bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterns of virus growth across the diversity of life
Authors: Jin Tianyi , Yin John 
Published: February 2021

AbstractAlthough viruses in their natural habitats add up to less than 10% of the biomass, they contribute more than 90% of the genome sequences [1]. These viral sequences or ‘viromes’ encode viruses that populate the Earth’s oceans [2, 3] and terrestrial environments [4, 5], where their infections impact life across diverse ecological niches and scales [6, 7], including humans [8–10]. Most viruses have yet to be isolated and cultured [11–13], and surprisingly few efforts have explored what analysis of available data might reveal about their nature. Here, we compiled and analyzed seven decades of one-step growth and other data for viruses from six major families, including their infections of archaeal, bacterial and eukaryotic hosts [14–191]. We found that the use of host cell biomass for virus production was highest for archaea at 10%, followed by bacteria at 1% and eukarya at 0.01%, highlighting the degree to which viruses of archaea and bacteria exploit their host cells. For individual host cells, the yield of virus progeny spanned a relatively narrow range (10–1000 infectious particles per cell) compared with the million-fold difference in size between the smallest and largest cells. Furthermore, healthy and infected host cells were remarkably similar in the time they needed to multiply themselves or their virus progeny. Specifically, the doubling time of healthy cells and the delay time for virus release from infected cells were not only correlated (r = 0.71, p &lt; 10−10, n = 101); they also spanned the same range from tens of minutes to about a week. These results have implications for better understanding the growth, spread and persistence of viruses in complex natural habitats that abound with diverse hosts, including humans and their associated microbes.
Informatics response to address the COVID-19 pandemic in a safety net healthcare system
Authors: Sadasivaiah Shobha , Shaffer Eric , Enanoria Wayne , Su George , Goldman Seth , Scarafia Jeff , Lee Tina , Yu Albert , Goldman L Elizabeth , Ratanawongsa Neda 
Published: February 2021

Abstract
In service of particularly vulnerable populations, safety net healthcare systems must nimbly leverage health information technology (IT), including electronic health records (EHRs), to coordinate the medical and public health response to the novel coronavirus (COVID-19). Six months after the San Francisco Department of Public Health implemented a new EHR across its hospitals and citywide clinics, California declared a state of emergency in response to COVID-19. This paper describes how the IT and informatics teams supported San Francisco Department of Public Health’s goals of expanding the safety net healthcare system capacity, meeting the needs of specific vulnerable populations, increasing equity in COVID-19 testing access, and expanding public health analytics and research capacity. Key enabling factors included critical partnerships with operational leaders, early identification of priorities, a clear governance structure, agility in the face of rapidly changing circumstances, and a commitment to vulnerable populations.
Coverage of the hospital-based cancer registries and the designated cancer care hospitals in Japan
Authors: Okuyama Ayako , Tsukada Yoichiro , Higashi Takahiro 
Published: February 2021

Abstract

Background
Hospital-based cancer registries were developed to describe and improve clinical care for cancer patients. We described the hospital-based cancer registry coverage as a reference for the users, including researchers, policymakers and clinicians.

Methods
The hospital-based cancer registry coverage was defined as the proportion of new cases registered in the hospital-based cancer registry to the National Cancer Registry as the denominator. To examine the coverage of respective cancer types, age groups and prefecture in the hospital-based cancer registry, cases were grouped based on the 10th International Statistical Classification of Diseases and Related Health Problems and were compared with the published report of the National Cancer Registry in 2017.

Results
The overall hospital-based cancer registries coverage was 71.7%, and 52.5% of patients were treated at designated cancer care hospitals. The hospital-based cancer registries coverage and treatment rates at designated cancer care hospitals varied per cancer type, age group, and prefecture. The hospital-based cancer registries covered over 80% of the patients with cancers of the larynx, uterus, oesophagus, lip, oral cavity, pharynx and skin, whereas patients’ coverage with thyroid cancer was relatively low. The hospital-based cancer registry coverage of young patients (&lt;15 years) was &gt;80%, whereas that for elderly patients (≥85 years) was &lt;55%. The range of coverage in each prefecture was from 43.0 to 89.7%. Over 70% of the patients with cancers of the larynx, lip, oral cavity and pharynx were treated at designated cancer care hospitals.

Conclusions
The hospital-based cancer registry coverage is ~70% of all cancers. Because the coverage differed across cancers and age groups, the respective target groups’ analysis should consider this factor.
Histone acetylation: a requirement for petunia floral scent
Authors: Vlachonasios Konstantinos E 
Published: February 2021

This article comments on:
Patrick RM, Huang X-Q, Dudareva N, Li Y. 2021. Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers. Journal of Experimental Botany 72, 3704–3722.
The environment of QSO triplets at 1 ≲ z ≲ 1.5
Authors: Vicentin Marcelo C , Araya-Araya Pablo , Sodré Laerte , Overzier Roderik , Carrasco Eleazar R , Cuevas Hector 
Published: February 2021

ABSTRACT
We present an analysis of the environment of six QSO triplets at 1 ≲ z ≲ 1.5 by analysing multiband (r, i, z, or g, r, i) images obtained with Megacam at the CFHT telescope, aiming to investigate whether they are associated or not with galaxy protoclusters. This was done by using photometric redshifts trained using the high-accuracy photometric redshifts of the COSMOS2015 catalogue. To improve the quality of our photometric redshift estimation, we included in our analysis near-infrared photometry (3.6 and 4.5$\, \mu$m) from the unWISE survey available for our fields and the COSMOS survey. This approach allowed us to obtain good photometric redshifts with dispersion, as measured with the robust σNMAD statistics (which scales as (1 + z)−1), of ∼0.04 for our six fields. Our analysis setup was reproduced on lightcones constructed from the Millennium Simulation data and the latest version of the L-GALAXIES semi-analytic model to verify the protocluster detectability in such conditions. The density field in a redshift slab containing each triplet was then analysed with a Gaussian kernel density estimator. We did not find any significant evidence of the triplets inhabiting dense structures, such as a massive galaxy cluster or protocluster.
Dark energy survey internal consistency tests of the joint cosmological probes analysis with posterior predictive distributions
Authors: Doux C , Baxter E , Lemos P , Chang C , Alarcon A , Amon A , Campos A , Choi A , Gatti M , Gruen D , Jarvis M , MacCrann N , Park Y , Prat J , Rau M M , Raveri M , Samuroff S , DeRose J , Hartley W G , Hoyle B , Troxel M A , Zuntz J , Abbott T M C , Aguena M , Allam S , Annis J , Avila S , Bacon D , Bertin E , Bhargava S , Brooks D , Burke D L , Carrasco Kind M , Carretero J , Cawthon R , Costanzi M , da Costa L N , Pereira M E S , Desai S , Diehl H T , Dietrich J P , Doel P , Everett S , Ferrero I , Fosalba P , Frieman J , García-Bellido J , Gerdes D W , Giannantonio T , Gruendl R A , Gschwend J , Gutierrez G , Hinton S R , Hollowood D L , Honscheid K , Huff E M , Huterer D , Jain B , James D J , Krause E , Kuehn K , Kuropatkin N , Lahav O , Lidman C , Lima M , Maia M A G , Menanteau F , Miquel R , Morgan R , Muir J , Ogando R L C , Palmese A , Paz-Chinchón F , Plazas A A , Sanchez E , Scarpine V , Schubnell M , Serrano S , Sevilla-Noarbe I , Smith M , Suchyta E , Swanson M E C , Tarle G , To C , Tucker D L , Varga T N , Weller J , Wilkinson R D ,   (DES Collaboration), Alarcon Alex , Compos Andresa , Park Youngsoo 
Published: February 2021

ABSTRACT
Beyond ΛCDM, physics or systematic errors may cause subsets of a cosmological data set to appear inconsistent when analysed assuming ΛCDM. We present an application of internal consistency tests to measurements from the Dark Energy Survey Year 1 (DES Y1) joint probes analysis. Our analysis relies on computing the posterior predictive distribution (PPD) for these data under the assumption of ΛCDM. We find that the DES Y1 data have an acceptable goodness of fit to ΛCDM, with a probability of finding a worse fit by random chance of p = 0.046. Using numerical PPD tests, supplemented by graphical checks, we show that most of the data vector appears completely consistent with expectations, although we observe a small tension between large- and small-scale measurements. A small part (roughly 1.5 per cent) of the data vector shows an unusually large departure from expectations; excluding this part of the data has negligible impact on cosmological constraints, but does significantly improve the p-value to 0.10. The methodology developed here will be applied to test the consistency of DES Year 3 joint probes data sets.
Unveiling the planet population at birth
Authors: Rogers James G , Owen James E 
Published: February 2021

ABSTRACT
The radius distribution of small, close-in exoplanets has recently been shown to be bimodal. The photoevaporation model predicted this bimodality. In the photoevaporation scenario, some planets are completely stripped of their primordial H/He atmospheres, whereas others retain them. Comparisons between the photoevaporation model and observed planetary populations have the power to unveil details of the planet population inaccessible by standard observations, such as the core mass distribution and core composition. In this work, we present a hierarchical inference analysis on the distribution of close-in exoplanets using forward models of photoevaporation evolution. We use this model to constrain the planetary distributions for core composition, core mass, and initial atmospheric mass fraction. We find that the core-mass distribution is peaked, with a peak-mass of ∼4M⊕. The bulk core-composition is consistent with a rock/iron mixture that is ice-poor and ‘Earth-like’; the spread in core-composition is found to be narrow ($\lesssim 16{{\ \rm per\ cent}}$ variation in iron-mass fraction at the 2σ level) and consistent with zero. This result favours core formation in a water/ice poor environment. We find the majority of planets accreted a H/He envelope with a typical mass fraction of $\sim 4{{\ \rm per\ cent}}$; only a small fraction did not accrete large amounts of H/He and were ‘born-rocky’. We find four times as many super-Earths were formed through photoevaporation, as formed without a large H/He atmosphere. Finally, we find core-accretion theory overpredicts the amount of H/He cores would have accreted by a factor of ∼5, pointing to additional mass-loss mechanisms (e.g. ‘boil-off’) or modifications to core-accretion theory.
Intron exon boundary junctions in human genome have in-built unique structural and energetic signals
Authors: Mishra Akhilesh , Siwach Priyanka , Misra Pallavi , Dhiman Simran , Pandey Ashutosh Kumar , Srivastava Parul , Jayaram B 
Published: February 2021

Abstract
Precise identification of correct exon–intron boundaries is a prerequisite to analyze the location and structure of genes. The existing framework for genomic signals, delineating exon and introns in a genomic segment, seems insufficient, predominantly due to poor sequence consensus as well as limitations of training on available experimental data sets. We present here a novel concept for characterizing exon–intron boundaries in genomic segments on the basis of structural and energetic properties. We analyzed boundary junctions on both sides of all the exons (3 28 368) of protein coding genes from human genome (GENCODE database) using 28 structural and three energy parameters. Study of sequence conservation at these sites shows very poor consensus. It is observed that DNA adopts a unique structural and energy state at the boundary junctions. Also, signals are somewhat different for housekeeping and tissue specific genes. Clustering of 31 parameters into four derived vectors gives some additional insights into the physical mechanisms involved in this biological process. Sites of structural and energy signals correlate well to the positions playing important roles in pre-mRNA splicing.
aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin
Authors: Stefos Georgios C , Szantai Eszter , Konstantopoulos Dimitris , Samiotaki Martina , Fousteri Maria 
Published: February 2021

AbstractSpecific capture of chromatin fractions with distinct and well-defined features has emerged as both challenging and a key strategy towards a comprehensive understanding of genome biology. In this context, we developed aniFOUND (accelerated native isolation of factors on unscheduled nascent DNA), an antibody-free method, which can label, capture, map and characterise nascent chromatin fragments that are synthesized in response to specific cues outside S-phase. We used the ‘unscheduled’ DNA synthesis (UDS) that takes place during the repair of UV-induced DNA lesions and coupled the captured chromatin to high-throughput analytical technologies. By mass-spectrometry we identified several factors with no previously known role in UVC-DNA damage response (DDR) as well as known DDR proteins. We experimentally validated the repair-dependent recruitment of the chromatin remodeller RSF1 and the cohesin-loader NIPBL at sites of UVC-induced photolesions. Developing aniFOUND-seq, a protocol for mapping UDS activity with high resolution, allowed us to monitor the landscape of UVC repair-synthesis events genome wide. We further resolved repair efficacy of the rather unexplored repeated genome, in particular rDNA and telomeres. In summary, aniFOUND delineates the proteome composition and genomic landscape of chromatin loci with specific features by integrating state-of-the-art ‘omics’ technologies to promote a comprehensive view of their function.
Police and Crime Commissioners: A Dislocated Expectation?
Authors: Cooper Simon 
Published: February 2021

AbstractThe calls in 2019 and 2020 for a Royal Commission, combined with the launch of The Strategic Review by The Police Foundation and the recommendation by Her Majesty’s Inspector of Constabulary and Fire & Rescue Services for ‘profound and far reaching police reform’, evidence a thirst for refinement, and potentially, significant change to the governance of policing. Using new empirical data obtained through elite research interviews with some of the most senior stakeholders in policing at a regional and national level, this article explores the ability of Police and Crime Commissioners (PCCs) to hold Chief Constables to account. Attention is drawn to how the accountability of Chief Constables to PCCs may have significant strengths, such as enhanced visibility, increased frequency, and improved scrutiny. However, the accountability of Chief Constables may also be frustrated and possibly compromised. Indeed, accountability might be exercised inconsistently, susceptible to significant variance and contingent on the calibre and vagaries of PCCs. As such, recommendations are made to strengthen governance arrangements to ensure Chief Constables are robustly held to account. Specifically, the Home Secretary is encouraged to review The Policing Protocol Order and issue an Accountability Code of Practice.
Meta-analysis of alcohol consumption and venous thromboembolism
Authors: Zhang Xingxia , Chen Xinrong , Yang Jie , Du Liang , Zhou Yong , Li Ka 
Published: February 2021

Abstract

Background
The associations of alcohol consumption and venous thromboembolism (VTE) have been investigated widely, but the conclusions were inconsistent.

Objective
To summarize the relationship of alcohol consumption and VTE.

Methods
This study has been registered in PROSPERO (ID: CRD42020164567). We searched the PubMed, Embase, Web of Science and the Cochrane Library databases from inception to September 2019 and reviewed the reference list of relevant articles to identify studies assessing the association between alcohol consumption and risk of VTE.

Results
Fourteen cohorts and four case-control studies were included in the meta-analysis. Compared with non-drinkers, the risk of VTE was decreased (RR: 0.93; 95% confidence interval [CI] 0.88–0.99) for alcohol drinkers. The pooled RRs of VTE were 0.91 (95% CI 0.84–0.99) for low to moderate alcohol intake (0.1–14.0 drinks/week) and 0.91 (95% CI 0.78–1.06) for high alcohol intake (&gt;14.0 drinks/week) compared with non-drinker. Subgroup analysis showed liquor intake might slightly increase the risk of VTE (1.01; 95% CI 0.85–1.21) although the difference was not significant.

Conclusions
Alcohol consumption in low to moderate was associated with a lower risk of VTE. However, precautions are needed when providing personal drinking advice considering the potential harm of alcohol. Further studies are warranted to determine whether moderate alcohol consumption has a causal role in VTE.
Rules without Commitment: Reputation and Incentives
Authors: Dovis Alessandro , Kirpalani Rishabh 
Published: February 2021

Abstract
This article studies the optimal design of rules in a dynamic model when there is a time inconsistency problem and uncertainty about whether the policy maker can commit to follow the rule ex post. The policy maker can either be a commitment type, which can always commit to follow rules, or an optimizing type, which sequentially decides whether to follow rules or not. This type is unobservable to private agents, who learn about it through the actions of the policy maker. Higher beliefs that the policy maker is the commitment type (i.e. the policy maker’s reputation) help promote good behaviour by private agents. We show that in a large class of economies, preserving uncertainty about the policy maker’s type is preferable from an ex ante perspective. If the initial reputation is not too high, the optimal rule is the strictest one that is incentive compatible for the optimizing type. We show that reputational considerations imply that the optimal rule is more lenient than the one that would arise in a static environment. Moreover, opaque rules are preferable to transparent ones if reputation is high enough.
Implementation of Cognitive Behavioral Therapy With Cognitive Restructuring Technique to Reduce Psychosocial Anxiety in the COVID-19 Outbreak
Authors: Fadhli Teuku , Situmorang Dominikus David Biondi 
Published: February 2021

Objectives:
Anxiety can cause someone to be counterproductive or experience psychological disorders, causing discomfort in social activities, less active participation in behavior. This study aims to prove the effectiveness of cognitive behavioral therapy (CBT) approach and the cognitive restructuring (CR) technique to reduce individual psychosocial anxiety through group counseling, which covers high school adolescents. The CBT approach with the CR technique for dealing with personal psychosocial anxiety provides valuable space for movement. The CBT approach with the CR technique will change the maladaptive beliefs that arise because of anxiety. This intervention aims to increase self-defense and self-control by stimulating rational problem-solving abilities, social skills, and active participation in social activities.

Methods:
The research method was a nonequivalent group pretest-posttest design with a control or comparison group. On the basis of the paired sample t test, there is a significant difference in the mean. The results showed that the CBT approach with the CR technique effectively reduced psychosocial anxiety in the COVID-19 outbreak.

Conclusions:
The results showed that the CBT approach with the CR technique effectively reduced psychosocial anxiety in the COVID-19 outbreak.
Fatty liver index and left ventricular mass: prospective associations from two independent cohorts
Authors: Li Xiang , Heiskanen Jarkko S. , Ma Hao , Heianza Yoriko , Guo Yajun , Kelly Tanika N. , He Hua , Fonseca Vivian A. , Chen Wei , Harville Emily W. , Ruohonen Saku , Hutri-Kähönen Nina , Bazzano Lydia A. , Raitakari Olli T. , Qi Lu 
Published: February 2021

Objectives:
Heart disease is the most common cause of death in patients with nonalcoholic fatty liver disease (NAFLD). Emerging data have shown that NAFLD may affect subclinical myocardial remodeling, mainly left ventricular hypertrophy; however, evidence from the prospective studies is still lacking.

Methods:
Prospective analyses were performed to investigate the association of fatty liver index (FLI) with left ventricular mass (LVM) among 1962 participants from the Bogalusa Heart Study (BHS, 1995–2010) and 1547 participants from the Cardiovascular Risk in Young Finns Study (YFS, 2001–2011) free of cardiovascular diseases (CVD) at baseline. LVM was assessed by two-dimensional guided M-mode echocardiography and indexed (LVMI) to body height (m2.7). Multivariable regression models were applied after adjustment for traditional CVD risk factors.

Results:
In both cohorts, we observed significant and positive associations between FLI and LVM (BHS: β=0.59, P < 0.001; YFS: β=0.41, P < 0.001) and LVMI (BHS: β=0.14, P < 0.001; YFS: β=0.09, P < 0.001). In addition, we found that the relationship between FLI and LVMI was stronger in women than men (BHS: P-interaction = 0.01; YFS: P-interaction < 0.01); and the relationship between FLI and LVM/LVMI was stronger in black than white individuals (LVM: P-interaction = 0.02; LVMI: P-interaction = 0.04). Moreover, we found that the associations of FLI with LVM and LVMI were attenuated by high physical activity, especially in BHS (P-interaction = 0.02).

Conclusion:
Our findings from two independent prospective cohorts indicate that FLI is positively associated with LVM/LVMI, independent of traditional cardiovascular risk factors. Such relationships are more pronounced among women and black individuals and are attenuated by high physical activity.