bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio pulsar emission-beam geometry at low frequency: LOFAR High-Band Survey sources studied using Arecibo at 1.4 GHz and 327 MHz
Authors: Wahl Haley , Rankin Joanna , Venkataraman Arun , Olszanski Timothy 
Published: December 2022

ABSTRACT
This paper continues our study of radio pulsar emission-beam configurations with the primary intent of extending study to the lowest possible frequencies. Here, we focus on a group of 133 more recently discovered pulsars, most of which were included in the (100–200 MHz) LOFAR High-Band Survey, observed with Arecibo at 1.4 GHz and 327 MHz, and some observed at decametre wavelengths. Our analysis framework is the core/double-cone beam model, and we took opportunity to apply it as widely as possible, both conceptually and quantitatively, while highlighting situations where modelling is difficult, or where its premises may be violated. In the great majority of pulsars, beam forms consistent with the core/double-cone model were identified. Moreover, we found that each pulsar’s beam structure remained largely constant over the frequency range available; where profile variations were observed, they were attributable to different component spectra and in some instances to varying conal beam sizes. As an Arecibo population, many or most of the objects tend to fall in the Galactic anticenter region and/or at high Galactic latitudes, so overall it includes a number of nearer, older pulsars. We found a number of interesting or unusual characteristics in some of the pulsars that would benefit from additional study. The scattering levels encountered for this group are low to moderate, apart from a few pulsars lying in directions more towards the inner Galaxy.
On rapid binary mass transfer – I. Physical model
Authors: Lu Wenbin , Fuller Jim , Quataert Eliot , Bonnerot Clément 
Published: December 2022

ABSTRACT
In some semidetached binary systems, the donor star may transfer mass to the companion at a very high rate. We propose that, at sufficiently high mass-transfer rates such that the accretion disc around the companion becomes geometrically thick (or advection-dominated) near the disc outer radius, a large fraction of the transferred mass may be lost through the outer Lagrangian (L2) point, as a result of the excessive energy generated by viscous heating that cannot be efficiently radiated away. A physical model is constructed where the L2 mass-loss fraction is given by the requirement that the remaining material in the disc has Bernoulli number equal to the L2 potential energy. Our model predicts significant L2 mass-loss at mass transfer rates exceeding $\mbox{a few}\, 10^{-4}\, {\mathrm{ M}_\odot \, \mathrm{yr}^{-1}}$. An equatorial circumbinary outflow (CBO) is formed in these systems. Implications for the orbital evolution and the observational appearance of the system are discussed. In particular, (1) rapid angular momentum loss from the system tends to shrink the orbit, and hence may increase the formation rate of mergers and gravitational-wave sources; and (2) photons from the hot disc wind are reprocessed by the CBO into longer wavelength emission in the infrared bands, consistent with Spitzer observations of some ultra-luminous X-ray sources.
Redshift drift and strong gravitational lensing
Authors: Helbig Phillip 
Published: December 2022

ABSTRACT
In general, the cosmological redshift of an object changes with time, a phenomenon known as redshift drift. Although long known theoretically, recently interest has been renewed because of the possibility of measuring it on a reasonable time-scale. Strong gravitational lensing offers a possibility to measure it on a much shorter time-scale, by making use of a time delay of n years rather than making observations separated by n years, but, perhaps at least in part because of the expectation that the signal would be swamped by a larger change in redshift due to transverse motion of the lens, that has not attracted much interest. I present a method to extract the small signal, making use of the fact that the light-travel time through different parts of an Einstein ring is the same (and hence the difference in redshift due to redshift drift vanishes), thus enabling the measurement of redshift drift on a much shorter time-scale, and show how that can help in the measurement of the distribution of (dark) matter.
Effect of geometrically thin discs on precessing, thick flows: relevance to type-C QPOs
Authors: Bollimpalli D A , Fragile P C , Kluźniak W 
Published: December 2022

ABSTRACT
Type-C quasi-periodic oscillations (QPOs) are the low-frequency QPOs most commonly observed during the hard spectral state of X-ray binary systems. The leading model for these QPOs is the Lense-Thirring precession of a hot geometrically thick accretion flow that is misaligned with respect to the black hole spin axis. However, none of the work done to date has accounted for the effects of a surrounding geometrically thin disc on this precession, as would be the case in the truncated disc picture of the hard state. To address this, we perform a set of general relativistic magnetohydrodynamics simulations of truncated discs misaligned with the spin axes of their central black holes. Our results confirm that the inner-hot flow still undergoes precession, though at a rate that is only 5 per cent of what is predicted for an isolated precessing torus. We find that the exchange of angular momentum between the outer thin and the inner thick disc causes this slow-down in the precession rate and discuss its relevance to type-C QPOs.
A correlation between accreted stellar kinematics and dark-matter halo spin in the artemis simulations
Authors: Dillamore Adam M , Belokurov Vasily , Evans N Wyn , Font Andreea S 
Published: December 2022

ABSTRACT
We report a correlation between the presence of a Gaia-Sausage-Enceladus (GSE) analogue and dark-matter (DM) halo spin in the artemis simulations of Milky Way-like galaxies. The haloes which contain a large population of accreted stars on highly radial orbits (like the GSE) have lower spin on average than their counterparts with more isotropic stellar velocity distributions. The median modified spin parameters λ′ differ by a factor of ∼1.7 at the present day, with a similar value when the haloes far from virial equilibrium are removed. We also show that accreted stars make up a smaller proportion of the stellar populations in haloes containing a GSE analogue, and are stripped from satellites with stellar masses typically ∼4 times smaller. Our findings suggest that the higher spin of DM haloes without a GSE-like feature is due to mergers with large satellites of stellar mass ∼1010 M⊙, which do not result in prominent radially anisotropic features like the GSE.
Racial/Ethnic Differences Among Tumor-Infiltrating Lymphocytes in Breast Cancer Tumors
Authors: Bansil Surbhi , Silva Anthony , Taniguchi Alana , Wiedmer Christina , Fernandez Mayumi , Pagano Ian , Vierkoetter Koah , Killeen Jeffrey , Fukui Jami 
Published: December 2022

AbstractPurposeTumor-infiltrating lymphocytes (TILs) have emerged as a predictor of breast cancer treatment response and patient outcomes. Current studies investigating racial/ethnic differences in TILs and immune profiles in breast cancer offer varying results. Our study provides some preliminary data in the breast cancer tumor microenvironment where there is a paucity of information, from Asian and Native Hawaiian/Pacific Islander (NHPI) racial/ethnic groups, not well represented in the literature.MethodsWe reviewed 183 cases of women diagnosed with early stage breast cancer who received neoadjuvant treatment at 2 large health systems in Hawaii between 2008 and 2020. We evaluated clinical and demographic information including: age at diagnosis, self-reported race/ethnicity, tumor stage, tumor subtype according to ER, PR, and HER2 receptor status, the amount of TILs and pathologic complete response (pCR).ResultsWe found a significantly greater amount of TILs in Asians (37.7%, P = .01) and NHPI (37.2%, P = .02) patients compared to White patients on multivariate analysis. We found no significant differences in pCR among the different racial/ethnic groups.ConclusionsRacial/ethnic differences in the amount of TILs in breast cancer tumors may suggest differences in the breast tumor microenvironment. This may in part contribute to known outcome disparities in these populations and should be further evaluated.
Using theHER2/CEP17FISH Ratio to Predict Pathologic Complete Response Following Neoadjuvant Anti-HER2 Doublet Therapy in HER2+ Breast Cancer
Authors: Lander Eric M , Rappazzo Katherine C , Huang Li-Ching , Hu Jiun-Ruey , Chen Heidi , Shyr Yu , Abramson Vandana G 
Published: December 2022

AbstractBackgroundClinical trials of HER2-directed therapy that omit neoadjuvant conventional chemotherapy for HER+ breast cancer demonstrate that a subset of patients still obtains a pCR. Identifying tumor characteristics which predict pCR may help select patients for de-escalated neoadjuvant dual HER2-targeted treatment without chemotherapy. This is the first study evaluating the HER2/CEP17 ratio by FISH as a biomarker to predict pCR among patients who received neoadjuvant anti-HER2 regimens without chemotherapy.Patients and MethodsData from patients with locally advanced HER2+ breast cancer who received neoadjuvant dual HER2-targeted therapy without conventional chemotherapy from a single center was retrospectively reviewed. All patients were enrolled in one of 3 clinical trials evaluating chemotherapy de-escalation. Logistic regression modeling assessed for a relationship between the HER2/CEP17 FISH ratio obtained from baseline tissue biopsy and pCR based on pathology at the time of definitive breast surgery following neoadjuvant treatment.ResultsFollowing neoadjuvant treatment with dual HER2-targeted therapies in 56 patients, the probability of pCR was 73% among patients with a HER2 ratio of 13.1 compared to a probability of 38% among patients with HER2 ratio of 5.5 (OR 4.14, 95% CI 1.44-11.89; P = .012). This positive association persisted after controlling for different treatment regimens administered (OR 2.87, 95% CI 0.9-9.18, P = .020).ConclusionsThese data found a positive association between the HER2/CEP17 FISH ratio and pCR following neoadjuvant dual HER2-targeted therapy without chemotherapy. Larger prospective studies are needed to validate the HER2 ratio as a biomarker to select patients for neoadjuvant dual anti-HER2 therapy without chemotherapy.
Kinase regulators evolved into two families by gain and loss of ability to bind plant steroid receptors
Authors: Wei Qiang , Liu Jing , Guo Feimei , Wang Zhuxia , Zhang Xinzhen , Yuan Lei , Ali Khawar , Qiang Fanqi , Wen Yueming , Li Wenjuan , Zheng Bowen , Bai Qunwei , Li Guishuang , Ren Hongyan , Wu Guang 
Published: December 2022

Abstract
All biological functions evolve by fixing beneficial mutations and removing deleterious ones. Therefore, continuously fixing and removing the same essential function to separately diverge monophyletic gene families sounds improbable. Yet, here we report that brassinosteroid insensitive1 kinase inhibitor1 (BKI1)/membrane-associated kinase regulators (MAKRs) regulating a diverse function evolved into BKI1 and MAKR families from a common ancestor by respectively enhancing and losing ability to bind brassinosteroid receptor brassinosteroid insensitive1 (BRI1). The BKI1 family includes BKI1, MAKR1/BKI1-like (BKL) 1, and BKL2, while the MAKR family contains MAKR2-6. Seedless plants contain only BKL2. In seed plants, MAKR1/BKL1 and MAKR3, duplicates of BKL2, gained and lost the ability to bind BRI1, respectively. In angiosperms, BKL2 lost the ability to bind BRI1 to generate MAKR2, while BKI1 and MAKR6 were duplicates of MAKR1/BKL1 and MAKR3, respectively. In dicots, MAKR4 and MAKR5 were duplicates of MAKR3 and MAKR2, respectively. Importantly, BKI1 localized in the plasma membrane, but BKL2 localized to the nuclei while MAKR1/BKL1 localized throughout the whole cell. Importantly, BKI1 strongly and MAKR1/BKL1 weakly inhibited plant growth, but BKL2 and the MAKR family did not inhibit plant growth. Functional study of the chimeras of their N- and C-termini showed that only the BKI1 family was partially reconstructable, supporting stepwise evolution by a seesaw mechanism between their C- and N-termini to alternately gain an ability to bind and inhibit BRI1, respectively. Nevertheless, the C-terminal BRI1-interacting motif best defines the divergence of BKI1/MAKRs. Therefore, BKI1 and MAKR families evolved by gradually gaining and losing the same function, respectively, extremizing divergent evolution and adding insights into gene (BKI1/MAKR) duplication and divergence.
The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion
Authors: Wang Hanhui , Lu Yanan , Zhang Tianxu , Liu Zhi , Cao Li , Chang Qiaoying , Liu Yueying , Lu Xin , Yu Song , Li Huiyu , Jiang Jing , Liu Guifeng , Sederoff Heike W , Sederoff Ronald R , Zhang Qingzhu , Zheng Zhimin 
Published: December 2022

AbstractAs essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through Bulked Segregant Analysis (BSA) sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees.
Pharmacological potentiators of the calcium signaling cascade identified by high-throughput screening
Authors: Genovese Michele , Guidone Daniela , Buccirossi Martina , Borrelli Anna , Rodriguez-Gimeno Alejandra , Bertozzi Fabio , Bandiera Tiziano , Galietta Luis J V 
Published: December 2022

Abstract
Pharmacological modulators of the Ca2+ signaling cascade are important research tools and may translate into novel therapeutic strategies for a series of human diseases. We carried out a screening of a maximally diverse chemical library using the Ca2+-sensitive Cl− channel TMEM16A as a functional readout. We found compounds that were able to potentiate UTP-dependent TMEM16A activation. Mechanism of action of these compounds was investigated by a panel of assays that looked at intracellular Ca2+ mobilization triggered by extracellular agonists or by caged-IP3 photolysis, PIP2 breakdown by phospholipase C, and ion channel activity on nuclear membrane. One compound appears as a selective potentiator of inositol triphosphate receptor type 1 (ITPR1) with a possible application for some forms of spinocerebellar ataxia. A second compound is instead a potentiator of the P2RY2 purinergic receptor, an activity that could promote fluid secretion in dry eye and chronic obstructive respiratory diseases.
Risky cascading transitions in international relationships
Authors: Zhang Mingyuan , Chen Shenwen , Du Wenbo , Cao Xianbin , Li Daqing , Zhang Jun , Havlin Shlomo 
Published: December 2022

Abstract
Changing attitudes in diplomatic relations is a common feature of international politics. However, such changes may trigger risky domino-like cascades of “friend-to-enemy” transitions among other counties and yielding catastrophic damage that could reshape the global network of international relationships. While previous attention has been focused on studying single pairs of international relationships, due to the lack of a systematic framework, it remains still unknown whether, and how, a single transition of attitude between two countries could trigger a cascade of attitude transitions among other countries. Here, we develop such a framework and construct a global evolving network of relations between country pairs based on 70,756,728 international events between 1,225 country pairs from January 1995 to March 2020. Our framework can identify and quantify the cascade of transitions following a given original transition. Surprisingly, weaker transitions are found to initiate most of the largest cascades. We also find that transitions are not only related to the balance of the local environment, but also global network properties such as betweenness centrality. Our results suggest that these transitions have a substantial impact on bilateral trade volumes and scientific collaborations. Our results reveal reaction chains of international relations, which could be helpful for designing early warning signals and mitigation methods for global international conflicts.
Paxillin tunes the relationship between cell–matrix and cell–cell adhesions to regulate stiffness-dependent dentinogenesis
Authors: Bai Mingru , Zhang Zhaowei , Chen Huiyu , Liu Xiaoyu , Xie Jing 
Published: December 2022

Abstract
Mechanical stiffness is recognized as a key physical factor and directs cell function via a mechanotransduction process, from extracellular physical cues to intracellular signaling cascades that affect transcriptional activity. Cells continually receive mechanical signals from both the surrounding matrix and adjacent cells. However, how mechanical stiffness cue at cell–substrate interfaces coordinates cell–cell junctions in guiding mesenchymal stem cell behaviors is poorly understood. Here, polydimethylsiloxane substrates with different stiffnesses were used to study mechanosensation/transduction mechanisms in controlling odontogenic differentiation of dental papilla cells (DPCs). DPC phenotypes (morphology and differentiation) changed in response to the applied force derived from stiff substrates. Significantly, higher expression of paxillin on stiffer substrates promoted DPC dentinogenesis. Upon treatment with siRNA to knockdown paxillin, N-cadherin increased mainly in the cytomembrane at the area of cell–cell contacts, whereas β-catenin decreased in the nuclei. The result of a double luciferase reporter assay showed that stiffness promoted β-catenin binding to TCF, which could coactivate the target genes associated with odontogenic differentiation, as evidenced by bioinformatics analysis. Finally, we determined that the addition of a β-catenin inhibitor suppressed DPC mineralization in all the stiffness groups. Thus, our results indicated that a mechanotransduction process from cell–substrate interactions to cell–cell adhesions was required for DPC odontogenic differentiation under the stimulation of substrate stiffness. This finding suggests that stem cell fate specification under the stimulus of stiffness at the substrates is based on crosstalk between substrate interactions and adherens junctions, which provides an essential mechanism for cell-based tissue engineering.
The PICC in Chinese Courts
Authors: Liu Qiao 
Published: December 2022

Abstract
This article offers, for the first time, a comprehensive survey of all accessible (28) Chinese cases in which Chinese judges or lawyers invoked the Unidroit Principles of International Commercial Contracts (PICC) as applicable law or otherwise made a reference to the PICC. The survey has a particular focus on the use of the PICC to interpret or supplement domestic law, which is widely assumed to have no direct impact on the decisions of local courts. Through a detailed analysis that explores the often-times subtle connection between the PICC and judicial reasoning in Chinese courtrooms, the survey rebuts the ‘no direct impact’ thesis and demonstrates and expounds a range of significant roles the PICC may play in this respect. In doing so, this article also illustrates the case-guiding effect of previously little-known case comments—the dominant vehicle by which Chinese judges presently make the above use of the PICC.
Polymorphisms predicting phylogeny in hepatitis B virus
Authors: Lourenço José , McNaughton Anna L , Pley Caitlin , Obolski Uri , Gupta Sunetra , Matthews Philippa C 
Published: December 2022

Abstract
Hepatitis B viruses (HBVs) are compact viruses with circular genomes of ∼3.2 kb in length. Four genes (HBx, Core, Surface, and Polymerase) generating seven products are encoded on overlapping reading frames. Ten HBV genotypes have been characterised (A–J), which may account for differences in transmission, outcomes of infection, and treatment response. However, HBV genotyping is rarely undertaken, and sequencing remains inaccessible in many settings. We set out to assess which amino acid (aa) sites in the HBV genome are most informative for determining genotype, using a machine learning approach based on random forest algorithms (RFA). We downloaded 5,496 genome-length HBV sequences from a public database, excluding recombinant sequences, regions with conserved indels, and genotypes I and J. Each gene was separately translated into aa, and the proteins concatenated into a single sequence (length 1,614 aa). Using RFA, we searched for aa sites predictive of genotype and assessed covariation among the sites with a mutual information–based method. We were able to discriminate confidently between genotypes A–H using ten aa sites. Half of these sites (5/10) sites were identified in Polymerase (Pol), of which 4/5 were in the spacer domain and one in reverse transcriptase. A further 4/10 sites were located in Surface protein and a single site in HBx. There were no informative sites in Core. Properties of the aa were generally not conserved between genotypes at informative sites. Among the highest co-varying pairs of sites, there were fifty-five pairs that included one of these ‘top ten’ sites. Overall, we have shown that RFA analysis is a powerful tool for identifying aa sites that predict the HBV lineage, with an unexpectedly high number of such sites in the spacer domain, which has conventionally been viewed as unimportant for structure or function. Our results improve ease of genotype prediction from limited regions of HBV sequences and may have future applications in understanding HBV evolution.