bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gender-sensitive word embeddings for healthcare
Authors: Agmon Shunit , Gillis Plia , Horvitz Eric , Radinsky Kira 
Published: December 2021

AbstractObjectiveTo analyze gender bias in clinical trials, to design an algorithm that mitigates the effects of biases of gender representation on natural-language (NLP) systems trained on text drawn from clinical trials, and to evaluate its performance.Materials and MethodsWe analyze gender bias in clinical trials described by 16 772 PubMed abstracts (2008–2018). We present a method to augment word embeddings, the core building block of NLP-centric representations, by weighting abstracts by the number of women participants in the trial. We evaluate the resulting gender-sensitive embeddings performance on several clinical prediction tasks: comorbidity classification, hospital length of stay prediction, and intensive care unit (ICU) readmission prediction.ResultsFor female patients, the gender-sensitive model area under the receiver-operator characteristic (AUROC) is 0.86 versus the baseline of 0.81 for comorbidity classification, mean absolute error 4.59 versus the baseline of 4.66 for length of stay prediction, and AUROC 0.69 versus 0.67 for ICU readmission. All results are statistically significant.DiscussionWomen have been underrepresented in clinical trials. Thus, using the broad clinical trials literature as training data for statistical language models could result in biased models, with deficits in knowledge about women. The method presented enables gender-sensitive use of publications as training data for word embeddings. In experiments, the gender-sensitive embeddings show better performance than baseline embeddings for the clinical tasks studied. The results highlight opportunities for recognizing and addressing gender and other representational biases in the clinical trials literature.ConclusionAddressing representational biases in data for training NLP embeddings can lead to better results on downstream tasks for underrepresented populations.
Tangential Immersion: Increasing Persistence in Boring Consumer Behaviors
Authors: Lieberman Alicea , Morales Andrea C , Amir On 
Published: December 2021

AbstractConsumers’ lives are filled with myriad behaviors that can be successfully executed with minimal attention. Many such low-attention behaviors benefit from persistence but are often not performed long enough (e.g., hygiene, exercise). The current work examines consumer persistence-failures through an attentional lens. Specifically, drawing on boredom and resource-matching frameworks, we suggest one key driver of poor consumer persistence is that many behaviors demand less attention than consumers have available, leaving excess attention that leads to boredom and premature abandonment. The current research thus proposes an attention-matching framework for persistence and suggests that concurrently performing a task that engages excess attention will improve the match between attentional demands and available resources, thereby increasing persistence. Five experiments across a range of low-attention behaviors (e.g., toothbrushing, coordination exercise) demonstrate that concurrently performing a task that occupies excess attention (e.g., reading, listening), delays boredom and increases persistence. Moreover, two important boundary conditions arise. First, the focal behavior must require minimal attention, leaving excess attention available to attend to the tangential task. Second, the tangential task must engage excess attention without exceeding attentional capacity. This research provides important theoretical and practical contributions, offering the potential to improve consumer well-being by increasing persistence in low-attention behaviors.
Leaf microscopy applications in photosynthesis research: identifying the gaps
Authors: Khoshravesh Roxana , Hoffmann Natalie , Hanson David T 
Published: December 2021

Abstract
Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure–function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.
Impact of point spread function higher moments error on weak gravitational lensing
Authors: Zhang Tianqing , Mandelbaum Rachel ,   The LSST Dark Energy Science Collaboration, Kannawadi Arun , Miyatake Hironao , Astier Pierre , Jarvis Mike , Meyers Josh , Schmitz Morgan , Clowe Douglas 
Published: December 2021

ABSTRACT
Weak gravitational lensing is one of the most powerful tools for cosmology, while subject to challenges in quantifying subtle systematic biases. The point spread function (PSF) can cause biases in weak lensing shear inference when the PSF model does not match the true PSF that is convolved with the galaxy light profile. Although the effect of PSF size and shape errors – i.e. errors in second moments – is well studied, weak lensing systematics associated with errors in higher moments of the PSF model require further investigation. The goal of our study is to estimate their potential impact for LSST weak lensing analysis. We go beyond second moments of the PSF by using image simulations to relate multiplicative bias in shear to errors in the higher moments of the PSF model. We find that the current level of errors in higher moments of the PSF model in data from the Hyper Suprime-Cam survey can induce a ∼0.05 per cent shear bias, making this effect unimportant for ongoing surveys but relevant at the precision of upcoming surveys such as LSST.
Unravelling the foretime of GRS 1915+105 using AstroSat observations: Wide-band spectral and temporal characteristics
Authors: Athulya M P , Radhika D , Agrawal V K , Ravishankar B T , Naik Sachindra , Mandal Samir , Nandi Anuj 
Published: December 2021

ABSTRACT
We present a comprehensive study of GRS 1915+105 in wide-energy band (0.5–60 keV) using AstroSat – SXT and LAXPC observations during the period of 2016–2019. The MAXI X-ray light curve of the source shows rise and decay profiles similar to canonical outbursting black holes. However, the source does not follow the exemplary ‘q’-diagram in the hardness–intensity diagram. Model independent analysis of light curves suggest that GRS 1915+105 displays various types of variability classes (δ, χ, ρ, κ, ω, and γ). We also report possible transitions from one class to another (χ → ρ, ρ → κ via an ‘unknown’ class and ω → γ → ω + γ) within a few hours duration. Detailed ‘spectrotemporal’ analysis indicates a gradual increase in the photon index (Γ) from 1.83 to 3.8, disc temperature (kTin) from 1.33 to 2.67 keV, and quasi-periodic oscillation frequency (ν) from 4 to 5.64 Hz during the rise, while the parameters decrease to Γ ∼1.18, kTin ∼1.18 keV, and ν ∼1.38 Hz, respectively, in the decline phase. The source shows maximum bolometric luminosity (Lbol) during the peak at ∼36 per cent of Eddington luminosity (LEdd), and a minimum of ∼2.4 per cent of LEdd during the decay phase. Further evolution of the source towards an obscured low-luminosity (Lbol of ∼1 per cent LEdd) phase, with a decrease in the intrinsic bolometric luminosity of the source due to obscuration, has also been indicated from our analysis. The implication of our results are discussed in the context of accretion disc dynamics around the black hole.
Atmospheric mass loss and stellar wind effects in young and old systems – II. Is TOI-942 the past of TOI-421 system?
Authors: Kubyshkina Daria , Vidotto Aline A , Villarreal D’Angelo Carolina , Carolan Stephen , Hazra Gopal , Carleo Ilaria 
Published: December 2021

ABSTRACT
The two planetary systems, TOI-942 and TOI-421, share many similar characteristics, apart from their ages (50 Myr and 9 Gyr). Each of the stars hosts two sub-Neptune-like planets at similar orbits and in similar mass ranges. In this paper, we aim to investigate whether the similarity of the host stars and configuration of the planetary systems can be taken as proof that the two systems were formed and evolved in a similar way. In paper I of this series, we performed a comparative study of these two systems using three-dimensional (3D) modelling of atmospheric escape and its interaction with the stellar wind, for the four planets. We demonstrated that though the strong wind of the young star has a crucial effect on observable signatures, its effect on the atmospheric mass loss is minor in the evolutionary context. Here, we use atmosphere evolution models to track the evolution of planets in the younger system TOI-942 and also to constrain the past of the TOI-421 system. We demonstrate that despite all the similarities, the two planetary systems are on two very different evolutionary pathways. The inner planet in the younger system, TOI-942, will likely lose all of its atmosphere and become a super-Earth-like planet, while the outer planet will become a typical sub-Neptune. Concerning the older system, TOI-421, our evolution modelling suggests that they must have started their evolution with very substantial envelopes, which can be a hint of formation beyond the snow line.
Neural-network assisted study of nitrogen atom dynamics on amorphous solid water – II. Diffusion
Authors: Zaverkin Viktor , Molpeceres Germán , Kästner Johannes 
Published: December 2021

ABSTRACT
The diffusion of atoms and radicals on interstellar dust grains is a fundamental ingredient for predicting accurate molecular abundances in astronomical environments. Quantitative values of diffusivity and diffusion barriers usually rely heavily on empirical rules. In this paper, we compute the diffusion coefficients of adsorbed nitrogen atoms by combining machine learned interatomic potentials, metadynamics, and kinetic Monte Carlo simulations. With this approach, we obtain a diffusion coefficient of nitrogen atoms on the surface of amorphous solid water of merely $(3.5 \pm 1.1)\, \times 10^{-34}$ cm2 s−1 at 10 K for a bare ice surface. Thus, we find that nitrogen, as a paradigmatic case for light and weakly bound adsorbates, is unable to diffuse on bare amorphous solid water at 10 K. Surface coverage has a strong effect on the diffusion coefficient by modulating its value over 9–12 orders of magnitude at 10 K and enables diffusion for specific conditions. In addition, we have found that atom tunnelling has a negligible effect. Average diffusion barriers of the potential energy surface (2.56 kJ mol−1) differ strongly from the effective diffusion barrier obtained from the diffusion coefficient for a bare surface (6.06 kJ mol−1) and are, thus, inappropriate for diffusion modelling. Our findings suggest that the thermal diffusion of N on water ice is a process that is highly dependent on the physical conditions of the ice.
First evidence of a collision between two unrelated open clusters in the Milky Way
Authors: Piatti Andrés E , Malhan Khyati 
Published: December 2021

Abstract
We report the first evidence of an ongoing collision between two star clusters in our Galaxy, namely IC 4665 and Collinder 350. These are open clusters located at a distance of ∼330 pc from the Sun and ∼100 pc above the Galactic plane, and they both have prograde motions with only a small difference in their velocities (Collinder 350 moves $\sim 5\, \rm {km\, s^{-1}}$ faster than IC 4665); as inferred from ESA/Gaia based catalogue. Interestingly, the two clusters are physically separated by only ∼36 pc in space; a distance that is smaller than the sum of their respective radii. Furthermore, the clusters exhibit signatures of elongated stellar density distributions, and we also detect an onset of an inter-cluster stellar bridge. Moreover, the orbit analysis suggests that the younger cluster IC 4665 (age = 53 Myr) must have formed at a distance &gt;500 pc away from Collinder 350 (age = 617 Myr). These findings together imply that the two clusters do not represent merging of two objects in a binary system; rather, what we are witnessing is an actual collision between two independently formed star clusters. This collision phenomenon provides a unique opportunity to explore new aspects of formation and evolution theory of star clusters.
Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors
Authors: Qiu Yichun , Köhler Claudia 
Published: December 2021

AbstractMADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules, and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS genes underpin the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.
Disrupting the Cdk9/Cyclin T1 heterodimer of 7SK snRNP for the Brd4 and AFF1/4 guided reconstitution of active P-TEFb
Authors: Zhou Kai , Zhuang Songkuan , Liu Fulong , Chen Yanheng , Li You , Wang Shihui , Li Yuxuan , Wen Huixin , Lin Xiaohua , Wang Jie , Huang Yue , He Cailing , Xu Nan , Li Zongshu , Xu Lang , Zhang Zixuan , Chen Lin-Feng , Chen Ruichuan , Liu Min 
Published: December 2021

Abstract
P-TEFb modulates RNA polymerase II elongation through alternative interaction with negative and positive regulation factors. While inactive P-TEFbs are mainly sequestered in the 7SK snRNP complex in a chromatin-free state, most of its active forms are in complex with its recruitment factors, Brd4 and SEC, in a chromatin-associated state. Thus, switching from inactive 7SK snRNP to active P-TEFb (Brd4/P-TEFb or SEC/P-TEFb) is essential for global gene expression. Although it has been shown that cellular signaling stimulates the disruption of 7SK snRNP, releasing dephosphorylated and catalytically inactive P-TEFb, little is known about how the inactive released P-TEFb is reactivated. Here, we show that the Cdk9/CycT1 heterodimer released from 7SK snRNP is completely dissociated into monomers in response to stress. Brd4 or SEC then recruits monomerized Cdk9 and CycT1 to reassemble the core P-TEFb. Meanwhile, the binding of monomeric dephosphorylated Cdk9 to either Brd4 or SEC induces the autophosphorylation of T186 of Cdk9. Finally, the same mechanism is employed during nocodazole released entry into early G1 phase of cell cycle. Therefore, our studies demonstrate a novel mechanism by which Cdk9 and CycT1 monomers are reassembled on chromatin to form active P-TEFb by its interaction with Brd4 or SEC to regulate transcription.
A minimal motif for sequence recognition by mitochondrial transcription factor A (TFAM)
Authors: Choi Woo Suk , Garcia-Diaz Miguel 
Published: December 2021

Abstract
Mitochondrial transcription factor A (TFAM) plays a critical role in mitochondrial transcription initiation and mitochondrial DNA (mtDNA) packaging. Both functions require DNA binding, but in one case TFAM must recognize a specific promoter sequence, while packaging requires coating of mtDNA by association with non sequence-specific regions. The mechanisms by which TFAM achieves both sequence-specific and non sequence-specific recognition have not yet been determined. Existing crystal structures of TFAM bound to DNA allowed us to identify two guanine-specific interactions that are established between TFAM and the bound DNA. These interactions are observed when TFAM is bound to both specific promoter sequences and non-sequence specific DNA. These interactions are established with two guanine bases separated by 10 random nucleotides (GN10G). Our biochemical results demonstrate that the GN10G consensus is essential for transcriptional initiation and contributes to facilitating TFAM binding to DNA substrates. Furthermore, we report a crystal structure of TFAM in complex with a non sequence-specific sequence containing a GN10G consensus. The structure reveals a unique arrangement in which TFAM bridges two DNA substrates while maintaining the GN10G interactions. We propose that the GN10G consensus is key to facilitate the interaction of TFAM with DNA.
The C nucleotide at the mature 5′ end of the Escherichia coli proline tRNAs is required for the RNase E cleavage specificity at the 3′ terminus as well as functionality
Authors: Mohanty Bijoy K , Maples Valerie , Kushner Sidney R 
Published: December 2021

Abstract
Proline tRNA 3′-maturation in Escherichia coli occurs through a one-step RNase E endonucleolytic cleavage immediately after the CCA determinant. This processing pathway is distinct from the 3′-end maturation of the other tRNAs by avoiding the widespread use of 3′ → 5′ exonucleolytic processing, 3′-polyadenylation and subsequent degradation. Here, we show that the cytosine (C) at the mature 5′-terminus of the proK and proL tRNAs is required for both the RNase E cleavage immediately after the CCA determinant and their functionality. Thus, changing the C nucleotide at the mature 5′-terminus of the proL and proK tRNAs to the more common G nucleotide led to RNase E cleavages 1–4 nucleotides downstream of the CCA determinant. Furthermore, the 5′-modified mutant tRNAs required RNase T and RNase PH for their 3′-maturation and became substrates for polyadenylation and degradation. Strikingly, the aminoacylation of the 5′-modified proline tRNAs was blocked due to the change in the recognition element for prolyl-tRNA-synthetase. An analogous modification of the pheV 5′-mature terminus from G to C nucleotide did not support cell viability. This result provides additional support for the importance of first nucleotide of the mature tRNAs in their processing and functionality.
CryoEM of RUVBL1–RUVBL2–ZNHIT2, a complex that interacts with pre-mRNA-processing-splicing factor 8
Authors: Serna Marina , González-Corpas Ana , Cabezudo Sofía , López-Perrote Andrés , Degliesposti Gianluca , Zarzuela Eduardo , Skehel J Mark , Muñoz Javier , Llorca Oscar 
Published: December 2021

Abstract
Biogenesis of the U5 small nuclear ribonucleoprotein (snRNP) is an essential and highly regulated process. In particular, PRPF8, one of U5 snRNP main components, requires HSP90 working in concert with R2TP, a cochaperone complex containing RUVBL1 and RUVBL2 AAA-ATPases, and additional factors that are still poorly characterized. Here, we use biochemistry, interaction mapping, mass spectrometry and cryoEM to study the role of ZNHIT2 in the regulation of the R2TP chaperone during the biogenesis of PRPF8. ZNHIT2 forms a complex with R2TP which depends exclusively on the direct interaction of ZNHIT2 with the RUVBL1–RUVBL2 ATPases. The cryoEM analysis of this complex reveals that ZNHIT2 alters the conformation and nucleotide state of RUVBL1–RUVBL2, affecting its ATPase activity. We characterized the interactions between R2TP, PRPF8, ZNHIT2, ECD and AAR2 proteins. Interestingly, PRPF8 makes a direct interaction with R2TP and this complex can incorporate ZNHIT2 and other proteins involved in the biogenesis of PRPF8 such as ECD and AAR2. Together, these results show that ZNHIT2 participates in the assembly of the U5 snRNP as part of a network of contacts between assembly factors required for PRPF8 biogenesis and the R2TP-HSP90 chaperone, while concomitantly regulating the structure and nucleotide state of R2TP.
Firefighting and melanoma, epidemiological and toxicological associations: a case report
Authors: Brinchmann Bendik C , Bugge Merete D , Nordby Karl-Christian , Alfonso Jose Hernán 
Published: December 2021

Summary
The International Agency for Research on Cancer (IARC) classifies firefighting as possibly carcinogenic to humans, and polychlorinated biphenyls (PCBs) as carcinogens with sufficient evidence for development of melanoma in humans. We present a case report of a firefighter with melanoma and history of 33 years of occupational exposure. Based on the available epidemiological and toxicological evidence of association between being a firefighter and developing melanoma, melanoma was recognized by the Norwegian Labour and Welfare Service as an occupational disease in our patient. In 2017, melanoma was acknowledged as an occupational disease in only 8 out of 28 surveyed European countries. Melanoma should be considered as a possible occupational disease among firefighters with a history of relevant exposure. Further recognition of the occupational exposures leading to increased risk of melanoma is still needed for preventive purposes.
Effectiveness of an intervention to reduce accidents in bus drivers
Authors: McCollum Emma 
Published: December 2021

Abstract

Background
Medical incapacity at the wheel is a small but significant factor in accident causation. To mitigate against this, in July 2017 a UK-based bus operator changed its medical assessment policy, requiring all future medicals to include a request to the General Practitioner (GP) for information about any conditions in the medical record which could affect fitness to drive.

Aims
To evaluate the impact of the change in policy on accident rates.

Methods
Accident data were obtained over a 5-year period, with information on age and length of service of drivers, from three bus depots. Monthly accident rates, before and after the change in policy were compared with the Wilcoxon matched pairs test, and a line of best fit/R2 obtained via a scatter graph.

Results
Although a general downward trend in accident rates was seen, there was no statistically significant difference between the overall accident rates in the 12 months before and after the policy change in July 2017 (P-value = 0.519, significance level P &lt; 0.05).

Conclusions
The downward trend in accident rates observed over the study period could not be attributed to the change of policy. However, this intervention warrants further scrutiny due to the potential consequences of passenger service vehicle accidents. Evidence suggests that professional awareness of the UK Driver and Vehicle Licensing Agency fitness to drive standards can be limited, so requesting GP input into driver medicals may raise awareness of these standards from an occupational health perspective.