-induction is equivalent to the uniform Kruskal theorem for $\textsf {WPO}$-dilators that are strongly normal.
ATOMS: ALMA Three-millimeter Observations of Massive Star-forming regions – XV. Steady accretion from global collapse to core feeding in massive hub-filament system SDC335
Authors: Xu Feng-Wei , Wang Ke , Liu Tie , Goldsmith Paul F , Zhang Qizhou , Juvela Mika , Liu Hong-Li , Qin Sheng-Li , Li Guang-Xing , Tej Anandmayee , Garay Guido , Bronfman Leonardo , Li Shanghuo , Wu Yue-Fang , Gómez Gilberto C , Vázquez-Semadeni Enrique , Tatematsu Ken’ichi , Ren Zhiyuan , Zhang Yong , Toth L Viktor , Liu Xunchuan , Yue Nannan , Zhang Siju , Baug Tapas , Issac Namitha , Stutz Amelia M , Liu Meizhu , Fuller Gary A , Tang Mengyao , Zhang Chao , Dewangan Lokesh , Lee Chang Won , Zhou Jianwen , Xie Jinjin , Jiao Wenyu , Wang Chao , Liu Rong , Luo Qiuyi , Soam Archana , Eswaraiah Chakali 
Published: February 2023

ABSTRACT
We present ALMA Band-3/7 observations towards ‘the Heart’ of a massive hub-filament system (HFS) SDC335, to investigate its fragmentation and accretion. At a resolution of ∼0.03 pc, 3 mm continuum emission resolves two massive dense cores MM1 and MM2, with $383(^{\scriptscriptstyle +234}_{\scriptscriptstyle -120})$ M⊙ (10–24 % mass of ‘the Heart’) and $74(^{\scriptscriptstyle +47}_{\scriptscriptstyle -24})$ M⊙, respectively. With a resolution down to 0.01 pc, 0.87 mm continuum emission shows MM1 further fragments into six condensations and multi-transition lines of H2CS provide temperature estimation. The relation between separation and mass of condensations at a scale of 0.01 pc favors turbulent Jeans fragmentation where the turbulence seems to be scale-free rather than scale-dependent. We use the H13CO+ J = 1 − 0 emission line to resolve the complex gas motion inside ‘the Heart’ in position-position-velocity space. We identify four major gas streams connected to large-scale filaments, inheriting the anti-clockwise spiral pattern. Along these streams, gas feeds the central massive core MM1. Assuming an inclination angle of 45(± 15)° and a H13CO+ abundance of 5(± 3) × 10−11, the total mass infall rate is estimated to be 2.40(± 0.78) × 10−3 M⊙ yr−1, numerically consistent with the accretion rates derived from the clump-scale spherical infall model and the core-scale outflows. The consistency suggests a continuous, near steady-state, and efficient accretion from global collapse, therefore ensuring core feeding. Our comprehensive study of SDC335 showcases the detailed gas kinematics in a prototypical massive infalling clump, and calls for further systematic and statistical studies in a large sample.
ATOMS: ALMA three-millimetre observations of massive star-forming regions – XIV. Properties of resolved ultra-compact H iiregions
Authors: Zhang C , Zhu Feng-Yao , Liu Tie , Ren Z-Y , Liu H-L , Wang Ke , Wu J-W , Zhang Y , Zhou J-W , Tatematsu K , Garay Guido , Tej Anandmayee , Li Shanghuo , Xu W F , Lee Chang Won , Bronfman Leonardo , Soam Archana , Li D 
Published: February 2023

ABSTRACTHydrogen radio recombination lines (RRLs) are one of the major diagnostics of the physical properties of H ii regions. We use RRL H40α, He40α, and 3 mm continuum emission to investigate the properties of a large sample of resolved UC H ii regions identified in the ATOMS survey. In total, we identify 94 UC H ii regions from H40α emission. The basic parameters for these UC H ii regions, such as electron density, emission measure, electron temperature, ionic abundance ratio (n$_{\rm He^+}$/n$_{\rm H^+}$), and line width are derived. The median electron density and the median n$_{\rm He^+}$/n$_{\rm H^+}$ ratio of these UC H ii regions derived from RRLs are ∼9000 cm−3 and 0.11, respectively. Within UC H ii regions, the n$_{\rm He^+}$/n$_{\rm H^+}$ ratios derived from the intensity ratio of the He40α and H40α lines seems to be higher in the boundary region than in the centre. The H40α line width is mainly broadened by thermal motion and microturbulence. The electron temperature of these UC H ii regions has a median value of ∼6700 K, and its dependence on galactocentric distance is weak.
Search for the Epoch of Reionization with HERA: upper limits on the closure phase delay power spectrum
Authors: Keller Pascal M , Nikolic Bojan , Thyagarajan Nithyanandan , Carilli Chris L , Bernardi Gianni , Charles Ntsikelelo , Bester Landman , Smirnov Oleg M , Kern Nicholas S , Dillon Joshua S , Hazelton Bryna J , Morales Miguel F , Jacobs Daniel C , Parsons Aaron R , Abdurashidova Zara , Adams Tyrone , Aguirre James E , Alexander Paul , Ali Zaki S , Baartman Rushelle , Balfour Yanga , Beardsley Adam P , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Bull Philip , Burba Jacob , Carey Steven , Cheng Carina , DeBoer David R , Acedo Eloy de Lera , Dexter Matt , Eksteen Nico , Ely John , Ewall-Wice Aaron , Fagnoni Nicolas , Fritz Randall , Furlanetto Steven R , Gale-Sides Kingsley , Glendenning Brian , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Halday Ziyaad , Hewitt Jacqueline N , Hickish Jack , Julius Austin , Kariseb MacCalvin , Kerrigan Joshua , Kittiwisit Piyanat , Kohn Saul A , Kolopanis Matthew , Lanman Adam , Plante Paul La , Liu Adrian , Loots Anita , Ma Yin-Zhe , MacMahon David Harold Edward , Malan Lourence , Malgas Cresshim , Malgas Keith , Marero Bradley , Martinot Zachary E , Mesinger Andrei , Molewa Mathakane , Mosiane Tshegofalang , Murray Steven G , Neben Abraham R , Nuwegeld Hans , Pascua Robert , Patra Nipanjana , Pieterse Samantha , Pober Jonathan C , Razavi-Ghods Nima , Robnett James , Rosie Kathryn , Santos Mario G , Sims Peter , Smith Craig , Swarts Hilton , Van Wyngaarden Pieter , Williams Peter K G , Zheng Haoxuan 
Published: February 2023

ABSTRACT
Radio interferometers aiming to measure the power spectrum of the redshifted 21 cm line during the Epoch of Reionization (EoR) need to achieve an unprecedented dynamic range to separate the weak signal from overwhelming foreground emissions. Calibration inaccuracies can compromise the sensitivity of these measurements to the effect that a detection of the EoR is precluded. An alternative to standard analysis techniques makes use of the closure phase, which allows one to bypass antenna-based direction-independent calibration. Similarly to standard approaches, we use a delay spectrum technique to search for the EoR signal. Using 94 nights of data observed with Phase I of the Hydrogen Epoch of Reionization Array (HERA), we place approximate constraints on the 21 cm power spectrum at z = 7.7. We find at 95 per cent confidence that the 21 cm EoR brightness temperature is ≤(372)2 ‘pseudo’ mK2 at 1.14 ‘pseudo’ h Mpc−1, where the ‘pseudo’ emphasizes that these limits are to be interpreted as approximations to the actual distance scales and brightness temperatures. Using a fiducial EoR model, we demonstrate the feasibility of detecting the EoR with the full array. Compared to standard methods, the closure phase processing is relatively simple, thereby providing an important independent check on results derived using visibility intensities, or related.
Planetary nurseries: vortices formed at smooth viscosity transition
Authors: Regály Zs , Kadam K , Tarczay-Nehéz D 
Published: February 2023

ABSTRACT
Excitation of Rossby wave instability and development of a large-scale vortex at the outer dead zone edge of protoplanetary discs is one of the leading theories that explains horseshoe-like brightness distribution in transition discs. Formation of such vortices requires a relatively sharp viscosity transition. Detailed modelling, however, indicates that viscosity transitions at the outer edge of the dead zone is relatively smooth. In this study, we present 2D global, non-isothermal, gas–dust coupled hydrodynamic simulations to investigate the possibility of vortex excitation at smooth viscosity transitions. Our models are based on a recently postulated scenario, wherein the recombination of charged particles on the surface of dust grains results in reduced ionization fraction and, in turn, the turbulence due to magnetorotational instability. Thus, the α-parameter for the disc viscosity depends on the local dust-to-gas mass ratio. We found that the smooth viscosity transitions at the outer edge of the dead zone can become Rossby unstable and form vortices. A single large-scale vortex develops if the dust content of the disc is well coupled to the gas; however, multiple small-scale vortices ensue for the case of less coupled dust. As both type of vortices are trapped at the dead zone outer edge, they provide sufficient time for dust growth. The solid content collected by the vortices can exceed several hundred Earth masses, while the dust-to-gas density ratio within often exceeds unity. Thus, such vortices function as planetary nurseries within the disc, providing ideal sites for formation of planetesimals and eventually planetary systems.
Three-dimensional core-collapse supernovae with complex magnetic structures – II. Rotational instabilities and multimessenger signatures
Authors: Bugli M , Guilet J , Foglizzo T , Obergaulinger M 
Published: February 2023

ABSTRACT
The gravitational collapse of rapidly rotating massive stars can lead to the onset of the low T/|W| instability within the central proto-neutron star (PNS), which leaves strong signatures in both the gravitational wave (GW) and neutrino emission. Strong large-scale magnetic fields are usually invoked to explain outstanding stellar explosions of rapidly rotating progenitors, but their impact on the growth of such instability has not yet been cleared. We analyse a series of three-dimensional magnetohydrodynamic models to characterize the effects of different magnetic configurations on the development of the low T/|W| and the related multimessenger features. In the absence of magnetic fields, we observe the growth on dynamical time-scales of the low T/|W|, associated with a strong burst of GW and a correlated modulation of the neutrino emission. However, models with a strong magnetic field show a quenching of the low T/|W|, due to a flattening of the rotation profile in the first ∼100 ms after shock formation caused by the magnetic transport of angular momentum. The associated GW emission is weakened by an order of magnitude, exhibits a broader spectral shape, and has no dominant feature associated with the PNS large-scale oscillation modes. Neutrino luminosities are damped along the equatorial plane due to a more oblate PNS, and the only clear modulation in the signal is due to Standing Accretion Shock Instability activity. Finally, magnetized models produce lower luminosities for νe than for $\bar{\nu }_e$, which is connected to a higher concentration of neutron-rich material in the PNS surroundings.