bluuebunny/crossref_metadata_2025_split huggingface dataset:
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes
Authors: Huang Yilei , Ringbauer Harald 
Published: June 2022

AbstractMotivationHuman ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (&lt;1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches.ResultsWe present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25–30% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries.Availability and implementationWe make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH.Supplementary informationSupplementary data are available at Bioinformatics online.
MetBP: a software tool for detection of interaction between metal ion–RNA base pairs
Authors: Roy Parthajit , Bhattacharyya Dhananjay 
Published: June 2022

AbstractMotivationThe role of metals in shaping and functioning of RNA is a well-established fact, and the understanding of that through the analysis of structural data has biological relevance. Often metal ions bind to one or more atoms of the nucleobase of an RNA. This fact becomes more interesting when such bases form a base pair with any other base. Furthermore, when metal ions bind to any residue of an RNA, the secondary structural features of the residue (helix, loop, unpaired, etc.) are also biologically important. The available metal-binding-related software tools cannot address such type-specific queries.ResultsTo fill this limitation, we have designed a software tool, called MetBP that meets the goal. This tool is a stand-alone command-line-based tool and has no dependency on the other existing software. It accepts a structure file in mmCIF or PDB format and computes the base pairs and thereafter reports all metals that bind to one or more nucleotides that form pairs with another. It reports binding distance, angles along with base pair stability. It also reports several other important aspects, e.g. secondary structure of the residue in the RNA. MetBP can be used as a generalized metal-binding site detection tool for Proteins and DNA as well.Availability and implementationhttps://github.com/computational-biology/metbpSupplementary informationSupplementary data are available at Bioinformatics online.
Low-voltage area substrate modification for atrial fibrillation ablation: a systematic review and meta-analysis of clinical trials
Authors: Junarta Joey , Siddiqui Muhammad U , Riley Joshua M , Dikdan Sean J , Patel Akash , Frisch Daniel R 
Published: June 2022

Abstract

Aims
The value of additional ablation beyond pulmonary vein isolation for atrial fibrillation (AF) ablation is unclear, especially for persistent AF. The optimal target for substrate modification to improve outcomes is uncertain. We investigate the utility of low-voltage area (LVA) substrate modification in patients undergoing catheter ablation for AF.

Methods and results
This meta-analysis was reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines. Medline, Scopus and Cochrane Central Register of Controlled Trials were systematically searched to identify relevant studies. Risk of bias was assessed using the Cochrane risk of bias tool. Only randomized studies were included. AF patients who underwent catheter ablation with voltage-guided substrate modification targeting LVA (LVA group) vs. conventional ablation approaches not targeting LVA (non-LVA group) were compared. Four studies comprising 539 patients were included (36% female). Freedom from arrhythmia (FFA) in patients with persistent AF was greater in the LVA group [risk ratio (RR) 1.30; 95% confidence interval (CI) 1.03–1.64]. There was no difference in FFA in patients with paroxysmal AF between groups (RR 1.30; 95% CI 0.89–1.91). There was no difference in total procedural time (mean difference −17.54 min; 95% CI −64.37 to 29.28 min) or total ablation time (mean difference −36.17 min; 95% CI −93.69 to 21.35 min) in all included patients regardless of AF type between groups. There was no difference in periprocedural complications between groups in all included patients regardless of AF type (RR 0.93; 95% CI 0.22–3.82).

Conclusion
This meta-analysis demonstrates improved FFA in persistent AF patients who underwent voltage-guided substrate modification targeting LVA.
Object Handling for People With Dementia: A Scoping Review and the Development of Intervention Guidance
Authors: D’Andrea Federica , Dening Tom , Tischler Victoria 
Published: June 2022

Abstract

Background and Objectives
Among the various psychosocial interventions aiming at improving behavior, quality of life, and the well-being of people with dementia, one that has attracted recent attention has been object handling. This scoping review synthesizes available studies on object handling for people with dementia, their effects, and methodological characteristics and describes its components and likely domains.

Research Design and Methods
The search was conducted using CINAHL, PsycINFO, MEDLINE, PsycARTICLES, Academic Search Elite, and Art Full Text, plus review of reference lists and hand search. Data from the studies included were chattered and reported in narrative form.

Results
Eleven studies were included; of which, 9 described a group intervention and 10 investigated the distinctive value of heritage items. Studies used a mixed-methods or qualitative design and varied in their procedures, including number of sessions and length of intervention. Most studies reported positive effects on well-being, mood, and emotion in those with dementia. Qualitative investigations revealed that the co-construction of an object’s meaning facilitated new learning, social inclusion, and change in attitudes toward dementia. From the review and stakeholder consultations, a definition of object handling is proposed, which includes three components: presenting, receiving, and responding.

Discussion and Implications
The findings suggest that people with dementia may benefit from object handling interventions as a means of improving well-being, mood, and social inclusion. The review highlighted a variety of approaches used and a small number of studies were identified under the term of “object handling.” Further studies are needed to examine the complexity of object handling, its impact within dementia care settings, and that explicitly use the term “object handling.” Given the focus to date on heritage, archive, and museum objects, more studies involving the handling of everyday material objects are needed because these are by definition highly accessible.
Aging and the Left Behind: Puerto Rico and Its Unconventional Rapid Aging
Authors: Matos-Moreno Amílcar , Verdery Ashton M , Mendes de Leon Carlos F , De Jesús-Monge Vivianna M , Santos-Lozada Alexis R 
Published: June 2022

Abstract
Puerto Rico is aging more rapidly than almost any country, with 2020 estimates placing its population share of adults older than 65 as being the 10th highest in the world. Unlike most locales, Puerto Rico’s aging is driven by both (a) the culmination of long-running fertility and mortality trends and (b) high levels of outmigration of working-age adults, which contributes both directly (removal of young people) and indirectly (reduced births) to its pace of population aging. This article offers an overview of the main issues surrounding population aging in Puerto Rico. Policymakers and government leaders must plan for Puerto Rico’s unconventional population aging, which will exacerbate traditional concerns about the sustainability of government services and long-term economic prospects. Additional concerns emerge related to reduced social support networks and their impact on caregiving dynamics and implications for health. Puerto Rico’s unique history and political relationship with the United States present challenges and benefits for its aging population. Research on aging in Puerto Rico and public health policies must adapt to the needs of the country’s aging society.
Establishing political priority for global mental health: a qualitative policy analysis
Authors: Iemmi Valentina 
Published: June 2022

AbstractMental disorders represent the leading cause of disability worldwide, yet they remain a low global health priority. This paper uses a case study methodology and different data sources (35 interviews and documents) to analyse factors that have shaped the generation of political priority for global mental health over the past three decades (1990–2020) and their changes over time. The Shiffman and Smith framework on determinants of political priority for global health issues is used to organize data into themes: actor power, ideas, political context and issue characteristics. Global mental health has gained political attention, especially over the past decade, yet support remains limited. Findings reveal that actor power is undermined by a fragmented policy community, the absence of one guiding institution or coordination mechanism and little civil society mobilization. Public portrayal of the issue is divided, hampered by the absence of a common understanding by the community and by stigma. Some policy windows have been missed and a strong global governance structure is lacking. Credible indicators and evidence on simple cost-effective solutions, especially in low- and middle-income countries, are scarce. However, opportunities are arising, including an increasing number of leaders and grassroots organizations, multiple arguments for action and integrated solutions resonating with broader audiences, widening political support at the national level, an emerging global governance structure and an expanding evidence base on the scale of the problem and available solutions. The results point to three technical and four political challenges that advocates need to address to increase political support over the next decade.
Post-traumatic stress disorder, anxiety, depression and related factors among COVID-19 patients during the fourth wave of the pandemic in Vietnam
Authors: Nguyen Hoang Bac , Nguyen Thi Hong Minh , Vo Thi Hong Nhan , Vo Thi Cam Nhung , Nguyen Duc Nguyet Quynh , Nguyen Huu-Thinh , Tang Tuan-Ngan , Nguyen Thi-Hiep , Do Van Trang , Truong Quang Binh 
Published: June 2022

Abstract

Background
This study investigated post-traumatic stress disorder (PTSD), anxiety, depression and their related factors among coronavirus disease 2019 (COVID-19) patients during the fourth wave of the pandemic in Vietnam.

Methods
Vietnamese-fluent confirmed COVID-19 patients for at least 3 d were recruited in this online cross-sectional study to answer a three-part questionnaire including participants’ sociodemographic characteristics, PTSD (Impact of Event Scale-Revised) and anxiety and depression (Hospital Anxiety and Depression Scale). Associated factors were determined using multivariable binary logistic regression models.

Results
Of 1544 responses, the majority were female (53.0%), ages 18–39 y (74.8%) and were isolated and treated at field hospitals (72.2%). Family or friends were the greatest sources of mental support (68.2%), followed by healthcare providers (51.1%). The overall prevalence rates of PTSD, anxiety and depression among COVID-19 patients were 22.9%, 11.2% and 17.4%, respectively. Risk factors included older age, higher education, getting infected from the public, knowing someone who died from COVID-19 and high perception of life threat. Meanwhile, mental assistance from family or friends, a greater number of supporters, living with someone not vulnerable and higher salaries were significantly protective factors.

Conclusions
The psychological responses associated with some sociodemographic details. Family or friends should be the first line of mental interventions for COVID-19 patients.
Distributions Distract: How Distributions on Attribute Filters and Other Tools Affect Consumer Judgments
Authors: Davis Derick F 
Published: June 2022

AbstractFirms and other entities provide category-level product attribute information via attribute filters and other tools to aid consumers in filtering, evaluating, comparing, and choosing products. This research examines how displaying this information as a range with or without the distribution of values systematically affects judgments involving attribute value comparisons. Specifically, distributions draw attention away from attribute values, reducing the importance of attribute value differences. With this reduced importance, consumers are less sensitive to attribute value differences; thus, consumers evaluate individual products more positively as they seem more similar to the best available option. Likewise, wider bands of attribute values are selected when filtering product options, as the minimum and maximum values chosen seem less different. Reduced sensitivity to differences also has implications for choices involving tradeoffs between attributes. Importantly, the presence of a distribution itself is the primary driver of this effect, more so than distribution type, as the effect is largely independent of the type of distribution displayed (e.g., normal, bimodal, skewed, uniform). Across six main and seven supplemental experiments, this research highlights a novel consideration for how consumers filter options, form preferences, and choose products. These findings have practical implications and highlight important topics for future research.
A survey of sodium absorption in 10 giant exoplanets with high-resolution transmission spectroscopy
Authors: Langeveld Adam B , Madhusudhan Nikku , Cabot Samuel H C 
Published: June 2022

ABSTRACT
The alkali metal sodium (Na) is one of the most commonly detected chemical species in the upper atmospheres of giant exoplanets. In this work, we conducted a homogeneous survey of Na in a diverse sample of 10 highly irradiated giant exoplanets using high-resolution transmission spectroscopy. Our sample includes nine planets with previous Na detections and one new detection. We confirm previous detections and assess multiple approaches for deriving Na line properties from high-resolution transmission spectra. The homogeneously measured sodium line depths were used to constrain the atmospheric heights (HNa) with respect to the planetary radii (Rp). We assess an empirical trend describing the relative atmospheric height (HNa/Rp) as a function of planetary equilibrium temperature (Teq) and surface gravity (g), in which HNa/Rp decreases exponentially with ξ ∝ gTeq, approaching a constant at large ξ. We also report the sodium D2/D1 line ratios across our sample and find that seven targets have line ratios that are consistent with unity. Finally, we measured net blueshifted offsets of the sodium absorption lines from their rest frame wavelengths for all 10 planets, corresponding to day–night wind velocities of a few km s−1. This suggests that the broad sample of exoplanets share common underlying processes that govern atmospheric dynamics. Our study highlights a promising avenue for using high-resolution transmission spectroscopy to further our understanding of how atmospheric characteristics vary over a diverse sample of exoplanets.
Discovering vanishing objects in POSS I red images using the Virtual Observatory
Authors: Solano Enrique , Villarroel B , Rodrigo C 
Published: June 2022

ABSTRACT
In this paper, we report a search for vanishing sources in POSS I red images using virtual observatory (VO) archives, tools, and services. The search, conducted in the framework of the VASCO project, aims at finding POSS I (red) sources not present in recent catalogues like Pan-STARRS DR2 (limiting magnitude r = 21.4) or Gaia EDR3 (limiting magnitude G = 21). We found 298 165 sources visible only in POSS I plates, out of which 288 770 had a cross-match within 5 arcsec in other archives (mainly in the infrared), 189 were classified as asteroids, 35 as variable objects, 3592 as artefacts from the comparison to a second digitization (Supercosmos), and 180 as high proper motion objects without information on proper motion in Gaia EDR3. The remaining unidentified transients (5399) as well as the 172 163 sources not detected in the optical but identified in the infrared regime are available from a VO compliant archive and can be of interest in searches for strong M-dwarf flares, high-redshift supernovae, asteroids, or other categories of unidentified red transients. No point sources were detected by both POSS-I and POSS-II before vanishing, setting the rate of failed supernovae in the Milky Way during 70 yr to less than one in one billion.
Formation of periodic FRB in binary systems with eccentricity
Authors: Barkov Maxim V , Popov Sergei B 
Published: June 2022

ABSTRACT
Long-term periodicity in the rate of flares is observed for two repeating sources of fast radio bursts (FRBs). In this paper, we present a hydrodynamical modelling of a massive binary consisting of a magnetar and an early-type star. We model the interaction of the pulsar wind from the magnetar with an intense stellar wind. It is shown that only during a fraction of the orbital period, radio emission can escape the system. This explains the duty cycle of the two repeating FRB sources with periodic activity. The width of the transparency window depends on the eccentricity, stellar wind properties, and the viewing angle. To describe the properties of the known sources, it is necessary to assume large eccentricities ≳0.5. We apply the maser cyclotron mechanism of the radio emission generation to model spectral properties of the sources. The produced spectrum is not wide: Δν/ν ∼ 0.2 and the typical frequency depends on the radius of the shock where the emission is generated. The shock radius changes along the orbit. This, together with changing parameters of the medium, allows us to explain the frequency drift during the phase of visibility. Frequency dependence of the degree of polarization at few GHz can be a consequence of a small-scale turbulence in the shocked stellar wind. It is much more difficult to explain huge (∼105 rad/m2) and variable value of the rotation measure observed for FRB 121102. We suggest that this can be explained if the supernova explosion, which produced the magnetar happened near a dense interstellar cloud with n ∼ 100 cm−3.
The peculiar spectral evolution of the new X-ray transient MAXI J0637–430
Authors: Ma R C , Soria R , Tao L , Zhang W , Qu J L , Zhang S N , Zhang L , Qiao E L , Zhao S J , Ge M Y , Li X B , Huang Y , Song L M , Zhang S , Bu Q C , Wang Y N , Ma X , Jia S M 
Published: June 2022

ABSTRACT
We studied the transient Galactic black hole candidate MAXI J0637−430 with data from Insight-HXMT, Swift, and XMM–Newton. The broad-band X-ray observations from Insight-HXMT help us constrain the power-law component. MAXI J0637–430 is located at unusually high Galactic latitude; if it belongs to the Galactic thick disc, we suggest a most likely distance ≲7 kpc. Compared with other black hole transients, MAXI J0637–430 is also unusual for other reasons: a fast transition to the thermal dominant state at the start of the outburst; a low peak temperature and luminosity (we estimate them at ≈0.7 keV and ≲0.1 times Eddington, respectively); a short decline time-scale; a low soft-to-hard transition luminosity (≲0.01 times Eddington). We argue that such properties are consistent with a small binary separation, short binary period (P ∼ 2 h), and low-mass donor star (M2 ∼ 0.2 M⊙). Moreover, spectral modelling shows that a single disc blackbody component is not a good fit to the thermal emission. Soft spectral residuals, and deviations from the standard $L_{\rm disc} \propto T_{\rm in}^4$ relation, suggest the need for a second thermal component. We propose and discuss various scenarios for such component, in addition to those presented in previous studies of this source. For example, a gap in the accretion disc between a hotter inner ring near the innermost stable orbit, and a cooler outer disc. Another possibility is that the second thermal component is the thermal plasma emission from an ionized outflow.
Role of aIF5B in archaeal translation initiation
Authors: Kazan Ramy , Bourgeois Gabrielle , Lazennec-Schurdevin Christine , Larquet Eric , Mechulam Yves , Coureux Pierre-Damien , Schmitt Emmanuelle 
Published: June 2022

Abstract
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.