bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling of multimode radially pulsating high-amplitude δ Scuti stars from the OGLE Galactic bulge sample
Authors: Netzel H , Smolec R 
Published: July 2022

ABSTRACT
Thanks to relatively firm mode identification, possible based only on period ratios, high-amplitude δ Scuti stars pulsating in at least three radial modes are promising targets for asteroseismic inference. In this study, we used the most numerous sample of HADS from the OGLE inner bulge fields that likely pulsate in either three or four radial modes simultaneously. We have computed a grid of pulsation models along evolutionary tracks and determined the physical parameters of stars by matching their pulsation periods and period ratios. For 176 HADS, we determined physical parameters, i.e. masses, luminosities, effective temperatures, metallicities, and ages. We present the distribution of physical parameters and discuss their properties. We selected 16 candidates for SX Phoenicis stars.
Investigation of rocket effect in bright-rimmed clouds using Gaia EDR3
Authors: Saha Piyali , Maheswar G , Ojha D K , Baug Tapas , Neha Sharma 
Published: July 2022

ABSTRACT
Bright-rimmed clouds (BRCs) are excellent laboratories to explore the radiation-driven implosion mode of star formation because they show evidence of triggered star formation. In our previous study, BRC 18 has been found to accelerate away from the direction of the ionizing H ii region because of the well-known ‘Rocket Effect’. Based on the assumption that both BRC 18 and the candidate young stellar objects (YSOs) are kinematically coupled and using the latest Gaia EDR3 measurements, we found that the relative proper motions of the candidate YSOs exhibit a tendency of moving away from the ionizing source. Using BRC 18 as a prototype, we made our further analysis for 21 more BRCs, a majority of which showed a similar trend. For most of the BRCs, the median angle of the relative proper motion of the candidate YSOs is similar to the angle of on-sky direction from the ionizing source to the central IRAS source of the BRC. Based on the Pearson’s and Spearman’s correlation coefficients, we found a strong correlation between these two angles, which is further supported by the Kolmogorov–Smirnov (K−S) test on them. The strong correlation between these two angles supports the ‘Rocket Effect’ in the BRCs on the sky plane.
The quintessence of metallomics: a harbinger of a different life science based on the periodic table of the bioelements
Authors: Maret Wolfgang 
Published: July 2022

Abstract
This year marks the 20th anniversary of the field of metallomics. As a landmark in time, it is an occasion to reflect on the past, present, and future of this integrated field of biometal sciences. A fundamental bias is one reason for having metallomics as a scientific discipline. The focus of biochemistry on the six non-metal chemical elements, collectively known with the acronym SPONCH (sulphur, phosphorus, oxygen, nitrogen, carbon, hydrogen), glosses over the fact that the lower quantities of many other elements have qualities that made them instrumental in the evolution of life and pivotal in numerous life processes. The metallome, alongside the genome, proteome, lipidome, and glycome, should be regarded as a fifth pillar of elemental—vis-à-vis molecular—building blocks in biochemistry. Metallomics as ‘global approaches to metals in the biosciences’ considers the biological significance of most chemical elements in the periodic table, not only the ones essential for life, but also the non-essential ones that are present in living matter—some at higher concentrations than the essential ones. The non-essential elements are bioactive with either positive or negative effects. Integrating the significance of many more chemical elements into the life sciences requires a transformation in learning and teaching with a focus on elemental biology in addition to molecular biology. It should include the dynamic interactions between the biosphere and the geosphere and how the human footprint is changing the ecology globally and exposing us to many additional chemical elements that become new bioelements.
Division of labor within the DNA damage tolerance system reveals non-epistatic and clinically actionable targets for precision cancer medicine
Authors: Spanjaard Aldo , Shah Ronak , de Groot Daniël , Buoninfante Olimpia Alessandra , Morris Ben , Lieftink Cor , Pritchard Colin , Zürcher Lisa M , Ormel Shirley , Catsman Joyce J I , de Korte-Grimmerink Renske , Siteur Bjørn , Proost Natalie , Boadum Terry , van de Ven Marieke , Song Ji-Ying , Kreft Maaike , van den Berk Paul C M , Beijersbergen Roderick L , Jacobs Heinz 
Published: July 2022

Abstract
Crosslink repair depends on the Fanconi anemia pathway and translesion synthesis polymerases that replicate over unhooked crosslinks. Translesion synthesis is regulated via ubiquitination of PCNA, and independently via translesion synthesis polymerase REV1. The division of labor between PCNA-ubiquitination and REV1 in interstrand crosslink repair is unclear. Inhibition of either of these pathways has been proposed as a strategy to increase cytotoxicity of platinating agents in cancer treatment. Here, we defined the importance of PCNA-ubiquitination and REV1 for DNA in mammalian ICL repair. In mice, loss of PCNA-ubiquitination, but not REV1, resulted in germ cell defects and hypersensitivity to cisplatin. Loss of PCNA-ubiquitination, but not REV1 sensitized mammalian cancer cell lines to cisplatin. We identify polymerase Kappa as essential in tolerating DNA damage-induced lesions, in particular cisplatin lesions. Polk-deficient tumors were controlled by cisplatin treatment and it significantly delayed tumor outgrowth and increased overall survival of tumor bearing mice. Our results indicate that PCNA-ubiquitination and REV1 play distinct roles in DNA damage tolerance. Moreover, our results highlight POLK as a critical TLS polymerase in tolerating multiple genotoxic lesions, including cisplatin lesions. The relative frequent loss of Polk in cancers indicates an exploitable vulnerability for precision cancer medicine.
De novoassembly of human genome at single-cell levels
Authors: Xie Haoling , Li Wen , Hu Yuqiong , Yang Cheng , Lu Jiansen , Guo Yuqing , Wen Lu , Tang Fuchou 
Published: July 2022

AbstractGenome assembly has been benefited from long-read sequencing technologies with higher accuracy and higher continuity. However, most human genome assembly require large amount of DNAs from homogeneous cell lines without keeping cell heterogeneities, since cell heterogeneity could profoundly affect haplotype assembly results. Herein, using single-cell genome long-read sequencing technology (SMOOTH-seq), we have sequenced K562 and HG002 cells on PacBio HiFi and Oxford Nanopore Technologies (ONT) platforms and conducted de novo genome assembly. For the first time, we have completed the human genome assembly with high continuity (with NG50 of ∼2 Mb using 95 individual K562 cells) at single-cell levels, and explored the impact of different assemblers and sequencing strategies on genome assembly. With sequencing data from 30 diploid individual HG002 cells of relatively high genome coverage (average coverage ∼41.7%) on ONT platform, the NG50 can reach over 1.3 Mb. Furthermore, with the assembled genome from K562 single-cell dataset, more complete and accurate set of insertion events and complex structural variations could be identified. This study opened a new chapter on the practice of single-cell genome de novo assembly.
Structure of the human RAD17–RFC clamp loader and 9–1–1 checkpoint clamp bound to a dsDNA–ssDNA junction
Authors: Day Matthew , Oliver Antony W , Pearl Laurence H 
Published: July 2022

Abstract
The RAD9–RAD1–HUS1 (9–1–1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5′-recessed end of a dsDNA–ssDNA junction by the RAD17–RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9–1–1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17–RFC clamp loader bound to human 9–1–1, engaged with a dsDNA–ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9–1–1 over PCNA, and how the clamp loader specifically recognises the recessed 5′ DNA end and fixes the orientation of 9–1–1 on the ssDNA.
Selective pericentromeric heterochromatin dismantling caused by TP53 activation during senescence
Authors: Mendez-Bermudez Aaron , Lototska Liudmyla , Pousse Melanie , Tessier Florent , Croce Oliver , Latrick Chrysa M , Cherdyntseva Veronica , Nassour Joe , Xiaohua Jiang , Lu Yiming , Abbadie Corinne , Gagos Sarantis , Ye Jing , Gilson Eric 
Published: July 2022

Abstract
Cellular senescence triggers various types of heterochromatin remodeling that contribute to aging. However, the age-related mechanisms that lead to these epigenetic alterations remain elusive. Here, we asked how two key aging hallmarks, telomere shortening and constitutive heterochromatin loss, are mechanistically connected during senescence. We show that, at the onset of senescence, pericentromeric heterochromatin is specifically dismantled consisting of chromatin decondensation, accumulation of DNA breakages, illegitimate recombination and loss of DNA. This process is caused by telomere shortening or genotoxic stress by a sequence of events starting from TP53-dependent downregulation of the telomere protective protein TRF2. The resulting loss of TRF2 at pericentromeres triggers DNA breaks activating ATM, which in turn leads to heterochromatin decondensation by releasing KAP1 and Lamin B1, recombination and satellite DNA excision found in the cytosol associated with cGAS. This TP53–TRF2 axis activates the interferon response and the formation of chromosome rearrangements when the cells escape the senescent growth arrest. Overall, these results reveal the role of TP53 as pericentromeric disassembler and define the basic principles of how a TP53-dependent senescence inducer hierarchically leads to selective pericentromeric dismantling through the downregulation of TRF2.
Endoplasmic reticulum oxidoreductin provides resilience against reductive stress and hypoxic conditions by mediating luminal redox dynamics
Authors: Ugalde José Manuel , Aller Isabel , Kudrjasova Lika , Schmidt Romy R , Schlößer Michelle , Homagk Maria , Fuchs Philippe , Lichtenauer Sophie , Schwarzländer Markus , Müller-Schüssele Stefanie J , Meyer Andreas J 
Published: July 2022

Abstract
Oxidative protein folding in the endoplasmic reticulum (ER) depends on the coordinated action of protein disulfide isomerases and ER oxidoreductins (EROs). Strict dependence of ERO activity on molecular oxygen as the final electron acceptor implies that oxidative protein folding and other ER processes are severely compromised under hypoxia. Here, we isolated viable Arabidopsis thaliana ero1 ero2 double mutants that are highly sensitive to reductive stress and hypoxia. To elucidate the specific redox dynamics in the ER in vivo, we expressed the glutathione redox potential (EGSH) sensor Grx1-roGFP2iL-HDEL with a midpoint potential of −240 mV in the ER of Arabidopsis plants. We found EGSH values of −241 mV in wild-type plants, which is less oxidizing than previously estimated. In the ero1 ero2 mutants, luminal EGSH was reduced further to −253 mV. Recovery to reductive ER stress induced by dithiothreitol was delayed in ero1 ero2. The characteristic signature of EGSH dynamics in the ER lumen triggered by hypoxia was affected in ero1 ero2 reflecting a disrupted balance of reductive and oxidizing inputs, including nascent polypeptides and glutathione entry. The ER redox dynamics can now be dissected in vivo, revealing a central role of EROs as major redox integrators to promote luminal redox homeostasis.
Neighborhood-Level Predictors of Age-at-First-Diagnosis of Psychotic Disorders: A Swedish Register-Based Cohort Study
Authors: Spyridonidis Spyros , Dykxhoorn Jennifer , Hollander Anna-Clara , Dalman Christina , Kirkbride James B 
Published: July 2022

Abstract
The relationship between neighborhood-level factors and the incidence of psychotic disorders is well established. However, it is unclear whether neighborhood characteristics are also associated with age-at-first-diagnosis of these disorders. We used linked Swedish register data to identify a cohort of persons first diagnosed with an ICD-10 non-affective or affective psychotic disorder (F20-33) between 1997 and 2016. Using multilevel mixed-effect linear modelling, we investigated whether neighborhood deprivation and population density at birth were associated with age-at-first diagnosis of a psychotic disorder. Our final cohort included 13,440 individuals, with a median age-at-first-diagnosis of 21.8 years for women (interquartile range [IQR]: 19.0–25.5) and 22.9 years for men (IQR: 20.1–26.1; P &lt; .0001). In an unadjusted model, we found no evidence of an association between neighborhood deprivation and age-at-first-diagnosis of psychotic disorder (P = .07). However, after multivariable adjustment, age-at-first-diagnosis increased by .13 years (95% CI: .05 to .21; P = .002) for a one standard deviation increase in neighborhood deprivation. This was equivalent to a later diagnosis of 47 days (95% CI: 18 to 77). We found no evidence of a different relationship for non-affective versus affective psychoses [LRT χ2(1) = .14; P = .71]. Population density was not associated with age-at-first-diagnosis in unadjusted (P = .81) or adjusted (P = .85) models. Later age-at-first-diagnosis for individuals born in more deprived neighborhoods suggests structural barriers in accessing equitable psychiatric care.
Bridging climate change science and policy through TMNs in Turkey: CoM as a boundary-object
Authors: Erbil Aslı Öğüt , Eroğlu Mehmet , Türk Ebru Gönül 
Published: July 2022

Abstract
This paper qualitatively investigates one of the influential transnational municipal networks, Covenant of Mayors for Climate and Energy (CoM)’s position in three Turkish municipal governments in bridging the climate change science and climate change policy gap. In the last two decades, the importance of science-based policymaking for climate mitigation and adaptation and transnational municipal networks empowered by municipalities that guide city policies linked to international agreements has been recognized. In this paper, we argue that CoM has acted as a boundary-object in producing climate change policies and plans in Turkish municipal governments. However, CoM has done so to a certain extent; their effectiveness was limited due to the general atmosphere on climate change policies in Turkey. We substantiate this claim through a two-layer examination: a case-specific analysis of three municipalities and semi-structured interviews with thirteen experts in climate change policy-related issues.
The Effects of Skin Temperature Changes on the Integrity of Skin Tissue: A Systematic Review
Authors: Mifsud Tiziana , Modestini Chiara , Mizzi Anabelle , Falzon Owen , Cassar Kevin , Mizzi Stephen 
Published: July 2022

ABSTRACT

OBJECTIVE
To determine whether changes in skin temperature can affect the integrity of skin.

METHODOLOGY
The authors conducted a systematic literature search as per the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) guidelines. They searched the CINAHL (Cumulative Index to Nursing and Allied Health Literature), Cochrane, MEDLINE Complete, Academic Search Ultimate, and HyDi databases for articles examining the effects of skin temperature on skin integrity published through April 2020. Two independent reviewers scored the methodologic quality of the 13 included studies.

RESULTS
Only 11 studies were included in the qualitative analysis, as the other two articles had a critical risk of bias. There is strong evidence to indicate that an increase in skin temperature leads to changes in skin structure and function. However, ulcer formation was more affected by intrinsic and extrinsic factors, rather than by temperature alone.

CONCLUSION
Further high-quality randomized controlled trials are required to investigate the direct effect of skin temperature on ulceration.
Understanding Research Methods: Up-and-down Designs for Dose-finding
Authors: Oron Assaf P. , Souter Michael J. , Flournoy Nancy 
Published: July 2022

Summary
For the task of estimating a target benchmark dose such as the ED50 (the dose that would be effective for half the population), an adaptive dose-finding design is more effective than the standard approach of treating equal numbers of patients at a set of equally spaced doses. Up-and-down is the most popular family of dose-finding designs and is in common use in anesthesiology. Despite its widespread use, many aspects of up-and-down are not well known, implementation is often misguided, and standard, up-to-date reference material about the design is very limited. This article provides an overview of up-and-down properties, recent methodologic developments, and practical recommendations, illustrated with the help of simulated examples. Additional reference material is offered in the Supplemental Digital Content.
The Effects of Lower Extremity Rotational Malalignment on Pediatric Patient-reported Outcomes Measurement and Information System (PROMIS) Scores
Authors: Chandrananth Janan , Hannan Richard , Bouton Daniel , Raney Ellen , Sienko Susan , Do Patrick , Bauer Jeremy P. 
Published: July 2022

Background:
There is sparse literature demonstrating the relationship between lower limb pediatric idiopathic rotational malalignment (IRM) and patient-reported outcomes measurement information system (PROMIS) scores. Our goal is to determine and quantify the amount that IRM deformities, as measured with the 3D gait analysis, affect childrens’ pain interference, mobility, and peer relationship PROMIS domains. Secondary outcomes include investigating the potential relationships between IRM and various subgroups (Pediatric Outcomes Data Collection Instrument (PODCI), gender, Body Mass Index (BMI), femur Versus tibia). We also examine whether the PROMIS domains correlate with PODCI in this population.

Methods:
This study was a retrospective cohort, single institution, and consecutively recruited cases series. We identified 47 children over a 3-year period who were evaluated at the motion analysis center at our tertiary care hospital, with increased torsion of the femur or tibia. After exclusions, 25 children with IRM, documented PROMIS data and gait analysis were considered.

Results:
Femoral malrotation had a significant relationship with female gender (P=0.001) and increased BMI (P<0.001). Femoral malrotation had a correlation with PROMIS pain interference (P=0.016), whereas tibial rotation did not achieve significance (P=0.084). In the ANOVA regression analysis, there was a strong prediction of the PROMIS mobility domain when both malrotation and pain interference were present (P=0.007). There were Pearson Correlations of PROMIS and PODCI domains for Mobility Versus Sports (P=0.007) and Pain Interference Versus Comfort/Pain (P=0.004), respectively.

Conclusion:
The evident relationship between lower limb rotational malalignment and PROMIS scores signifies the likelihood for gait and pain disturbance. This in turn could show us that children are likely to be more debilitated and thus may benefit from timely correction. We aim to conduct this as a multicentre trial to confirm our findings.

Level of Evidence:
Level IV.
Aberrant Circulating SNHG1 Serves as a Biomarker to Distinguish Acute Myocardial Infarction and Construction of a Risk Model for Secondary Heart Failure
Authors: Yang Guanghu , Gai Xin , Han Maozhi , Gao Feng , Qiao Lujun , Tian Yonggang 
Published: July 2022

Abstract:
Acute myocardial infarction (AMI) is a severe condition observed in patients with coronary heart disease, and heart failure (HF) often occurs after AMI. This study aimed to evaluate the clinical significance of long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) in the diagnosis and prognosis of AMI and to construct a logistic predict model to determine the risk of post-AMI HF. This study analyzed the data of 229 patients with AMI. Serum SNHG1 levels were examined using quantitative real-time PCR, and its diagnostic value was evaluated using receiver operating characteristic analysis. The predictive value of SNHG1 for HF onset was evaluated using the Kaplan–Meier method and Cox regression analysis. The risk factors and predictive parameters included in the predictive model of post-AMI HF were determined using multivariate logistic regression analysis. In this study, we found that reduced serum SNHG1 was negatively correlated with the Gensini score of patients with AMI. The diagnostic performance of combining cardiac troponin I (cTnI) and creatine kinase (CK)-MB and SNHG1 was the best. Lower SNHG1 expression served as an independent indicator for HF secondary to AMI. A logistic risk model was constructed with the following equation:

, and the predictive accuracy of this model was relatively high with an area under the curve of 0.890. Taken together, our results revealed that reduced SNHG1 combining cTnI and CK-MB had the best diagnostic performance in patients with AMI. A logistic risk model based on SNHG1, age, cTnI, CK-MB, left ventricular ejection fraction, and Gensini score may help to determine the development of HF in patients with AMI.
Uterine arcuate artery calcification as a potential marker of cardiovascular risk—a preliminary study
Authors: Akilli Rabia , Kucukgoz Gulec Umran , Deniz Ali , Aikimbaev Kairqueldy , Akcabay Cigdem , Seydaoglu Gulsah 
Published: July 2022

Abstract

Objective
Atherosclerotic cardiovascular disease is the most common cause of death in postmenopausal women. As this is a progressive disease, it is important to identify markers at an early stage during the subclinical period. Arterial calcifications are an indicator of overall atherosclerotic disease and therefore may be used as a marker for the estimation of future atherosclerotic cardiovascular events. The aims of this study are to investigate the relationship between uterine myometrial calcification (UMC) and carotid artery intima-media thickness (CIMT) and to evaluate whether UMC can be a predictive marker for the estimation of future atherosclerotic cardiovascular risk in asymptomatic postmenopausal women.

Methods
In this cross-sectional study, we assessed 81 postmenopausal women without gynecological complaints for cardiovascular risk factors, UMC, and CIMT. Participants were divided into two risk groups according to their cardiovascular risk factors. The level of UMC was determined using a new scoring system, which was based on transvaginal ultrasonography. Demographic, clinical, and laboratory parameters, UMC scores, and measurements of CIMT were evaluated.

Results
A moderately positive correlation was detected between CIMT and UMC scores (r = 0.62). There was a significant relationship between UMC scores and atherosclerotic cardiovascular risk; the risk of atherosclerosis was 15.4 times higher (OR: 15.4, 95% CI: 5.1–46.8; P = 0.001) in participants with a high UMC score (≥2). According to the multivariable logistic regression model adjusted by age and duration of menopause, the risk of cardiovascular atherosclerosis increased 27.8 fold for those with CIMT of 0.075 or greater (OR: 27.8, 95% CI: 5.3–147.1; P = 0.001) and 9.2 fold for those with a UMC score of 2 or greater (OR: 9.2, CI: 1.22–69.3; P = 0.032).

Conclusions
The presence of UMC has been identified as an independent predictive factor for atherosclerotic risk. Accordingly, considering UMC as an atherosclerotic cardiovascular risk factor may provide an opportunity to identify cardiovascular disease in asymptomatic postmenopausal women. When UMC is detected, women should be assessed for cardiovascular risk.