bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
Authors: Jarnot Patryk , Ziemska-Legiecka Joanna , Grynberg Marcin , Gruca Aleksandra 
Published: August 2022

Abstract
Low complexity regions are fragments of protein sequences composed of only a few types of amino acids. These regions frequently occur in proteins and can play an important role in their functions. However, scientists are mainly focused on regions characterized by high diversity of amino acid composition. Similarity between regions of protein sequences frequently reflect functional similarity between them. In this article, we discuss strengths and weaknesses of the similarity analysis of low complexity regions using BLAST, HHblits and CD-HIT. These methods are considered to be the gold standard in protein similarity analysis and were designed for comparison of high complexity regions. However, we lack specialized methods that could be used to compare the similarity of low complexity regions. Therefore, we investigated the existing methods in order to understand how they can be applied to compare such regions. Our results are supported by exploratory study, discussion of amino acid composition and biological roles of selected examples. We show that existing methods need improvements to efficiently search for similar low complexity regions. We suggest features that have to be re-designed specifically for comparing low complexity regions: scoring matrix, multiple sequence alignment, e-value, local alignment and clustering based on a set of representative sequences. Results of this analysis can either be used to improve existing methods or to create new methods for the similarity analysis of low complexity regions.
Reversible Circuit Synthesis Method Using Sub-graphs of Shared Functional Decision Diagrams
Authors: Bu Dengli , Deng Junyi , Tang Pengjie , Yang Shuhong 
Published: August 2022

AbstractReversible circuit synthesis methods based on decision diagrams achieve low quantum costs but do not account for quantum bit (qubit) limits for the application of reversible logic in quantum computing. Here, a synthesis method using sub-graphs of shared functional decision diagrams (SFDDs) is proposed for reducing the number of lines when synthesizing reversible circuits. An SFDD is partitioned into sub-graphs by exploiting the longest dominant-active paths, and the sub-graphs are mapped to reversible gate cascades. To further reduce the number of lines, template root matching is presented for reusing circuit lines. Experimental results indicate that the proposed method achieves the known minimum number of lines in many cases and has good scalability. Although the proposed method increases the quantum cost over a prior method based on functional decision diagrams, it significantly reduces the number of lines in most cases. Compared with the one-pass method using quantum multiple-valued decision diagrams, the proposed method reduces the quantum cost without increasing the number of lines in many cases. When compared with the lookup table-based method using a direct mapping flow, the method reduces the number of lines in a few cases. Thus, the method aids in the physical realization of a quantum circuit.
MyMD-1 Improves Health Span and Prolongs Life Span in Old Mice: A Noninferiority Study to Rapamycin
Authors: Sabini Elena , O’Mahony Alison , Caturegli Patrizio 
Published: August 2022

AbstractAging and age-related diseases represent a compelling therapeutic goal for senolytics and drugs targeting inflammatory or metabolic pathways. We compared MyMD-1, a synthetic derivative of the alkaloid myosmine capable of suppressing TNF-α production, to rapamycin, the best characterized drug endowed with antiaging properties. In vivo, a longitudinal cohort of 54 C57BL/6 mice, 19-month-old at the start, was randomized to receive MyMD-1, high-dose (126 ppm) rapamycin, or low-dose (14 ppm) rapamycin plus metformin. Each treatment arm included 18 mice (10 females and 8 males) and was followed for 16 months or until death. Life span was significantly longer in MyMD-1 than rapamycin (p = .019 vs high-dose and .01 vs low-dose) in a Cox survival model that accounted for sex and serum levels of IL-6, TNF-α, and IL-17A. MyMD-1 also improved several health span characteristics, resulting in milder body weight loss, greater muscle strength, and slower progression to frailty. In vitro, MyMD-1 and rapamycin were compared using a panel of 12 human primary cell systems (BioMAP Diversity PLUS), where a total of 148 biomarkers were measured. MyMD-1 possessed antiproliferative, anti-inflammatory, and antifibrotic properties. Many were shared with rapamycin, but MyMD-1 was more active in the inhibition of proinflammatory and profibrotic biomarkers. Overall, MyMD-1 emerges as a new compound that, even when begun at an advanced age, induces beneficial effects on health and life span by modulating inflammation and tissue remodeling.
Characteristics Associated With 5-Year Fracture Risk Versus 5-Year Mortality Risk Among Late-Life Men
Authors: Langsetmo Lisa , Schousboe John T , Taylor Brent C , Cauley Jane A , Fink Howard A , Cawthon Peggy M , Stefanick Marcia L , Kado Deborah M , Kats Allyson M , Ensrud Kristine E 
Published: August 2022

AbstractBackgroundIdentifying late-life men who might benefit from treatment to prevent fracture is challenging given high mortality. Our objective was to evaluate risks of clinical fracture, hip fracture, and mortality prior to fracture among men aged at least 80 years.MethodsStudy participants included 3 145 community-dwelling men (mean [standard deviation] age 83 [2.8] years) from the Osteoporotic Fractures in Men (MrOS) Study. We used separate multivariable Fine-Gray competing risk models with prespecified risk factors (age, hip bone mineral density [BMD], recent fracture [&lt;5 years], fall history [previous year], and multimorbidity [# conditions]) to estimate subdistribution hazard ratios and absolute 5-year risks of any clinical fracture and mortality prior to clinical fracture. Secondary analysis considered a hip fracture.ResultsThere were 414 incident clinical fractures and 595 deaths without prior fracture within 5 years. BMD, fall history, and recent fracture were strong predictors of clinical fracture. Age and multimorbidity were strong predictors of mortality before fracture. After accounting for competing risks, age, BMD, and fall history were each associated with both risks of hip fracture and mortality before hip fracture. Model discrimination varied from 0.65 (mortality before fracture) to 0.79 (hip fracture). Estimated mortality differed substantially among men with similar clinical fracture risk due to a modest correlation between fracture risk and competing mortality risk = 0.37.ConclusionIn late-life men, strong risk factors for clinical fracture and hip fracture include fall history, BMD, and recent fracture. Osteoporosis drug treatment decisions may be further enhanced by consideration of fracture risk versus overall life expectancy.
Work Expectations, Depressive Symptoms, and Passive Suicidal Ideation Among Older Adults: Evidence From the Health and Retirement Study
Authors: Mezuk Briana , Dang Linh , Jurgens David , Smith Jacqui 
Published: August 2022

Abstract

Background and Objectives
Employment and work transitions (e.g., retirement) influence mental health. However, how psychosocial contexts such as anticipation and uncertainty about work transitions, irrespective of the transitions themselves, relate to mental health is unclear. This study examined the relationships of work expectations with depressive symptoms, major depression episodes (MDE), and passive suicidal ideation over a 10-year period among the “Baby Boom” cohort of the Health and Retirement Study.

Research Design and Methods
Analysis was limited to 13,247 respondents aged 53–70 observed from 2008 to 2018. Past-year depressive symptoms, MDE, and passive suicidal ideation were indexed using the Composite International Diagnostic Interview—Short Form. Expectations regarding working full-time after age 62 were assessed using a probability scale (0%–100%). Mixed-effect logistic regressions with time-varying covariates were used to assess the relationship of work expectations with mental health, accounting for demographics, health status, and functioning, and stratified by baseline employment status.

Results
At baseline, higher work expectations were inversely associated with depressive symptoms. Longitudinally, higher expectations were associated with lower odds of depressive symptoms (odds ratio [OR] = 0.93, 95% CI: 0.91, 0.94). This association was more pronounced among respondents not working at baseline (ORNot working = 0.93 vs ORWorking = 0.96). Greater uncertainty (i.e., expectations near 50%) was also inversely associated with depressive symptoms. Results were similar for past-year MDE and passive suicidal ideation.

Discussion and Implications
Expectations (overall likelihood and uncertainty), as indicators of psychosocial context, provide insight into the processes that link work transitions with depression risk.
Deductive databases in four-valued logic: rule semantics and models
Authors: Laurent Dominique , Spyratos Nicolas 
Published: August 2022

AbstractIn this paper, we investigate rule semantics for deductive databases in the context of four-valued logic. In our approach, a database is a pair $\varDelta =(E,R)$, where $E$ is a set of pairs, each pair associating a ground fact with a truth value (thus, allowing to store true, false or inconsistent facts) and $R$ is a set of rules generalizing standard Datalog rules in the following sense: (i) the head of a rule can be a positive or a negative atom and (ii) the body can involve any among the connectors of four-valued logic. We define the database semantics as the least fixed point of a monotonic operator and we compare this semantics with that of k-existential programs defined by Fitting and paraconsistent extended logic programs defined by Arieli. Our main contribution is to show that, if we consider rules as implications (i.e. if we view the database as a set of formulas) then the semantics of the database is the unique minimal model of the set of database formulas. Here, minimality is understood with respect to the knowledge ordering of four-valued logic satisfying a monotonicity property whereby the truth value of the head of an instantiated rule is greater than that of the body. Moreover, we characterize databases having finite semantics and then, we address the issue of database updating. We argue that our approach allows for a new kind of updates, in which the update result depends not only on the fact involved in the update but also on its current truth value in the database.
Legal Determinants of Health
Authors: Thomson Michael 
Published: August 2022

Abstract
Social determinants of health are the social and economic conditions that have a determining impact on health at an individual and population level. Working within this framework, in 2019 the O’Neill Institute for National and Global Health Law at Georgetown University and The Lancet published The legal determinants of health: Harnessing the power of law for global health and sustainable development. This report identifies and promotes four legal determinants: provision of universal health coverage under the Sustainable Development Goals; governance of national and global health institutions; implementation of evidence-based health interventions; and building legal capacity. These determinants are dominated by the role of law in founding and governing health institutions and regulating their interventions. Such work is essential. However, the relationship between law, health improvement, and health equity articulated through these four determinants risks marginalising questions of disadvantage and inequality that social determinants of health research—and the report itself—mandate we attend to. Addressing the UK experience of COVID-19, and how social inequalities profoundly impacted experiences and outcomes in the first year of the pandemic, this article builds on the Lancet-O’Neill Commission’s important work to argue that any articulation of legal determinants of health must foreground law’s role in improving fairness in social arrangements and the distribution of resources.
The evolution of protoplanetary disc radii and disc masses in star-forming regions
Authors: Marchington Bridget , Parker Richard J 
Published: August 2022

ABSTRACT
Protoplanetary discs are crucial to understanding how planets form and evolve, but these objects are subject to the vagaries of the birth environments of their host stars. In particular, photoionizing radiation from massive stars has been shown to be an effective agent in disrupting protoplanetary discs. External photoevaporation leads to the inward evolution of the radii of discs, whereas the internal viscous evolution of the disc causes the radii to evolve outwards. We couple N-body simulations of star-forming regions with a post-processing analysis of disc evolution to determine how the radius and mass distributions of protoplanetary discs evolve in young star-forming regions. To be consistent with observations, we find that the initial disc radii must be of the order of 100 au, even though these discs are readily destroyed by photoevaporation from massive stars. Furthermore, the observed disc radius distribution in the Orion Nebula Cluster (ONC) is more consistent with moderate initial stellar densities (100 M⊙ pc−3), in tension with dynamical models that posit much higher initial densities for the ONC. Furthermore, we cannot reproduce the observed disc radius distribution in the Lupus star-forming region if its discs are subject to external photoevaporation. A more detailed comparison is not possible due to the well-documented uncertainties in determining the ages of pre-main-sequence (disc-hosting) stars.
Beginning: China's national park system
Authors: Zhao Weijie 
Published: August 2022

Abstract
At the leaders’ summit of the 15th Meeting of the Conference of the Parties to the Convention on Biological Diversity (COP15) on 12 October 2021, China's President Xi Jinping declared that China has officially designated its first group of national parks—the Three-River-Source National Park, the Giant Panda National Park, the Northeast China Tiger and Leopard National Park, the Hainan Tropical Forests National Park, and the Wuyishan National Park. The five national parks cover a total area of ∼230 000 square kilometers and protect nearly 30% of the key terrestrial wildlife species found in China.
Since the establishment of the United States’ Yellowstone National Park in 1872, national parks have been founded in many countries, and some of them have become distinctive ‘national signatures’ and important ecological security shelters. As a large country with rich biodiversity, China now begins to establish its first five national parks, with a total of about 50 planned for the future, and to form a national-park-centric protected-area system. How will national parks change the landscape of China's ecological conservation? Is China well prepared to scientifically establish and administrate national parks? In this panel discussion, six Chinese ecological conservationists introduce the background, plans and challenges of China's national park system, and provide their scientific perspectives.
Guangchun Lei

Professor, School of Ecology and Nature Conservation, Beijing Forestry University
Zhiyun Ouyang

Professor, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences
Yang Su

Research Fellow, Development Research Center of the State Council of China
Rui Yang

Professor, Institute for National Parks, Tsinghua University
Yujun Zhang

Professor, School of Landscape Architecture, Beijing Forestry University
Keping Ma (Chair)

Professor, Institute of Botany, Chinese Academy of Sciences
Nestling Savannah Sparrows and Tree Swallows differ in their sensitivity to weather
Authors: Wheelwright Nathaniel T , Freeman-Gallant Corey R , Mauck Robert A 
Published: August 2022

AbstractSavannah Sparrows (Passerculus sandwichensis) and Tree Swallows (Tachycineta bicolor) breed and forage in the same habitat on Kent Island, a boreal island in the Bay of Fundy, New Brunswick, but respond differently to the same weather conditions. The 2 passerines are similar in body size but because Tree Swallows depend upon small flying insects captured on the wing, they may be more sensitive to weather than Savannah Sparrows, which forage on insects and seeds on the ground and in shrubs and trees. To compare how reproductive success in the 2 species was affected by weather conditions, we took advantage of an 18-year dataset and used a model-building approach that controlled for year, adult sex and age, and field where they nested. We focused on 3 measures of reproductive success (hatching success, fledging success, and nestling condition) and different time periods (3- to 18-day time windows) before hatching or fledging. The responses of the 2 species differed in magnitude and direction. In Tree Swallows, adding weather variables to the basic model increased the explanatory power of fixed effects by 19.1%, illustrating the swallows’ sensitivity to weather. In contrast, in Savannah Sparrows, the addition of weather variables only increased the model’s explanatory power by 0.4% and the proportion of variation attributed to fixed factors by only 1.5%, which reflected the species’ hardiness in the face of inclement weather. Our results suggest that how a bird species forages and the nature of its prey may influence its sensitivity to weather and indicate that increased rainfall, strong winds and other events associated with climate change may affect Tree Swallows and other aerial insectivores more than ground-foraging birds such as Savannah Sparrows.
Self-reported sleepiness associates with greater brain and cortical volume and lower prevalence of ischemic covert brain infarcts in a community sample
Authors: Baril Andrée-Ann , Beiser Alexa S , DeCarli Charles , Himali Dibya , Sanchez Erlan , Cavuoto Marina , Redline Susan , Gottlieb Daniel J , Seshadri Sudha , Pase Matthew P , Himali Jayandra J 
Published: August 2022

AbstractStudy ObjectivesWe evaluated if self-reported sleepiness was associated with neuroimaging markers of brain aging and ischemic damage in a large community-based sample.MethodsParticipants from the Framingham Heart Study Offspring cohort (n = 468, 62.5 ± 8.7 years old, 49.6%M) free of dementia, stroke, and neurological diseases, completed sleep questionnaires and polysomnography followed by magnetic resonance imaging (MRI), 3 years later on average. We used linear and logistic regression models to evaluate the associations between Epworth Sleepiness Scale (ESS) scores and total brain, cortical and subcortical gray matter, and white matter hyperintensities volumes, and the presence of covert brain infarcts.ResultsHigher sleepiness scores were associated with larger total brain volume, greater cortical gray matter volume, and a lower prevalence of covert brain infarcts, even when adjusting for a large array of potential confounders, including demographics, sleep profiles and disorders, organic health diseases, and proxies for daytime cognitive and physical activities. Interactions indicated that more sleepiness was associated with larger cortical gray matter volume in men only and in APOE ε4 noncarriers, whereas a trend for smaller cortical gray matter volume was observed in carriers. In longitudinal analyses, those with stable excessive daytime sleepiness over time had greater total brain and cortical gray matter volumes, whereas baseline sleepiness scores were not associated with subsequent atrophy or cognitive decline.ConclusionOur findings suggest that sleepiness is not necessarily a marker of poor brain health when not explained by diseases or sleep debt and sleep disorders. Rather, sleepiness could be a marker of preserved sleep-regulatory processes and brain health in some cases.
Buprenorphine-naloxone versus Buprenorphine for Treatment of Opioid Use Disorder in Pregnancy
Authors: Perry Briana N. , Vais Simone , Boateng Jeffery O. , Jain Mayuri , Wachman Elisha M. , Saia Kelley A. 
Published: August 2022

Objectives
Data regarding treatment outcomes with the use of buprenorphine-naloxone (BUP-NX) in pregnancy are scarce. The objective of this study is to examine the outcomes in a cohort of pregnancies treated with BUP-NX versus buprenorphine (BUP).

Methods
This single-center, retrospective cohort study examined birthing person-infant dyads treated with BUP-NX versus BUP. The primary birthing person outcome was return to opioid use in pregnancy. The primary neonatal outcome was the need for pharmacologic treatment for neonatal opioid withdrawal syndrome (NOWS).

Results
The BUP-NX and the BUP treatment groups included 33 and 73 dyads, respectively. Except for psychiatric medication use, all demographics were similar between groups. In the final regression models, neither the birthing person nor the neonatal outcomes differed. The adjusted odds ratio for return to use during pregnancy for the BUP-NX versus BUP groups was 1.93 (95% confidence interval, 0.78–4.76). The adjusted odds ratio for pharmacologic treatment of NOWS for the BUP-NX versus BUP groups was 0.65 (95% confidence interval, 0.27–1.54). Among a subgroup of persons who transitioned from BUP to BUP-NX mid-pregnancy, there was no proximate return to use or need for dose increase.

Conclusions
Compared with BUP, the use of BUP-NX in pregnancy is not associated with a higher risk of return to opioid use or a higher need for pharmacological treatment for NOWS.
Circumstances Around Cigarette Use After Enforced Abstinence From Smoking in an American Prison
Authors: Martin Rosemarie A. , Stein L. A. R. , Kang Augustine , Rohsenow Damaris J. , Bock Beth , Martin Stephen A. , Clarke Jennifer G. 
Published: August 2022

Objectives
Most adults return to smoking after enforced tobacco abstinence when incarcerated in US prisons. Little is known about the specific relapse triggers on reentry. This study examines situational, affective, and motivational antecedents of return to smoking immediately after release from a tobacco-free prison.

Methods
Assessments were administered before release and 1 and 7 days after release to 190 incarcerated adults who were smokers before incarceration. Those reporting smoking within 7 days after release were asked about circumstances surrounding their first cigarette.

Results
Two-thirds reported smoking in the 7 days after release (76% of those in the first day) with the first cigarette smoked 21 hours after release on average. Smoking occurred more quickly for women than men and for those who planned to smoke after release (P values from 0.05 to 0.001). Forty-one percent of participants smoked while waiting for a ride or on the way home, 68% were given their first cigarette, 28% reported first smoking when reuniting with others, 42% first smoked with smokers, and 26% first smoked as celebration. The moods most reported before smoking were happy (60%) or excited (41.5%). Factors reported that could have prevented smoking were avoiding other smokers (27%), avoiding stress (16%), not drinking/using drugs (12%), and not having access to cigarettes (11%).

Conclusions
High rates of return to smoking occurred rapidly when around other smokers, using other substances, and in a positive mood. Interventions that focus specifically on these factors and can be immediately accessed upon release are required to help sustain people's desired abstinence.