bluuebunny/crossref_metadata_2025_split huggingface dataset:
The DESI One-Percent Survey: exploring a generalized SHAM for multiple tracers with the UNIT simulation
Authors: Yu Jiaxi , Zhao Cheng , Gonzalez-Perez Violeta , Chuang Chia-Hsun , Brodzeller Allyson , de Mattia Arnaud , Kneib Jean-Paul , Krolewski Alex , Rocher Antoine , Ross Ashley , Wang Yunchong , Yuan Sihan , Zhang Hanyu , Zhou Rongpu , Aguilar Jessica Nicole , Ahlen Steven , Brooks David , Dawson Kyle , de la Macorra Alex , Doel Peter , Fanning Kevin , Font-Ribera Andreu , Forero-Romero Jaime , Gontcho Satya Gontcho A , Honscheid Klaus , Kehoe Robert , Kisner Theodore , Kremin Anthony , Landriau Martin , Manera Marc , Martini Paul , Meisner Aaron , Miquel Ramon , Moustakas John , Nie Jundan , Percival Will , Poppett Claire , Raichoor Anand , Rossi Graziano , Seo Hee-Jong , Tarlé Gregory , Zhou Zhimin , Zou Hu 
Published: November 2023

ABSTRACT
We perform SubHalo Abundance Matching (SHAM) studies on UNIT simulations with {σ, Vceil, vsmear}-SHAM and {σ, Vceil, fsat}-SHAM. They are designed to reproduce the clustering on 5–30 $\, {\, h^{-1}\, {\rm Mpc}}$ of luminous red galaxies (LRGs), emission-line galaxies (ELGs), and quasi-stellar objects (QSOs) at 0.4 &lt; z &lt; 3.5 from DESI (Dark Energy Spectroscopic Instrument) One Percent Survey. Vceil is the incompleteness of the massive host (sub)haloes and is the key to the generalized SHAM. vsmear models the clustering effect of redshift uncertainties, providing measurements consistent with those from repeat observations. A free satellite fraction fsat is necessary to reproduce the clustering of ELGs. We find ELGs present a more complex galaxy–halo mass relation than LRGs reflected in their weak constraints on σ. LRGs, QSOs, and ELGs show increasing Vceil values, corresponding to the massive galaxy incompleteness of LRGs, the quenched star formation of ELGs and the quenched black hole accretion of QSOs. For LRGs, a Gaussian vsmear presents a better profile for subsamples at redshift bins than a Lorentzian profile used for other tracers. The impact of the statistical redshift uncertainty on ELG clustering is negligible. The best-fitting satellite fraction for DESI ELGs is around 4 per cent, lower than previous estimations for ELGs. The mean halo mass log10(〈Mvir〉) in ${{\, h^{-1}\, \mbox{M}_\odot }}{}$ for LRGs, ELGs, and QSOs are 13.16 ± 0.01, 11.90 ± 0.06, and 12.66 ± 0.45, respectively. Our generalized SHAM algorithms facilitate the production of multitracer galaxy mocks for cosmological tests.
Orbit injection of planet-crossing asteroids
Authors: Namouni F 
Published: November 2023

ABSTRACT
Solar system Centaurs originate in trans-Neptunian space from where planet orbit crossing events inject their orbits inside the giant planets’ domain. Here, we examine this injection process in the three-body problem by studying the orbital evolution of trans-Neptunian asteroids located at Neptune’s collision singularity as a function of the Tisserand invariant, T. Two injection modes are found, one for T &gt; 0.1, or equivalently prograde inclinations far from the planet, where unstable motion dominates injection, and another for T ≤ 0.1, or equivalently polar and retrograde inclinations far from the planet, where stable motion dominates injection. The injection modes are independent of the initial semimajor axis and the dynamical time at the collision singularity. The simulations uncovered a region in the polar corridor where the dynamical time exceeds the Solar system’s age suggesting the possibility of long-lived primordial polar trans-Neptunian reservoirs that supply Centaurs to the giant planets’ domain.
Kinetic rate coefficients for electron-driven collisions with CH+: dissociative recombination and rovibronic excitation
Authors: Forer Joshua , Hvizdoš Dávid , Ayouz Mehdi , Greene Chris H , Kokoouline Viatcheslav 
Published: November 2023

ABSTRACT
Cross-sections and rate coefficients for rovibronic excitation of the CH+ ion by electron impact and dissociative recombination of CH+ with electrons are evaluated using a theoretical approach combining an R-matrix method and molecular quantum defect theory. The method has been developed and tested, comparing the theoretical results with the data from the recent Cryogenic Storage Ring experiment. The obtained cross-sections and rate coefficients evaluated for temperatures from 1 to 10 000 K could be used for plasma modelling in the interpretation of astrophysical observations and also in the technological applications where the molecular hydrocarbon plasma is present.
ATLAS: protein flexibility description from atomistic molecular dynamics simulations
Authors: Vander Meersche Yann , Cretin Gabriel , Gheeraert Aria , Gelly Jean-Christophe , Galochkina Tatiana 
Published: November 2023

Abstract
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.
DRMref: comprehensive reference map of drug resistance mechanisms in human cancer
Authors: Liu Xiaona , Yi Jiahao , Li Tina , Wen Jianguo , Huang Kexin , Liu Jiajia , Wang Grant , Kim Pora , Song Qianqian , Zhou Xiaobo 
Published: November 2023

Abstract
Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial–mesenchymal transition, cell–cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug’s Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user’s exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation
Authors: Icking Leon-Samuel , Riedlberger Andreas Martin , Krause Fabian , Widder Jonas , Frederiksen Anne Smedegaard , Stockert Fabian , Spädt Michael , Edel Nikita , Armbruster Daniel , Forlani Giada , Franchini Selene , Kaas Paulina , Kırpat Konak Büşra Merve , Krier Fabrice , Lefebvre Maïwenn , Mazraeh Daniel , Ranniger Jeremy , Gerstenecker Johanna , Gescher Pia , Voigt Karsten , Salavei Pavel , Gensch Nicole , Di Ventura Barbara , Öztürk Mehmet Ali 
Published: November 2023

Abstract
The incorporation of non-canonical amino acids (ncAAs) into proteins is a powerful technique used in various research fields. Genetic code expansion (GCE) is the most common way to achieve this: a specific codon is selected to be decoded by a dedicated tRNA orthogonal to the endogenous ones. In the past 30 years, great progress has been made to obtain novel tRNA synthetases (aaRSs) accepting a variety of ncAAs with distinct physicochemical properties, to develop robust in vitro assays or approaches for codon reassignment. This sparked the use of the technique, leading to the accumulation of publications, from which gathering all relevant information can appear daunting. Here we present iNClusive (https://non-canonical-aas.biologie.uni-freiburg.de/), a manually curated, extensive repository using standardized nomenclature that provides organized information on ncAAs successfully incorporated into target proteins as verified by mass spectrometry. Since we focused on tRNA synthetase-based tRNA loading, we provide the sequence of the tRNA and aaRS used for the incorporation. Derived from more than 687 peer-reviewed publications, it currently contains 2432 entries about 466 ncAAs, 569 protein targets, 500 aaRSs and 144 tRNAs. We foresee iNClusive will encourage more researchers to experiment with ncAA incorporation thus contributing to the further development of this exciting technique.
The Use of Packaging Descriptors in a Rapidly Growing Market for Capsule Cigarettes: Evidence From Mexico
Authors: Tseng Tuo-Yen , Welding Kevin , Saenz-de-Miera Belen , Grilo Graziele , Cohen Joanna E 
Published: November 2023

Abstract

Introduction
The global market for capsule cigarettes has grown rapidly, especially in Latin America. This research examined the sales trends and patterns as well as packaging characteristics of capsule cigarette in Mexico in recent years.

Methods
National data on cigarette sales in Mexico between October 2018 and September 2021 licensed from NielsenIQ were supplemented with cigarette pack pictures and Internet searches to determine whether characterizing flavor, concept flavor, and action descriptors were used. Market share in sales value and volume was calculated by capsule and flavor status, descriptors, price tier, manufacturer, pack size, and cigarette length for the whole time period and for each month. Number of unique brand variants was also examined.

Results
Capsule cigarette sales totaled US$4.29 billion or 30.99 billion sticks during the assessed period, comprising 37.7% of the cigarette market share in sales value or 35.5% in sales volume. Over half of capsule cigarettes sold during this time period had concept flavor descriptors, 17.8% contained characterizing flavor descriptors, and 15.1% contained action descriptors that were suggestive of the interactive aspects of capsules. The monthly market share of capsule cigarette sales volume among all cigarette sales in Mexico increased steadily from 33.3% in October 2018 to 37.3% in September 2021.

Conclusions
The expanding capsule cigarette market in Mexico is concerning, given the product’s associated misconceptions of reduced harm and greater appeal among youth. Findings underline the need for enhanced regulations to address the public health threat posed by capsule cigarettes.

Implications
Capsule cigarettes have a substantial market share in Mexico, with increasing popularity. Descriptors and other product characteristics such as cigarette length might be used to increase the appeal and target particular populations. Policy makers should consider banning capsules and flavors in cigarettes including descriptors or other indication in product presentation that could be perceived as denoting a taste, aroma, or sensation, and making the appearance and design of tobacco products more commensurate with the harm they cause by adopting plain and standardized packaging.
A semiconducting hybrid of RhOx/GaN@InGaN for simultaneous activation of methane and water toward syngas by photocatalysis
Authors: Li Dongke , Wu Zewen , Li Yixin , Fan Xiaoxing , Hasan S M Najib , Arafin Shamsul , Rahman Md Afjalur , Li Jinglin , Wang Zhouzhou , Yu Tianqi , Kong Xianghua , Zhu Lei , Sadaf Sharif Md , Zhou Baowen 
Published: November 2023

Abstract
Prior to the eventual arrival of carbon neutrality, solar-driven syngas production from methane steam reforming presents a promising approach to produce transportation fuels and chemicals. Simultaneous activation of the two reactants, i.e. methane and water, with notable geometric and polar discrepancy is at the crux of this important subject yet greatly challenging. This work explores an exceptional semiconducting hybrid of RhOx/GaN@InGaN nanowires for overcoming this critical challenge to achieve efficient syngas generation from methane steam reforming by photocatalysis. By coordinating density functional theoretical calculations and microscopic characterizations, with in situ spectroscopic measurements, it is found that the multifunctional RhOx/GaN interface is effective for simultaneously activating both CH4 and H2O by stretching the C–H and O–H bonds because of its unique Lewis acid/base attribute. With the aid of energetic charge carriers, the stretched C–H and O–H bonds of reactants are favorably cleaved, resulting in the key intermediates, i.e. *CH3, *OH, and *H, to sit on Rh sites, Rh sites, and N sites, respectively. Syngas is subsequently produced via energetically favored pathway without additional energy inputs except for light. As a result, a benchmarking syngas formation rate of 8.1 mol·gcat−1·h−1 is achieved with varied H2/CO ratios from 2.4 to 0.8 under concentrated light illumination of 6.3 W·cm−2, enabling the achievement of a superior turnover number of 10,493 mol syngas per mol Rh species over 300 min of long-term operation. This work presents a promising strategy for green syngas production from methane steam reforming by utilizing unlimited solar energy.
Gender stereotypes embedded in natural language are stronger in more economically developed and individualistic countries
Authors: Napp Clotilde 
Published: November 2023

Abstract
Gender stereotypes contribute to gender imbalances, and analyzing their variations across countries is important for understanding and mitigating gender inequalities. However, measuring stereotypes is difficult, particularly in a cross-cultural context. Word embeddings are a recent useful tool in natural language processing permitting to measure the collective gender stereotypes embedded in a society. In this work, we used word embedding models pre-trained on large text corpora from more than 70 different countries to examine how gender stereotypes vary across countries. We considered stereotypes associating men with career and women with family as well as those associating men with math or science and women with arts or liberal arts. Relying on two different sources (Wikipedia and Common Crawl), we found that these gender stereotypes are all significantly more pronounced in the text corpora of more economically developed and more individualistic countries. Our analysis suggests that more economically developed countries, while being more gender equal along several dimensions, also have stronger gender stereotypes. Public policy aiming at mitigating gender imbalances in these countries should take this feature into account. Besides, our analysis sheds light on the “gender equality paradox,” i.e. on the fact that gender imbalances in a large number of domains are paradoxically stronger in more developed/gender equal/individualistic countries.
Examining the Effects of Prunus Necrotic Ringspot Virus (PNRSV) and Prune Dwarf Virus (PDV) on Peach (Prunus persica) Pollen Health
Authors: Tayal Mandeep , Ratay Alexandra , Swift Nina , Kaur Satinderpal , Russo Olivia , Kariyat Rupesh , Cieniewicz Elizabeth 
Published: November 2023

Pollen health is a key determinant of successful plant reproduction and crop yield. Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV) are pollen-borne viruses of stone fruits, including peaches, primarily transmitted through vegetative propagation (i.e., grafting) and pollen. Here, we investigated the effects of PNRSV and PDV infection on peach pollen morphology, viability, and germination. Our scanning electron microscopy on pollen morphology, as well as pollen viability and germination assays, showed that PNRSV has cultivar-specific effects on pollen health; compared with pollen from virus-negative trees, PNRSV infection resulted in distorted shape, reduced viability, and germination of pollen grains of peach cultivar Red Top, but no significant effects on viability or germination were detected on cultivar Zee Lady pollen grains. PDV infection affected pollen width and reduced pollen viability but did not affect pollen germination when compared between PDV-positive and PDV-negative pollen grains. We discuss our results in terms of potential evolutionary consequences and implications on virus epidemiology and disease management in orchards. Investigating the effects of viral infection on pollen health will ultimately enhance our understanding of the transmission of pollen-borne viruses. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
“Meiosis arrester” C‐natriuretic peptide directly stimulates oocytemtDNAaccumulation and is implicated in aging‐associated oocytemtDNAloss
Authors: Tang Yawen , Cui Jian , Wang Xiaodong , Yang Qianying , Yue Yuan , Gao Chunxiao , Wang Yue , Wang Wenjing , Zhang Shuai , Tian Jianhui , Xi Guangyin , An Lei 
Published: November 2023

AbstractC‐natriuretic peptide (CNP) is the central regulator of oocyte meiosis progression, thus coordinating synchronization of oocyte nuclear‐cytoplasmic maturation. However, whether CNP can independently regulate cytoplasmic maturation has been long overlooked. Mitochondrial DNA (mtDNA) accumulation is the hallmark event of cytoplasmic maturation, but the mechanism underlying oocyte mtDNA replication remains largely elusive. Herein, we report that CNP can directly stimulate oocyte mtDNA replication at GV stage, and deficiency of follicular CNP may contribute largely to lower mtDNA copy number in in vitro matured oocytes. The mechanistic study showed that cAMP‐PKA‐CREB1 signaling cascade underlies the regulatory role of CNP in stimulating mtDNA replication and upregulating related genes. Of interest, we also report that CNP‐NPR2 signaling is inhibited in aging follicles, and this inhibition is implicated in lower mtDNA copy number in oocytes from aging females. Together, our study provides the first direct functional link between follicular CNP and oocyte mtDNA replication, and identifies its involvement in aging‐associated mtDNA loss in oocytes. These findings, not only update the current knowledge of the functions of CNP in coordinating oocyte maturation but also present a promising strategy for improving in vitro fertilization outcomes of aging females.
Depression, anxiety, and stress in pregnant Black people
Authors: Gennaro Susan , Melnyk Bernadette Mazurek , Szalacha Laura A. , Hoying Jacqueline , Cooper Andrea , Aviles Melanie Milagros , O'Connor Caitlin , Gibeau Anne 
Published: November 2023

Abstract

Background:
Guidelines call for pregnant people to be screened for depression and anxiety. Screening may be particularly important for pregnant Black individuals who are reported to be more likely than non-Hispanic White pregnant people to experience prenatal stress, anxiety, and depressive symptoms. The purpose of this study was to determine if depression, anxiety, and stress co-occur in pregnant Black people and to identify which demographic factors are related to these mental health concerns.

Methods:
A subset analysis of an ongoing randomized controlled trial examined the risk of coexisting mental health conditions in pregnant Black people who screened eligible to participate (that is, they had high levels of depression, anxiety, and/or stress) in two urban clinics using a descriptive correlational design.

Results:
Of the 452 pregnant Black people who were screened for eligibility, 194 (42.9%) had elevated scores on depression, anxiety, and/or stress measures and were enrolled in the larger study. The average scores of the 194 enrolled participants were anxiety, mean (M) = 9.16 (standard deviation [SD] = 4.30); depression, M = 12.80 (SD = 4.27); and stress, M = 21.79 (SD = 4.76). More than one-third (n = 70, 36.1%) experienced two symptoms and 64 (33.0%) reported all three symptoms.

Conclusion:
Pregnant Black individuals experience high levels of comorbid mental health distress including depression, anxiety, and stress. The findings indicate that treatment for mental health concerns needs to be broad-based and effective for all three conditions. Prenatal interventions should aim to address mental health distress through screening and treatment of depression, anxiety, and stress, especially for pregnant Black individuals. This study furthers understanding of the prevalence of prenatal mental health conditions in pregnant Black people.
Cardiometabolic outcomes in Kronos Early Estrogen Prevention Study continuation: 14-year follow-up of a hormone therapy trial
Authors: Kantarci Kejal , Tosakulwong Nirubol , Lesnick Timothy G. , Kara Firat , Kendall-Thomas June , Kapoor Ekta , Fields Julie A. , James Taryn T. , Lobo Rogerio A. , Manson JoAnn E. , Pal Lubna , Hammers Dustin B. , Malek-Ahmadi Michael , Cedars Marcelle I. , Naftolin Frederick N. , Santoro Nanette , Miller Virginia M. , Harman Sherman M. , Dowling N. Maritza , Gleason Carey E. 
Published: November 2023

Abstract

Objective
This study aimed to determine long-term cardiometabolic effects of hormone therapies initiated within 3 years of onset of menopause after a 14-year follow-up study of participants of the Kronos Early Estrogen Prevention Study (KEEPS).

Methods
KEEPS was a multisite clinical trial that recruited recently menopausal women with good cardiovascular health for randomization to oral conjugated equine estrogens (Premarin, 0.45 mg/d) or transdermal 17β-estradiol (Climara, 50 μg/d) both with micronized progesterone (Prometrium, 200 mg/d) for 12 d/mo, or placebo pills and patch for 4 years. KEEPS continuation recontacted KEEPS participants 14 years after randomization and 10 years after the completion of the 4-year clinical trial to attend in-person clinic visits.

Results
Participants of KEEPS continuation (n = 299 of the 727 KEEPS participants; 41%) had an average age of 67 years (range, 58-73 y). Measurements of systolic and diastolic blood pressures, waist-to-hip ratio, fasting levels of glucose, insulin, lipid profiles, and homeostasis model assessment of insulin resistance were not different among the treatment groups at either KEEPS baseline or at KEEPS continuation visits, or for change between these two visits. The frequency of self-reported diabetes (P = 0.007) and use of diabetes medications was higher in the placebo than the oral conjugated equine estrogens (P = 0.045) or transdermal 17β-estradiol (P = 0.02) groups, but these differences were not supported by the laboratory measurements of glycemia or insulin resistance.

Conclusions
There was no evidence of cardiovascular and/or metabolic benefits or adverse effects associated with 4 years use of oral or transdermal forms of hormone therapy by recently menopausal women with good cardiovascular health after 10 years.