bluuebunny/crossref_metadata_2025_split huggingface dataset:
The XMM Cluster Survey analysis of the SDSS DR8 redMaPPer catalogue: implications for scatter, selection bias, and isotropy in cluster scaling relations
Authors: Giles P A , Romer A K , Wilkinson R , Bermeo A , Turner D J , Hilton M , Upsdell E W , Rooney P J , Bhargava S , Ebrahimpour L , Farahi A , Mann R G , Manolopoulou M , Mayers J , Vergara C , Viana P T P , Collins C A , Hollowood D , Jeltema T , Miller C J , Nichol R C , Noorali R , Splettstoesser M , Stott J P 
Published: August 2022

ABSTRACT
In this paper, we present the X-ray analysis of Sloan Digital Sky Survey DR8 redMaPPer (SDSSRM) clusters using data products from the XMM Cluster Survey (XCS). In total, 1189 SDSSRM clusters fall within the XMM–Newton footprint. This has yielded 456 confirmed detections accompanied by X-ray luminosity (LX) measurements. Of these clusters, 381 have an associated X-ray temperature measurement (TX). This represents one of the largest samples of coherently derived cluster TX values to date. Our analysis of the X-ray observable to richness scaling relations has demonstrated that scatter in the TX–λ relation is roughly a third of that in the LX–λ relation, and that the LX–λ scatter is intrinsic, i.e. will not be significantly reduced with larger sample sizes. Analysis of the scaling relation between LX and TX has shown that the fits are sensitive to the selection method of the sample, i.e. whether the sample is made up of clusters detected ‘serendipitously’ compared to those deliberately targeted by XMM. These differences are also seen in the LX–λ relation and, to a lesser extent, in the TX–λ relation. Exclusion of the emission from the cluster core does not make a significant impact on the findings. A combination of selection biases is a likely, but yet unproven, reason for these differences. Finally, we have also used our data to probe recent claims of anisotropy in the LX–TX relation across the sky. We find no evidence of anistropy, but stress this may be masked in our analysis by the incomplete declination coverage of the SDSS.
ATLASGAL - star forming efficiencies and the Galactic star formation rate
Authors: Wells M R A , Urquhart J S , Moore T J T , Browning K E , Ragan S E , Rigby A J , Eden D J , Thompson M A 
Published: August 2022

ABSTRACT
The ATLASGAL survey has characterized the properties of approximately 1000 embedded H ii regions and found an empirical relationship between the clump mass and bolometric luminosity that covers 3–4 orders of magnitude. Comparing this relation with simulated clusters drawn from an initial mass function and using different star formation efficiencies we find that a single value is unable to fit the observed luminosity to mass (L/M) relation. We have used a Monte Carlo simulation to generate 200 000 clusters using the L/M-ratio as a constraint to investigate how the star formation efficiency changes as a function of clump mass. This has revealed that the star formation efficiency decreases with increasing clump mass with a value of 0.2 for clumps with masses of a few hundred solar masses and dropping to 0.08 for clumps with masses of a few thousand solar masses. We find good agreement between our results and star formation efficiencies determined from counts of embedded objects in nearby molecular clouds. Using the star formation efficiency relationship and the infrared excess time for embedded star formation of 2 ± 1 Myr we estimate the Galactic star formation rate to be approximately 0.9 ± 0.45 M⊙ yr−1, which is in good agreement with previously reported values. This model has the advantage of providing a direct means of determining the star formation rate and avoids the difficulties encountered in converting infrared luminosities to stellar mass that affect previous galactic and extragalactic studies.
Pulsar death line revisited – II. ‘The death valley’
Authors: Beskin V S , Istomin A Yu 
Published: August 2022

ABSTRACTIn this paper, which is the second in a series of papers, we analyse what parameters can determine the width of the radio pulsar ‘death valley’ in the P–${\dot{P}}$ diagram. Using exact expression for the maximum potential drop, which can be realized over magnetic polar caps and the corresponding threshold for the secondary plasma production determined in Paper I, we analyse in detail the observed distribution of pulsars taking into account all the possible parameters (radius R and moment of inertia of a neutron star Ir, high-energy tail in the γ-quanta energy distribution giving rise to secondary particles, etc.) which could broaden ‘the death line’. We show that the consistent allowance for all these effects leads to a sufficiently wide of ‘the death valley’ containing all the observed pulsars even for dipole magnetic field of a neutron star. We emphasize that the main goal of this work is to demonstrate that the original Ruderman–Sutherland idea of the death line (dipole magnetic field, vacuum gap) is in good agreement with observations. The comparison with other models is beyond the scope of this paper.
The Pristine survey – XVI. The metallicity of 26 stellar streams around the Milky Way detected with the STREAMFINDER in Gaia EDR3
Authors: Martin Nicolas F , Ibata Rodrigo A , Starkenburg Else , Yuan Zhen , Malhan Khyati , Bellazzini Michele , Viswanathan Akshara , Aguado David , Arentsen Anke , Bonifacio Piercarlo , Carlberg Ray , González Hernández Jonay I , Hill Vanessa , Jablonka Pascale , Kordopatis Georges , Lardo Carmela , McConnachie Alan W , Navarro Julio , Sánchez-Janssen Rubén , Sestito Federico , Thomas Guillaume F , Venn Kim A , Vitali Sara , Voggel Karina T 
Published: August 2022

ABSTRACT
We use the photometric metallicities provided by the panoramic Pristine survey to study the veracity and derive the metallicities of the numerous stellar streams found by the application of the STREAMFINDER algorithm to the Gaia Early Data Release 3 data. All 26 streams present in Pristine show a clear metallicity distribution function, which provides an independent check of the reality of these structures, supporting the reliability of STREAMFINDER in finding streams and the power of Pristine to measure precise metallicities. We further present six candidate structures with coherent phase-space and metallicity signals that are very likely streams. The majority of studied streams are very metal-poor (14 structures with [Fe/H] &lt; −2.0) and include three systems with [Fe/H] &lt; −2.9 (C-11, C-19, and C-20). These streams could be the closest debris of low-luminosity dwarf galaxies or may have originated from globular clusters of significantly lower metallicity than any known current Milky Way globular cluster. Our study shows that the promise of the Gaia data for Galactic Archeology studies can be substantially strengthened by quality photometric metallicities, allowing us to peer back into the earliest epochs of the formation of our Galaxy and its stellar halo constituents.
Chromatin fiber breaks into clutches under tension and crowding
Authors: Liu Shuming , Lin Xingcheng , Zhang Bin 
Published: August 2022

Abstract
The arrangement of nucleosomes inside chromatin is of extensive interest. While in vitro experiments have revealed the formation of 30 nm fibers, most in vivo studies have failed to confirm their presence in cell nuclei. To reconcile the diverging experimental findings, we characterized chromatin organization using a residue-level coarse-grained model. The computed force–extension curve matches well with measurements from single-molecule experiments. Notably, we found that a dodeca-nucleosome in the two-helix zigzag conformation breaks into structures with nucleosome clutches and a mix of trimers and tetramers under tension. Such unfolded configurations can also be stabilized through trans interactions with other chromatin chains. Our study suggests that unfolding from chromatin fibers could contribute to the irregularity of in vivo chromatin configurations. We further revealed that chromatin segments with fibril or clutch structures engaged in distinct binding modes and discussed the implications of these inter-chain interactions for a potential sol–gel phase transition.
Dichotomouscis-regulatory motifs mediate the maturation of the neuromuscular junction by retrograde BMP signaling
Authors: Vuilleumier Robin , Miao Mo , Medina-Giro Sonia , Ell Clara-Maria , Flibotte Stephane , Lian Tianshun , Kauwe Grant , Collins Annie , Ly Sophia , Pyrowolakis George , Haghighi A Pejmun , Allan Douglas W 
Published: August 2022

AbstractRetrograde bone morphogenetic protein (BMP) signaling at the Drosophila neuromuscular junction (NMJ) has served as a paradigm to study TGF-β-dependent synaptic function and maturation. Yet, how retrograde BMP signaling transcriptionally regulates these functions remains unresolved. Here, we uncover a gene network, enriched for neurotransmission-related genes, that is controlled by retrograde BMP signaling in motor neurons through two Smad-binding cis-regulatory motifs, the BMP-activating (BMP-AE) and silencer (BMP-SE) elements. Unpredictably, both motifs mediate direct gene activation, with no involvement of the BMP derepression pathway regulators Schnurri and Brinker. Genome editing of candidate BMP-SE and BMP-AE within the locus of the active zone gene bruchpilot, and a novel Ly6 gene witty, demonstrated the role of these motifs in upregulating genes required for the maturation of pre- and post-synaptic NMJ compartments. Our findings uncover how Smad-dependent transcriptional mechanisms specific to motor neurons directly orchestrate a gene network required for synaptic maturation by retrograde BMP signaling.
Topoisomerase IIA in adult NSCs regulates SVZ neurogenesis by transcriptional activation of Usp37
Authors: Qin Shangyao , Yuan Yimin , Huang Xiao , Tan Zijian , Hu Xin , Liu Hong , Pu Yingyan , Ding Yu-qiang , Su Zhida , He Cheng 
Published: August 2022

Abstract
Topoisomerase IIA (TOP2a) has traditionally been known as an important nuclear enzyme that resolves entanglements and relieves torsional stress of DNA double strands. However, its function in genomic transcriptional regulation remains largely unknown, especially during adult neurogenesis. Here, we show that TOP2a is preferentially expressed in neurogenic niches in the brain of adult mice, such as the subventricular zone (SVZ). Conditional knockout of Top2a in adult neural stem cells (NSCs) of the SVZ significantly inhibits their self-renewal and proliferation, and ultimately reduces neurogenesis. To gain insight into the molecular mechanisms by which TOP2a regulates adult NSCs, we perform RNA-sequencing (RNA-Seq) plus chromatin immunoprecipitation sequencing (ChIP-Seq) and identify ubiquitin-specific protease 37 (Usp37) as a direct TOP2a target gene. Importantly, overexpression of Usp37 is sufficient to rescue the impaired self-renewal ability of adult NSCs caused by Top2a knockdown. Taken together, this proof-of-principle study illustrates a TOP2a/Usp37-mediated novel molecular mechanism in adult neurogenesis, which will significantly expand our understanding of the function of topoisomerase in the adult brain.
Association of branched chain fatty acids with cardiometabolic disorders in humans: a systematic review
Authors: Yehia Nagam Anna , Lai Kira Zhi Hua , Semnani-Azad Zhila , Blanco Mejia Sonia , Bazinet Richard P , Beaudry Jacqueline L , Hanley Anthony J 
Published: August 2022

Abstract

Context
Despite advances in treatments for cardiometabolic disorders such as type 2 diabetes mellitus and obesity, the increasing frequency of these conditions is of major clinical and public health concern. Therefore, primary prevention including diet and lifestyle approaches continues to play a key role in risk reduction. Meta-analyses of prospective cohort studies have documented inverse associations of dairy consumption with the incidence of different cardiometabolic disorders. Dairy is the largest dietary contributor of branched chain fatty acids (BCFAs), which have been suggested to not only serve as biomarkers of dairy consumption but may also have bioactive properties contributing to reducing the risk of cardiometabolic outcomes. To date, however, the literature on this topic has not been systematically reviewed.

Objective
The aim here was to report the results of a systematic review of the association of BCFAs with cardiometabolic disorders in humans.

Data Sources
Search terms were developed and run through the Ovid MEDLINE, Ovid Embase, and the Cochrane Library databases.

Data Extraction
Articles were selected on the basis of prespecified inclusion criteria and assessed for risk of bias by independent reviewers.

Results
Four studies (n = 2 cross sectional; n = 1 randomized feeding trial and n = 1 pre–post study) were identified. Two studies reported significant inverse associations between serum BCFAs and insulin resistance, triglycerides and/or body mass index. One study identified an inverse association between adipose tissue monomethyl BCFAs and skeletal muscle insulin resistance. In contrast, the randomized feeding trial reported no significant differences to stool BCFA concentrations or body mass index in obese participants following assignment to fruit–vegetable or whole-grain diet groups compared with a refined-grain control group.

Conclusions
Current evidence suggests beneficial associations of circulating BCFAs with cardiometabolic risk phenotypes, although data in human participants are limited, indicating that additional research is required.

PROSPERO registration no
CRD42021224975.
Underestimated Neotropical diversity: Integrative taxonomy reveals two unrelated look-alike species in a suboscine bird (Pachyramphus albogriseus)
Authors: Musher Lukas J , Krabbe Niels K , Areta Juan I 
Published: August 2022

Abstract
We applied an integrative taxonomic framework to evaluate the systematics of the Neotropical Black-and-white Becard (Pachyramphus albogriseusSclater 1857). Combining phylogenomic (ultraconserved elements), morphological, and vocalization data, we confirmed that this species is polyphyletic; some individuals form a clade sister to P. polychopterus and should be afforded species rank as P. salviniRichmond 1899 (Slender-billed Becard), whereas the remaining subspecies of P. albogriseus (Broad-banded Becard) are sister to P. major. We found that P. salvini differs from P. albogriseus in song, color of the lores, wing-bar width, body size, and bill width. Whereas P. albogriseus occurs in montane forest in Costa Rica and Panama (ssp. ornatus) and along the eastern slope of the Andes from northern Venezuela to southern Peru (ssp. albogriseus), P. salvini is found in the lowlands from Pacific Colombia south to northwest Peru and in the Río Marañón drainage. The latter also occurs, possibly only seasonally, along the eastern slope of the Andes, where the two species’ ranges approach closely. We treat P. a. guayaquilensisZimmer 1936 as a junior synonym of P. salviniRichmond 1899, and P. a. coronatusPhelps and Phelps 1953 as a junior synonym of P. a. albogriseusSclater 1857. This study provides a striking example of a major problem for comparative biology: underestimated and mischaracterized diversity. We argue that there are likely many more cases like this awaiting discovery.
Unperceived motor actions of the balance system interfere with the causal attribution of self-motion
Authors: Tisserand Romain , Rasman Brandon G , Omerovic Nina , Peters Ryan M , Forbes Patrick A , Blouin Jean-Sébastien 
Published: August 2022

AbstractThe instability of human bipedalism demands that the brain accurately senses balancing self-motion and determines whether movements originate from self-generated actions or external disturbances. Here, we challenge the longstanding notion that this process relies on a single representation of the body and world to accurately perceive postural orientation and organize motor responses to control balance self-motion. Instead, we find that the conscious sense of balance can be distorted by the corrective control of upright standing. Using psychophysics, we quantified thresholds to imposed perturbations and balance responses evoking cues of self-motion that are (in)distinguishable from corrective balance actions. When standing immobile, participants clearly perceived imposed perturbations. Conversely, when freely balancing, participants often misattributed their own corrective responses as imposed motion because their balance system had detected, integrated, and responded to the perturbation in the absence of conscious perception. Importantly, this only occurred for perturbations encoded ambiguously with balance-correcting responses and that remained below the natural variability of ongoing balancing oscillations. These findings reveal that our balance system operates on its own sensorimotor principles that can interfere with causal attribution of our actions, and that our conscious sense of balance depends critically on the source and statistics of induced and self-generated motion cues.
Ask the Doctor: Mental Hygiene Among the Young in Fin-de-Siècle Finland
Authors: Laine-Frigren Tuomas 
Published: August 2022

Summary
The turn of the twentieth century in Finland saw an increasing number of popular articles and books on health, which were published within the broader framework of ‘social hygiene’ and aimed at children, young people and their families. This article examines how young people articulated concerns about their own mental health in the context of these campaigns to improve social hygiene. Based on an extensive body of original sources consisting of medical advisory material and letters written by the young, the study reveals how young people saw themselves in this health context—especially when writing about their ‘nerves’ or ‘nervousness’. Drawing on more recent methodological investigations in the history of childhood, this study adds the much-needed perspective of the young people themselves as subjects experiencing these problems, to counterbalance the otherwise exclusively expert discourses on the subject of mental hygiene.
Lessons from distance education
Authors: Habala Petr , Demlová Marie 
Published: August 2022

Abstract
The recent transfer to distance education caused by the pandemic forced higher education to reshape courses and adopt new educational tools. Many teachers became aware of and acquired valuable first-hand experience with alternative techniques of teaching. In this contribution we look at advantages and disadvantages of some popular approaches, assessing them not only from the point of view of distance education (which could still be useful), but also regarding their potential for improving on-site education. This is based on the authors’ personal observations and student surveys at our institution (a kind of case study in our department and university), influenced by discussions with colleagues in formal and informal networks across Europe and supplemented with published results when possible.
Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi
Authors: Hugaboom Miya , Hatmaker E. Anne , LaBella Abigail L. , Rokas Antonis 
Published: August 2022

AbstractThe fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species—including 18 newly assembled mitogenomes—and compare their evolutionary history and codon usage bias (CUB) patterns to their nuclear counterparts. CUB refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of CUB between mitochondrial and nuclear genomes showed that species grouped differently by patterns of CUB depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of CUB at gene-level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes—both nuclear and mitochondrial—deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.
An alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs: Primer design for folD and ftfL and transformation of E. coli
Authors: Schmitz Rob A. , Pelsma Koen A.J. , Op den Camp Huub J.M. 
Published: August 2022

ABSTRACTMethylotrophs make a living by using one-carbon compounds as energy and carbon source. Methanol (CH3OH) is utilized by various methylotrophs and is oxidized by a methanol dehydrogenase. The calcium-dependent methanol dehydrogenase MxaFI converts methanol to formaldehyde (CH2O). In addition to MxaFI, the lanthanide-dependent methanol dehydrogenase XoxF is found in a wide range of bacteria. XoxF isolated from the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV possesses an unusually high affinity for both methanol and formaldehyde and converts methanol to formate (HCOOH) in vitro. However, genomic analyses and biochemical studies on related XoxF methanol dehydrogenases have questioned whether these enzymes are dedicated to the conversion of formaldehyde to formate in vivo. Instead, the genes encoding the bifunctional enzyme FolD and the enzyme FtfL, which we detected in all verrucomicrobial methanotrophs, were proposed to form a formaldehyde oxidation pathway utilizing tetrahydrofolate as C1-carrier. folD and ftfL are expressed in M. fumariolicum SolV and most closely related to homologues found in the phyla Verrucomicrobia and Proteobacteria, respectively. Here, we designed primers targeting Mf-folD and Mf-ftfL and amplified these genes through PCR. The amplified genes were ligated into pET30a(+) vectors which were subsequently used for the successful transformation of E. coli XL1-Blue cells. The vectors can be used for heterologous expression and subsequent His-tag purification to biochemically investigate whether FolD and FtfL could form an alternative tetrahydrofolate pathway for formaldehyde oxidation in verrucomicrobial methanotrophs.