bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why are we still using 3D masses for cluster cosmology?
Authors: Debackere Stijn N B , Hoekstra Henk , Schaye Joop , Heitmann Katrin , Habib Salman 
Published: June 2022

ABSTRACT
The abundance of clusters of galaxies is highly sensitive to the late-time evolution of the matter distribution, since clusters form at the highest density peaks. However, the 3D cluster mass cannot be inferred without deprojecting the observations, introducing model-dependent biases and uncertainties due to the mismatch between the assumed and the true cluster density profile and the neglected matter along the sightline. Since projected aperture masses can be measured directly in simulations and observationally through weak lensing, we argue that they are better suited for cluster cosmology. Using the Mira–Titan suite of gravity-only simulations, we show that aperture masses correlate strongly with 3D halo masses, albeit with large intrinsic scatter due to the varying matter distribution along the sightline. Nonetheless, aperture masses can be measured ≈2–3 times more precisely from observations, since they do not require assumptions about the density profile and are only affected by the shape noise in the weak lensing measurements. We emulate the cosmology dependence of the aperture mass function directly with a Gaussian process. Comparing the cosmology sensitivity of the aperture mass function and the 3D halo mass function for a fixed survey solid angle and redshift interval, we find the aperture mass sensitivity is higher for Ωm and $w_a$, similar for σ8, ns, and $w_0$, and slightly lower for h. With a carefully calibrated aperture mass function emulator, cluster cosmology analyses can use cluster aperture masses directly, reducing the sensitivity to model-dependent mass calibration biases and uncertainties.
Explaining prolonged fluctuations in light curves of classical novae via modelling
Authors: Hillman Yael 
Published: June 2022

ABSTRACT
Fluctuations during a prolonged maximum have been observed in several nova eruptions, although it is not clear, and cannot be deduced directly from observations, whether the phenomenon is an actual physical reaction to some mechanism originating in the erupting white dwarf, whether it is occurring in the expanding ejected shell, or whether it is a form of interaction with the red dwarf companion. A handful of erupting nova models are investigated in this work, in order to assess the possibility of this sort of feature being an actual part of the eruption itself. The results explain that the mechanism that may produce these fluctuations is the repeated approach and recession of the convective front from the surface. The efficiency of this mechanism, being dependent on the mass of the WD (white dwarf) envelope and the time-scale of the nova cycle, favours low-mass WDs and long accretion phases.
Investigation of stellar magnetic activity using variational autoencoder based on low-resolution spectroscopic survey
Authors: Xiang Yue , Gu Shenghong , Cao Dongtao 
Published: June 2022

ABSTRACT
We apply the variational autoencoder (VAE) to the LAMOST-K2 low-resolution spectra to detect the magnetic activity of the stars in the K2 field. After the training on the spectra of the selected inactive stars, the VAE model can efficiently generate the synthetic reference templates needed by the spectral subtraction procedure, without knowing any stellar parameters. Then, we detect the peculiar spectral features, such as chromospheric emissions, strong nebular emissions, and lithium absorptions, in our sample. We measure the emissions of the chromospheric activity indicators, Hα and Ca ii infrared triplet (IRT) lines, to quantify the stellar magnetic activity. The excess emissions of Hα and Ca ii IRT lines of the active stars are correlated well to the rotational periods and the amplitudes of light curves derived from the K2 photometry. We degrade the LAMOST spectra to simulate the slitless spectra of the China Space Station Telescope (CSST) and apply the VAE to the simulated data. For cool active stars, we reveal a good agreement between the equivalent widths of Hα line derived from the spectra with two resolutions. The result indicates the ability of identifying the magnetically active stars in the future CSST survey, which will deliver an unprecedented large data base of low-resolution spectra as well as simultaneous multiband photometry of stars.
MOCCA-survey data base: extra galactic globular clusters – II. Milky Way and Andromeda
Authors: Leveque A , Giersz M , Arca-Sedda M , Askar Abbas 
Published: June 2022

ABSTRACT
A comprehensive study of the co-evolution of globular cluster systems (GCS) in galaxies requires the ability to model both the large-scale dynamics (0.01–10 kpc) regulating their orbital evolution, and the small-scale dynamics (sub-pc – au) regulating the internal dynamics of each globular cluster (GC). In this work, we present a novel method that combine semi-analytic models of GCS with fully self-consistent Monte Carlo models to simultaneously evolve large GCSs. We use the population synthesis code MASinGa and the MOCCA-Survey Database I to create synthetic GC populations aimed at representing the observed features of GCs in the Milky Way (MW) and Andromeda (M31). Our procedure enables us to recover the spatial and mass distribution of GCs in such galaxies, and to constrain the amount of mass that GCs left either in the halo as dispersed debris, or in the galactic centre, where they can contribute to the formation of a nuclear star cluster (NSC) and can bring stellar and possibly intermediate mass black holes there. The final masses reported by our simulations are of a few order of magnitudes smaller than the observed values. These differences show that mass build-up of an NSC and central BHs in galaxies like MW and M31 cannot be solely explained by the infalling GC scenario. This build-up is likely to depend on the interplay between interactions and mergers of infalling GCs and gas. The latter can contribute to both in situ star formation in the NSC and growth of the central BH.
Human Follicular Mites: Ectoparasites Becoming Symbionts
Authors: Smith Gilbert , Manzano-Marín Alejandro , Reyes-Prieto Mariana , Antunes Cátia Sofia Ribeiro , Ashworth Victoria , Goselle Obed Nanjul , Jan Abdulhalem Abdulsamad A , Moya Andrés , Latorre Amparo , Perotti M Alejandra , Braig Henk R 
Published: June 2022

AbstractMost humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans that continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic, or endosymbiotic lifestyle. Somatic nuclei show under-replication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.
A New Paradigm of Multiheme Cytochrome Evolution by Grafting and Pruning Protein Modules
Authors: Soares Ricardo , Costa Nazua L , Paquete Catarina M , Andreini Claudia , Louro Ricardo O 
Published: June 2022

AbstractMultiheme cytochromes play key roles in diverse biogeochemical cycles, but understanding the origin and evolution of these proteins is a challenge due to their ancient origin and complex structure. Up until now, the evolution of multiheme cytochromes composed by multiple redox modules in a single polypeptide chain was proposed to occur by gene fusion events. In this context, the pentaheme nitrite reductase NrfA and the tetraheme cytochrome c554 were previously proposed to be at the origin of the extant octa- and nonaheme cytochrome c involved in metabolic pathways that contribute to the nitrogen, sulfur, and iron biogeochemical cycles by a gene fusion event. Here, we combine structural and character-based phylogenetic analysis with an unbiased root placement method to refine the evolutionary relationships between these multiheme cytochromes. The evidence show that NrfA and cytochrome c554 belong to different clades, which suggests that these two multiheme cytochromes are products of truncation of ancestral octaheme cytochromes related to extant octaheme nitrite reductase and MccA, respectively. From our phylogenetic analysis, the last common ancestor is predicted to be an octaheme cytochrome with nitrite reduction ability. Evolution from this octaheme framework led to the great diversity of extant multiheme cytochromes analyzed here by pruning and grafting of protein modules and hemes. By shedding light into the evolution of multiheme cytochromes that intervene in different biogeochemical cycles, this work contributes to our understanding about the interplay between biology and geochemistry across large time scales in the history of Earth.
Association of disease activity using SDAI and DAS28, but not JADAS-27, with subsequent changes in physical function in adult patients with juvenile idiopathic arthritis
Authors: Miyamae Takako , Inoue Eisuke , Tanaka Eiichi , Kawabe Tomohiro , Ikari Katsunori , Harigai Masayoshi 
Published: June 2022

ABSTRACT

Objectives
To investigate an optimal composite score for disease activity in adult JIA from the viewpoint of the subsequent changes in physical function.

Methods
Patients with JIA under the following conditions were enrolled: 1) disease onset &lt; 18 years; 2) registered in the database by Tokyo Women’s Medical University for the first time between 2000 and 2020; and 3) ≥18 years old at the time of registration. Patients were stratified according to mean disease activity scores in SDAI, DAS28, and JADAS-27 during the first year from baseline. Trends of estimated mean change in Japanese-HAQ score (ΔJ-HAQ) from baseline to 2 years later was examined across the stratified groups of each index.

Results
We included 294 eligible individuals (median age at onset, 14.0 years; RF positive in 64.7%). A significant increasing trend of the estimated mean ΔJ-HAQ at 2 years after baseline was observed along with an increase in the mean disease activity during the first year measured using DAS28 (p = 0.01) and SDAI (p = 0.018), but not using JADAS-27.

Conclusions
Disease activity measured using SDAI and DAS28, but not using JADAS27, was significantly associated with subsequent changes in physical function in adult patients with JIA.
Controllable assembly of synthetic constructs with programmable ternary DNA interaction
Authors: Cui Huangchen , Zhang Tianqing , Kong Yuhan , Xing Hang , Wei Bryan 
Published: June 2022

Abstract
Compared with the dual binding components in a binary interaction, the third component of a ternary interaction often serves as modulator or regulator in biochemical processes. Here, we presented a programmable ternary interaction strategy based on the natural DNA triplex structure. With the DNA triplex-based ternary interaction, we have successfully demonstrated controllable hierarchical assemblies from nanometer scale synthetic DNA nanostructure units to micrometer scale live bacteria. A selective signaling system responsive to orthogonal nucleic acid signals via ternary interaction was also demonstrated. This assembly method could further enrich the diversified design schemes of DNA nanotechnology.
Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair
Authors: Fu Iwen , Mu Hong , Geacintov Nicholas E , Broyde Suse 
Published: June 2022

Abstract
In nucleotide excision repair (NER), the xeroderma pigmentosum D helicase (XPD) scans DNA searching for bulky lesions, stalls when encountering such damage to verify its presence, and allows repair to proceed. Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6−4) pyrimidone UV photoproduct (6−4PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215−221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.
Progesterone Increases Nicotine Withdrawal and Anxiety in Male but Not Female Smokers During Brief Abstinence
Authors: Novick Andrew M , Duffy Korrina A , Johnson Rachel L , Sammel Mary D , Cao Wen , Strasser Andrew A , Sofuoglu Mehmet , Kuzma Alexandra , Loughead James , Epperson C Neill 
Published: June 2022

Abstract

Introduction
Although exogenous progesterone may hold promise as a treatment for nicotine use disorders, it is unclear whether it is similarly effective in males and females. This study examined the effects of progesterone on nicotine use disorder comprehensively using behavioral, psychological, and neural measures in male and female smokers exposed to brief abstinence.

Aims and Methods
Thirty-three male and 33 female non-treatment-seeking smokers participated in a double-blind, randomized, placebo-controlled crossover study of 200 mg of progesterone or placebo daily over a four-day abstinence period. Smoking behavior and subjective effects of nicotine were assessed at baseline and after final drug administration. Nicotine withdrawal, smoking urges, mood states, and neural response to smoking cues were measured at baseline, after the first drug administration, and after the final drug administration.

Results
No main effect of drug (progesterone vs. placebo) emerged for any outcome. Significant sex by drug interactions emerged for nicotine withdrawal (p = .020), perceived strength of nicotine (p = .040), and perceived bad effects of nicotine (p = .029). Males receiving progesterone reported worse nicotine withdrawal (p = .046) and a trend towards decreased bad effects of nicotine (p = .070). Males on progesterone also reported greater tension and anxiety relative to placebo (p = .021). Females on progesterone perceived nicotine’s effects as being stronger relative to placebo (p = .046).

Conclusions
Progesterone causes sex-dependent effects on smoking-related outcomes during brief abstinence. Specifically, progesterone in males may increase rather than decrease nicotine withdrawal and negative affect during abstinence, potentially hindering efforts to quit smoking.

Implications
In male and female smokers undergoing a brief period of abstinence, we examined the effects of progesterone on smoking outcomes. While progesterone had limited effects in female smokers, in males, it worsened nicotine withdrawal and negative affect. Our findings emphasize the importance of analyzing sex differences in future studies examining progesterone as a potential treatment and suggest that progesterone in males could potentially exacerbate aspects of nicotine dependence.

Clinicaltrials.gov registration
NCT01954966. https://clinicaltrials.gov/ct2/show/NCT01954966
Epidemiology of Antimicrobial Resistance Among Blood and Respiratory Specimens in the United States Using Genotypic Analysis From a Cloud-Based Population Surveillance Network
Authors: Timbrook Tristan T , Olin Katherine E , Spaulding Usha , Galvin Ben W , Cox Charles B 
Published: June 2022

Abstract

Background
Antimicrobial resistance (AMR) surveillance is critical in informing strategies for infection control in slowing the spread of resistant organisms and for antimicrobial stewardship in the care of patients. However, significant challenges exist in timely and comprehensive AMR surveillance.

Methods
Using BioFire Pneumonia and Blood Culture 2 Panels data from BioFire Syndromic Trends (Trend), a cloud-based population surveillance network, we described the detection rate of AMR among a US cohort. Data were included from 2019 to 2021 for Gram-positive and -negative organisms and their related AMR genomic-resistant determinants as well as for detections of Candida auris. Regional and between panel AMR detection rate differences were compared. In addition, AMR codetections and detection rate per organism were evaluated for Gram-negative organisms.

Results
A total of 26 912 tests were performed, primarily in the Midwest. Overall, AMR detection rate was highest in the South and more common for respiratory specimens than blood. methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus detection rates were 34.9% and 15.9%, respectively, whereas AMR for Gram-negative organisms was lower with 7.0% CTX-M and 2.9% carbapenemases. In addition, 10 mcr-1 and 4 C auris detections were observed. For Gram-negative organisms, Klebsiella pneumoniae and Escherichia coli were most likely to be detected with an AMR gene, and of Gram-negative organisms, K pneumoniae was most often associated with 2 or more AMR genes.

Conclusions
Our study provides important in-depth evaluation of the epidemiology of AMR among respiratory and blood specimens for Gram-positive and -negative organism in the United States. The Trend surveillance network allows for near real-time surveillance of AMR.
Anatomic Site–Specific Gonorrhea and Chlamydia Testing and Incidence Among People With HIV Engaged in Care at 4 US Clinical Centers, 2014–2018
Authors: Menza Timothy W , Berry Stephen A , Dombrowski Julie , Cachay Edward , Crane Heidi M , Kitahata Mari M , Mayer Kenneth H 
Published: June 2022

Abstract

Background
The incidence of Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) is increasing in the United States; however, there are limited data on anatomic site–specific GC/CT among people with HIV (PWH).

Methods
We reviewed records of all PWH in care between January 1, 2014, and November 16, 2018, at 4 sites in the CFAR Network of Integrated Clinical Systems Cohort (CNICS; n = 8455). We calculated anatomic site–specific GC/CT testing and incidence rates and used Cox proportional hazards models modified for recurrent events to examine sociodemographic and clinical predictors of GC/CT testing and incidence at urogenital, rectal, and pharyngeal sites. We also calculated site-specific number needed to test (NNT) to detect a positive GC/CT test.

Results
Of 8455 PWH, 2460 (29.1%) had at least yearly GC/CT testing at any anatomic site. The rates of urogenital, rectal, and pharyngeal GC were 1.7 (95% CI, 1.6–1.9), 3.2 (95% CI, 3.0–3.5), and 2.7 (95% CI, 2.5–2.9) infections per 100 person-years, respectively. The rates of urogenital, rectal, and pharyngeal CT were 1.9 (95% CI, 1.7–2.1), 4.3 (95% CI, 4.0–4.5), and 0.9 (95% CI, 0.8–1.0) infections per 100 person-years, respectively. PWH 16–39 years old experienced greater GC/CT rates at all anatomic sites, while men who have sex with men experienced greater rates of extragenital infections. NNTs for urogenital, rectal, and pharyngeal GC/CT were 20 (95% CI, 19–21), 5 (95% CI, 5–5), and 9 (95% CI, 8–9), respectively.

Conclusions
Many PWH are not tested annually for GC/CT, and rates of GC/CT infection, particularly rates of extragenital infections, are high. We identified groups of PWH who may benefit from increased site-specific GC/CT testing.
Mass gain and stopover dynamics among migrating songbirds are linked to seasonal, environmental, and life-history effects
Authors: de Zwaan Devin R , Huang Andrew , McCallum Quinn , Owen Kiirsti , Lamont Myles , Easton Wendy 
Published: June 2022

Abstract
During migration, birds must stopover at refueling sites to replenish energy stores, with the rate of refueling linked to stopover length, migration speed, and the timing of critical life stages, such as breeding. Under optimal migration theory, birds are expected to maximize fuel intake and minimize stopover length (the time minimization hypothesis). Within a multi-species framework, we demonstrate that time minimization behavior is context-dependent, as refueling rate, stopover length, and departure decisions vary between seasons, among species with different ecological traits (e.g., diet and migration distance), and in response to density-dependent factors and prevailing environmental conditions. Using long-term banding data (10 years) from southwestern British Columbia, Canada, we investigated the ecological processes shaping stopover dynamics among 5 warbler (Parulidae) and 5 sparrow species (Passerellidae). Specifically, we assessed variation in fuel deposition rates (FDRs) as well as the associations between mass gain, stopover length, and departure probability. FDR was greater in insectivorous warblers during spring migration and in species migrating long distances. FDR responded positively to temperature and habitat productivity, but negatively to precipitation events, particularly for insectivorous, long-distance migrants during spring migration. Similarly, density-dependent refueling rate was only observed in insectivores and long-distance migrants during spring migration, where higher densities of foliage-gleaning insectivores were associated with a lower FDR. Stopover duration was more closely associated with body condition upon arrival and subsequent mass gain than direct environmental effects, especially during northward spring migration, providing support for time minimization and a mass threshold influencing departure decisions. These results highlight that refueling rates and stopover quality vary among species depending on their life-history strategies, with particular implications for long-distance, migratory insectivores, which may be most susceptible to climate shifts.