bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new method to measure the spectra of transiting exoplanet atmospheres using multi-object spectroscopy
Authors: Panwar Vatsal , Désert Jean-Michel , Todorov Kamen O , Bean Jacob L , Stevenson Kevin B , Huitson C M , Fortney Jonathan J , Bergmann Marcel 
Published: December 2021

ABSTRACT
Traditionally, ground-based spectrophotometric observations probing transiting exoplanet atmospheres have employed a linear map between comparison and target star light curves (e.g. via differential spectrophotometry) to correct for systematics contaminating the transit signal. As an alternative to this conventional method, we introduce a new Gaussian Processes (GP) regression-based method to analyse ground-based spectrophotometric data. Our new method allows for a generalized non-linear mapping between the target transit light curves and the time-series used to detrend them. This represents an improvement compared to previous studies because the target and comparison star fluxes are affected by different telluric and instrumental systematics, which are complex and non-linear. We apply our method to six Gemini/GMOS transits of the warm (Teq = 990 K) Neptune HAT-P-26b. We obtain on average ∼20 per cent better transit depth precision and residual scatter on the white light curve compared to the conventional method when using the comparison star light curve as a GP regressor and ∼20 per cent worse when explicitly not using the comparison star. Ultimately, with only a cost of 30 per cent precision on the transmission spectra, our method overcomes the necessity of using comparison stars in the instrument field of view, which has been one of the limiting factors for ground-based observations of the atmospheres of exoplanets transiting bright stars. We obtain a flat transmission spectrum for HAT-P-26b in the range of 490–900 nm that can be explained by the presence of a grey opacity cloud deck, and indications of transit timing variations, both of which are consistent with previous measurements.
Inferring the rotation period distribution of stars from their projected rotation velocities and radii: Application to late-F/early-G Kepler stars
Authors: Masuda Kento , Petigura Erik A , Hall Oliver J 
Published: December 2021

ABSTRACT
While stellar rotation periods Prot may be measured from broad-band photometry, the photometric modulation becomes harder to detect for slower rotators, which could bias measurements of the long-period tail of the Prot distribution. Alternatively, the Prot distribution of stars can be inferred from their projected rotation velocities vsin i and radii R, without being biased against photometrically quiet stars. We solve this inference problem using a hierarchical Bayesian framework, which (i) is applicable to heteroscedastic measurements of vsin i and R with non-Gaussian uncertainties and (ii) does not require a simple parametric form for the true Prot distribution. We test the method on simulated data sets and show that the true Prot distribution can be recovered from ≳ 100 sets of vsin i and R measured with precisions of $1\, \mathrm{km\, s}^{-1}$ and 4 per cent, respectively, unless the true distribution includes sharp discontinuities. We apply the method to a sample of 144 late-F/early-G dwarfs in the Kepler field with vsin i measured from Keck/HIRES spectra, and find that the typical rotation periods of these stars are similar to the photometric periods measured from Kepler light curves: we do not find a large population of slow rotators that are missed in the photometric sample, although we find evidence that the photometric sample is biased for young, rapidly rotating stars. Our results also agree with asteroseismic measurements of Prot for Kepler stars with similar ages and effective temperatures, and show that $\approx 1.1\, \mathrm{M}_\odot$ stars beyond the middle of their main-sequence lifetimes rotate faster than predicted by standard magnetic braking laws.
Cooling flows around cold clouds in the circumgalactic medium: steady-state models and comparison with TNG50
Authors: Dutta Alankar , Sharma Prateek , Nelson Dylan 
Published: December 2021

ABSTRACT
Cold, non-self-gravitating clumps occur in various astrophysical systems, ranging from the interstellar and circumgalactic medium (CGM), to active galactic nucleus outflows and solar coronal loops. Cold gas has diverse origins such as turbulent mixing or precipitation from hotter phases. We obtain the analytical solution for a steady pressure-driven 1D cooling flow around cold, local overdensities, irrespective of their origin. Our solutions describe the slow and steady radiative cooling-driven gas inflow in the saturated regime of non-linear thermal instability in clouds, sheets, and filaments. Such a cooling flow develops when the gas around small clumps undergoes radiative cooling. These small-scale, cold ‘seeds’ are embedded in a large volume-filling hot CGM maintained by feedback. We use a simple two-fluid treatment to include magnetic fields as an additional polytropic fluid. To test the limits of applicability of these analytical solutions, we compare with the gas structure found in and around small-scale cold clouds in the CGM of massive haloes in the TNG50 cosmological magnetohydrodynamic simulation from the IllustrisTNG suite. Despite qualitative resemblance of the gas structure, we find deviations from steady-state profiles generated by our model. Complex geometries and turbulence all add complexity beyond our analytical solutions. We derive an exact relation between the mass cooling rate ($\dot{\rm M}_{\rm cool}$) and the radiative cooling rate ($\dot{\rm E}_{\rm cool}$) for a steady cooling flow. A comparison with the TNG50 clouds shows that this cooling flow relation only applies in a narrow temperature range around $\rm \sim 10^{4.5}$ K where the isobaric cooling time is the shortest. In general, turbulence and mixing, instead of radiative cooling, may dominate the transition of gas between different temperature phases.
Molecular mechanisms in IL-1β-mediated decorin production by decidual cells
Authors: Halari C D , Renaud S J , Lala P K 
Published: December 2021

AbstractDecorin, a small leucine-rich proteoglycan produced by decidual cells restrains trophoblast differentiation, migration and invasiveness of extra-villous trophoblast cells. Decidual overproduction of decorin is associated with preeclampsia, and elevated decorin levels in maternal plasma are a predictive biomarker of preeclampsia. Furthermore, decorin plays an autocrine role in maturation of human endometrial stromal cells into decidual cells. Thus, a balanced decorin production by the decidua is critical for healthy pregnancy. However, the molecular mechanisms regulating decorin production by the decidua are unclear. Interleukin-1 beta is an inflammation-associated multi-functional cytokine, and is reported to induce decidualization in primates. Hence, the present study was designed: (i) to test if exogenous Interleukin-1 beta stimulated decorin production by human endometrial stromal cells; and if so, (ii) to identify the cellular source of Interleukin-1 beta in first trimester decidual tissue; (iii) to identify the downstream molecular partners in Interleukin-1 beta mediated decorin production by human endometrial stromal cells. Results revealed that (i) amongst multiple pro-inflammatory cytokines tested, Interleukin-1 beta alone stimulated decorin production by these cells; (ii) both macrophages and decidual cells in first trimester decidua produced Interleukin-1 beta; (iii) Interleukin-1 beta mediated decorin production was dependent on Interleukin-1 receptor activation, followed by activation and nuclear translocation of nuclear factor kappa B and its binding to the decorin promoter. These results reveal that Interleukin-1 beta plays a novel role in inducing decorin production by human endometrial stromal cells by activating nuclear factor kappa B.
Expression profiling and function analysis identified new microRNAs regulating cumulus expansion and apoptosis in cumulus cells
Authors: Han Xiao , Zhang Min , Yuan Hong-Jie , Wang Guo-Liang , Zhao Xin-Yue , Li Zhi-Bin , Gong Shuai , Tan Jing-He 
Published: December 2021

Abstract
Although miRNAs expressed in cumulus cells (CCs) may be used to select competent oocytes/embryos, only a limited number of such miRNAs has been reported. To identify more miRNAs that regulate cumulus expansion (CE) and CC apoptosis, we first established that mouse cumulus-oocyte complexes (COCs) cultured in expansion-supporting medium supported full CE while undergoing mild apoptosis, whereas mouse oocytectomized COCs (OOXs) cultured in apoptosis-triggering medium underwent severe apoptosis while supporting no CE. RNA- and miRNA-sequencing and bioinformatics using CCs from these cultured COCs/OOXs identified candidate apoptosis- and/or CE-regulating miRNAs. Transfection of COCs/OOXs with miRNA mimic or inhibitor validated that miR-212-5p and 149-5p promoted CE by facilitating Has2 expression; miR-31-5p and 27a-3p promoted CE by increasing both Has2 and Ptx3 expression; and miR-351-5p and 503-5p inhibited CE by suppressing Ptx3 expression. Furthermore, miR-212-5p, 149-5p and Nov798 inhibited CC apoptosis, involving both Bcl2/Bax and Fas signaling. Analysis using in vivo matured COCs further verified the above apoptosis- and/or CE-regulating miRNAs, except for miR-149-5p. In conclusion, this study identified and validated new CE- and apoptosis-regulating miRNAs in CCs, which could be used as biomarkers to select competent oocytes/embryos and for elucidating how the oocyte-derived factors regulate CE and CC apoptosis.
Genomic landscape of single-stranded DNA gapped intermediates inEscherichia coli
Authors: Pham Phuong , Shao Yijun , Cox Michael M , Goodman Myron F 
Published: December 2021

AbstractSingle-stranded (ss) gapped regions in bacterial genomes (gDNA) are formed on W- and C-strands during replication, repair, and recombination. Using non-denaturing bisulfite treatment to convert C to U on ssDNA, combined with deep sequencing, we have mapped gDNA gap locations, sizes, and distributions in Escherichia coli for cells grown in mid-log phase in the presence and absence of UV irradiation, and in stationary phase cells. The fraction of ssDNA on gDNA is similar for W- and C-strands, ∼1.3% for log phase cells, ∼4.8% for irradiated log phase cells, and ∼8.5% for stationary phase cells. After UV irradiation, gaps increased in numbers and average lengths. A monotonic reduction in ssDNA occurred symmetrically between the DNA replication origin of (OriC) and terminus (Ter) for log phase cells with and without UV, a hallmark feature of DNA replication. Stationary phase cells showed no OriC → Ter ssDNA gradient. We have identified a spatially diverse gapped DNA landscape containing thousands of highly enriched ‘hot’ ssDNA regions along with smaller numbers of ‘cold’ regions. This analysis can be used for a wide variety of conditions to map ssDNA gaps generated when DNA metabolic pathways have been altered, and to identify proteins bound in the gaps.
“Bind, cleave and leave”: multiple turnover catalysis of RNA cleavage by bulge–loop inducing supramolecular conjugates
Authors: Amirloo Bahareh , Staroseletz Yaroslav , Yousaf Sameen , Clarke David J , Brown Tom , Aojula Harmesh , Zenkova Marina A , Bichenkova Elena V 
Published: December 2021

Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge–loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge–loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
scMAGIC: accurately annotating single cells using two rounds of reference-based classification
Authors: Zhang Yu , Zhang Feng , Wang Zekun , Wu Siyi , Tian Weidong 
Published: December 2021

Abstract
Here, we introduce scMAGIC (Single Cell annotation using MArker Genes Identification and two rounds of reference-based Classification [RBC]), a novel method that uses well-annotated single-cell RNA sequencing (scRNA-seq) data as the reference to assist in the classification of query scRNA-seq data. A key innovation in scMAGIC is the introduction of a second-round RBC in which those query cells whose cell identities are confidently validated in the first round are used as a new reference to again classify query cells, therefore eliminating the batch effects between the reference and the query data. scMAGIC significantly outperforms 13 competing RBC methods with their optimal parameter settings across 86 benchmark tests, especially when the cell types in the query dataset are not completely covered by the reference dataset and when there exist significant batch effects between the reference and the query datasets. Moreover, when no reference dataset is available, scMAGIC can annotate query cells with reasonably high accuracy by using an atlas dataset as the reference.
Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA
Authors: Gao Yuan , Lin Kuan-Ting , Jiang Tao , Yang Yang , Rahman Mohammad A , Gong Shuaishuai , Bai Jialin , Wang Li , Sun Junjie , Sheng Lei , Krainer Adrian R , Hua Yimin 
Published: December 2021

Abstract
Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5′ splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action.
Theoretical and practical approaches for dietary behavior change in urban socioeconomically disadvantaged adolescents: a systematic review
Authors: Bel-Serrat Silvia , Greene Ellen , Mullee Amy , Murrin Celine M 
Published: December 2021

Abstract

Context
There is limited evidence on strategies used to promote dietary behavior changes in socioeconomically disadvantaged urban adolescents and on their effectiveness.

Objective
A synthesis of nutrition interventions used in this group of adolescents is provided in this systematic review.

Data Sources
Five electronic databases (PubMed, Web of Science, CINAHL, PsycINFO, and ERIC) were searched until November 2020 to identify relevant studies.

Data Extraction
Forty-six manuscripts (n = 38 intervention studies) met the inclusion criteria. Quality was assessed with the Effective Public Health Practice Project Quality Assessment Tool. A qualitative synthesis summarizing data on study characteristics was conducted.

Data Analysis
Studies were classified by intervention type as those focusing on hedonic determinants of dietary intake (n = 1), environmental changes to promote a specific dietary intake (n = 3), cognitive determinants (n = 29), and multicomponent strategies (n = 13). The social cognitive theory was the most applied theoretical framework, either alone or combined with other frameworks. Most of the intervention studies targeted multiple dietary outcomes, and success was not always reported for each.

Conclusions
Despite the heterogeneity of the studies and lack of combination of dietary outcomes into dietary scores or patterns to evaluate changes on the individuals’ whole diets, long-term, theory-driven interventions targeting a single dietary factor seem promising in obtaining sustainable dietary behavior changes.

Systematic Review Registration
PROSPERO registration no. CRD42020188219.
Ocular occupational injuries in the United States between 2011–2018
Authors: Hom Grant L , Kalur Aneesha , Iyer Amogh , Singh Rishi P 
Published: December 2021

Abstract

Background
Current advocacy literature in occupational eye injury focuses on demographics and industries with the largest number of injuries. Additional demographics may also benefit from targeted advocacy that experience a greater proportion of eye injuries relative to all other occupational injuries.

Aims
To characterize which demographic groups are experiencing occupational ocular injuries in the United States.

Methods
This cross-sectional study examined de-identified individuals who experienced ocular workplace injuries from 2011 to 2018 and were reported to the survey of occupational injuries and illnesses (SOII). Data were stratified and analysed based on SOII reported characteristics.

Results
197 160 out of 9 197 350 (2%) ocular workplace injuries were reported. 152 940 (78%) injuries occurred in males. Relative to all workplace injuries experienced by industry, farming, fishing and forestry saw the highest percentage of ocular injuries (6%), followed by production, and installation (4%), maintenance and repairs (4%). Employers cited contact with objects (65%) and exposure to harmful substances (26%) as leading reasons for eye injury. Relative to all injuries, chemicals frequently injured the eye (27%).

Conclusions
A disproportionate number of American ocular workplace injuries occur in males who are likely relatively young. Industries such as fishing, farming and forestry see a high frequency of ocular injury relative to all occupational injuries. Hispanics see a slight increase in ocular occupational injury relative to other injuries. Advocates of occupational ocular safety should consider expanding their targeted audiences to include individuals who are part of demographics and occupations that more frequently experience an ocular workplace injury relative to all injuries.
Narrative Criminology and Ethnography
Authors: Fleetwood Jennifer , Sandberg Sveinung 
Published: December 2021

Abstract
This chapter outlines how criminological researchers can attend to narrative as part of their ethnographic practice. Attention to the narrativity of speech, conversations, and texts pertaining to both individuals and groups has the potential to enrich ethnographic research on crime, criminal justice, and victims/survivors. It accentuates that stories told in field, between research participants—and to the researcher—are paramount for most ethnographic fieldwork. Ethnographers can draw much from contemporary developments in narrative criminology. We outline two insights in particular: talk is a kind of social action that does things and, second, stories motivate and guide behaviour. We review research in narrative criminology to demonstrate the importance of stories for understanding crime and justice: they delineate insiders and outsiders, convey identity, supply know-how, and display criminal capital. Vengeance and violence are also a way to tell or enact stories. This chapter also explores questions of methodology and discusses some practical issues such as how to invite storytelling and how to use recording devices in the field. We conclude with some thoughts about future directions for narrative criminology and ethnography.
Nightlife Ethnography: A Phenomenological Approach
Authors: Tutenges Sébastien 
Published: December 2021

Abstract
This chapter offers advice on how to conduct phenomenological ethnographic research in nightlife settings such as bars, nightclubs, and music festivals. It argues that phenomenological ethnography focuses on studying experiences as they occur to the people living them. Phenomenological ethnographers use their bodies as research instruments to develop an experiential connection and understanding of the people they are studying. Priority is given to clarifying essential properties of embodied, emotional, and sensory experiences, and to describing these as precisely as possible. The chapter proposes that the Durkheimian concept of collective effervescence may be used as a sensitizing tool to understand and describe some of the essence of what people search for, and sometimes experience, in nightlife settings. In particular, the concept is helpful in the study of intensive forms of celebration and intoxication. The chapter concludes with policy recommendations and suggestions to direct future research.
Mining and Minerals in South Africa
Authors: Makgetla Neva Seidman 
Published: December 2021

Abstract
Although the mining value chain only accounted for around 13% of the GDP and 6% of employment in 2020, it remained a central link between the South African economy and international markets. As a result, it had an outsized impact on the production structure, income distribution, infrastructure and legal frameworks. After the transition to democracy in 1994, the value chain underwent significant changes, notably a shift away from coal into platinum, iron ore, coal and ferroalloys, and significant divestment by international mining companies. Still, deep-seated developmental challenges persisted, including limited mining-based industrialisation, the exercise of monopoly power within value chains, and deeply inequitable and oppressive payscales and work organisation. These structural weaknesses emerged clearly in the 2010s, as the end of the global metals prices boom (2002 to 2011) brought plummeting revenues, revealing a range of economic, workplace, and policy conflicts across the value chain.