bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical and X-ray GRB Fundamental Planes as cosmological distance indicators
Authors: Dainotti M G , Nielson V , Sarracino G , Rinaldi E , Nagataki S , Capozziello S , Gnedin O Y , Bargiacchi G 
Published: June 2022

ABSTRACT
Gamma-ray bursts (GRBs), can be employed as standardized candles, extending the distance ladder beyond Type Ia supernovae (SNe Ia, z = 2.26). We standardize GRBs using the three-dimensional (3D) Fundamental Plane relation (the Dainotti relation) among the rest-frame end time of the X-ray plateau emission, its corresponding luminosity, and the peak prompt luminosity. Combining SNe Ia and GRBs, we constrain ΩM = 0.299 ± 0.009 assuming a flat Λ cold dark matter (ΛCDM) cosmology with and without correcting GRBs for selection biases and redshift evolution. Using a 3D optical Dainotti correlation, we find this sample is as efficacious in the determination of ΩM as the X-ray sample. We trimmed our GRB samples to achieve tighter planes to simulate additional GRBs. We determined how many GRBs are needed as stand-alone probes to achieve a comparable precision on ΩM to the one obtained by SNe Ia only. We reach the same error measurements derived using SNe Ia in 2011 and 2014 with 142 and 284 simulated optical GRBs, respectively, considering the error bars on the variables halved. These error limits will be reached in 2038 and in 2047, respectively. Using a doubled sample (obtained by future machine learning approaches allowing a light-curve reconstruction and the estimates of GRB redshifts when z is unknown) compared to the current sample, with error bars halved we will reach the same precision as SNe Ia in 2011 and 2014, now and in 2026, respectively. If we consider the current SNe precision, this will be reached with 390 optical GRBs by 2054.
WISDOM project – XI. Star formation efficiency in the bulge of the AGN-host Galaxy NGC 3169 with SITELLE and ALMA
Authors: Lu Anan , Boyce Hope , Haggard Daryl , Bureau Martin , Liang Fu-Heng , Liu Lijie , Choi Woorak , Cappellari Michele , Chemin Laurent , Chevance Mélanie , Davis Timothy A , Drissen Laurent , Elford Jacob S , Gensior Jindra , Kruijssen J M Diederik , Martin Thomas , Massé Etienne , Robert Carmelle , Ruffa Ilaria , Rousseau-Nepton Laurie , Sarzi Marc , Savard Gabriel , Williams Thomas G 
Published: June 2022

ABSTRACT
The star formation efficiency (SFE) has been shown to vary across different environments, particularly within galactic starbursts and deep within the bulges of galaxies. Various quenching mechanisms may be responsible, ranging from galactic dynamics to feedback from active galactic nuclei (AGNs). Here, we use spatially resolved observations of warm ionized gas emission lines (Hβ, [O iii] λλ4959,5007, [N ii] λλ6548,6583, Hα and [S ii] λλ6716,6731) from the imaging Fourier transform spectrograph SITELLE at the Canada–France–Hawaii Telescope (CFHT) and cold molecular gas (12CO(2-1)) from the Atacama Large Millimeter/sub-millimeter Array (ALMA) to study the SFE in the bulge of the AGN-host galaxy NGC 3169. After distinguishing star-forming regions from AGN-ionized regions using emission-line ratio diagnostics, we measure spatially resolved molecular gas depletion times (τdep ≡1/SFE) with a spatial resolution of ≈100 pc within a galactocentric radius of 1.8 kpc. We identify a star-forming ring located at radii 1.25 ± 0.6 kpc with an average τdep of 0.3 Gyr. At radii &lt;0.9 kpc, however, the molecular gas surface densities and depletion times increase with decreasing radius, the latter reaching approximately 2.3 Gyr at a radius ≈500 pc. Based on analyses of the gas kinematics and comparisons with simulations, we identify AGN feedback, bulge morphology and dynamics as the possible causes of the radial profile of SFE observed in the central region of NGC 3169.
Stringent limits on 28SiO maser emission from the recurrent nova T Coronae Borealis
Authors: Evans A , Pimpanuwat B , Richards A M S , Banerjee D P K , Munari U , Gray M D , Hutawarakorn Kramer B , Kraus A 
Published: June 2022

ABSTRACT
There are indications that the third-known eruption of the recurrent nova T CrB is imminent, and multiwavelength observations prior to the eruption are important to characterize the system before it erupts. T CrB is known to display the SiO fundamental vibrational feature at 8 $\, \mu$m. When the anticipated eruption occurs, it is possible that the shock produced when the ejected material runs into the wind of the red giant in the system may be traced using SiO maser emission. We have used the 100 m Effelsberg Radio Telescope to search for 28SiO emission in the υ = 1, υ = 2, J = 1 → 0 transitions, at 43.122 GHz and 42.820 GHz, respectively, while the system is in quiescence. We find no evidence for such emission. We set stringent 3σ upper limits of 1.66 mJy on emission in the υ = 1, J = 1 → 0 transition, and 1.72 mJy in the υ = 2, J = 1 → 0 transition, respectively, for a noise bandwidth of 250 kHz. The corresponding limits for a 31.25 kHz bandwidth are 4.69 and 4.86 mJy, respectively. These upper limits improve on previous upper limits for this system by more than two orders of magnitude.
Noncanonical NF-κB factor p100/p52 regulates homologous recombination and modulates sensitivity to DNA-damaging therapy
Authors: Budke Brian , Zhong Alison , Sullivan Katherine , Park Chanyoung , Gittin David I , Kountz Timothy S , Connell Philip P 
Published: June 2022

AbstractHomologous recombination (HR) serves multiple roles in DNA repair that are essential for maintaining genomic stability, including double-strand DNA break (DSB) repair. The central HR protein, RAD51, is frequently overexpressed in human malignancies, thereby elevating HR proficiency and promoting resistance to DNA-damaging therapies. Here, we find that the non-canonical NF-κB factors p100/52, but not RelB, control the expression of RAD51 in various human cancer subtypes. While p100/p52 depletion inhibits HR function in human tumor cells, it does not significantly influence the proficiency of non-homologous end joining, the other key mechanism of DSB repair. Clonogenic survival assays were performed using a pair DLD-1 cell lines that differ only in their expression of the key HR protein BRCA2. Targeted silencing of p100/p52 sensitizes the HR-competent cells to camptothecin, while sensitization is absent in HR-deficient control cells. These results suggest that p100/p52-dependent signaling specifically controls HR activity in cancer cells. Since non-canonical NF-κB signaling is known to be activated after various forms of genomic crisis, compensatory HR upregulation may represent a natural consequence of DNA damage. We propose that p100/p52-dependent signaling represents a promising oncologic target in combination with DNA-damaging treatments.
Insight into RNA–DNA primer length counting by human primosome
Authors: Baranovskiy Andrey G , Lisova Alisa E , Morstadt Lucia M , Babayeva Nigar D , Tahirov Tahir H 
Published: June 2022

Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58C) with the primer 5′-end, and (ii) flexible tethering of p58C and the DNA polymerase alpha catalytic core domain (p180core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.
Imaging in patients with glioblastoma: A national cohort study
Authors: Dumba Maureen , Fry Anna , Shelton Jon , Booth Thomas C , Jones Brynmor , Shuaib Haris , Williams Matt 
Published: June 2022

Abstract

Background
Glioblastoma is the most common malignant brain tumor in adults and has a poor prognosis. This cohort of patients is diverse and imaging is vital to formulate treatment plans. Despite this, there is relatively little data on patterns of use of imaging and imaging workload in routine practice.

Methods
We examined imaging patterns for all patients aged 15–99 years resident in England who were diagnosed with a glioblastoma between 1st January 2013 and 31st December 2014. Patients without imaging and death-certificate-only registrations were excluded.

Results
The analytical cohort contained 4,307 patients. There was no significant variation in pre- or postdiagnostic imaging practice by sex or deprivation quintile. Postdiagnostic imaging practice was varied. In the group of patients who were treated most aggressively (surgical debulking and chemoradiation) and were MRI compatible, only 51% had a postoperative MRI within 72 hours of surgery. In patients undergoing surgery who subsequently received radiotherapy, only 61% had a postsurgery and preradiotherapy MRI.

Conclusions
Prediagnostic imaging practice is uniform. Postdiagnostic imaging practice was variable. With increasing evidence and clearer recommendations regarding debulking surgery and planning radiotherapy imaging, the reason for this is unclear and will form the basis of further work.
Nicotine Delivery and Pharmacokinetics of an Electronic Cigarette Compared With Conventional Cigarettes in Chinese Adult Smokers: A Randomized Open-Label Crossover Clinical Study
Authors: Guo Yi , Li Shoufeng , Wang Zhi , Jiang Fulin , Guan Yanping , Huang Min , Zhong Guoping 
Published: June 2022

Abstract

Introduction
To evaluate the nicotine pharmacokinetics of a commercial electronic cigarette (e-cigarette) relative to conventional cigarettes in Chinese adult smokers.

Aims and Methods
A randomized, open-label, crossover clinical study was conducted on 23 healthy adult Chinese smokers. In two sessions, subjects used either the e-cigarettes with 30 mg/g nicotine in e-liquid or conventional cigarettes of a given brand, at one puff every 30 seconds for a total of 10 puffs. Blood samples were collected at specified time points for 4 hours after the first puff. Subjective effects on desire-to-smoke and physiological parameters such as heart rate and oxyhemoglobin saturation levels were also examined before and after using the two products.

Results
The baseline-adjusted maximum nicotine concentration (Cmax-BL), time-to-peak nicotine concentration (Tmax), and nicotine absorption rate (Cmax-BL divided by Tmax) were found to be similar for the e-cigarette versus those of conventional cigarettes (p &gt; .05). Total nicotine exposure measured as the area-under-curve (AUC0-t-BL) was significantly lower for the e-cigarette relative to that of conventional cigarettes. In addition, the subjects found that e-cigarettes were well tolerated under controlled puffing conditions.

Conclusions
The test e-cigarettes achieved similar nicotine delivery and pharmacokinetic profiles to those of the comparator cigarettes, indicating that this e-cigarette could be a potential alternative to conventional cigarettes for those adult smokers.

Implications
There are no data in the published literature on the nicotine pharmacokinetics of e-cigarettes in Chinese smokers. To the best of our knowledge, this is the first study to evaluate the nicotine delivery and pharmacokinetic profile of a commercial e-cigarette brand compared with conventional cigarettes in Chinese adult smokers. After the use of test e-cigarettes, nicotine delivery and pharmacokinetic profile were similar to those of conventional cigarettes in Chinese adult smokers.
Perspectives of Zambian Clinical Oncology Trainees in the MD Anderson and Zambia Virtual Clinical Research Training Program (MOZART)
Authors: Diao Kevin , Kizub Darya A , Ausat Noveen , Mwaba Catherine K , Anakwenze Akinfenwa Chidinma P , Cameron Carrie A , Chiao Elizabeth Y , Lombe Dorothy C , Msadabwe Susan C , Lin Lilie L 
Published: June 2022

Abstract

Background
African countries are underrepresented in cancer research, partly because of a lack of structured curricula on clinical research during medical education. To address this need, the MD Anderson and Zambia Virtual Clinical Research Training Program (MOZART) was developed jointly by MD Anderson Cancer Center (MDA) and the Cancer Diseases Hospital in Zambia (CDH) for Zambian clinical oncology trainees. We explored participant perspectives to provide insight for implementation of similar efforts.

Materials and Methods
The MD Anderson and Zambia Virtual Clinical Research Training Program consisted of weekly virtual lectures and support of Zambian-led research protocols through longitudinal mentorship groups that included CDH faculty and MDA peer and faculty mentors. Participants were contacted via email to take part in semi-structured interviews, which were conducted via teleconference and audio-recorded, transcribed, and coded. Emergent themes were extracted and are presented with representative verbatim quotations.

Results
Thirteen of the 14 (93%) trainees were interviewed. Emergent themes included (1) participants having diverse educational backgrounds but limited exposure to clinical research, (2) importance of cancer research specific to a resource-constrained setting, (3) complementary roles of peer mentors and local and international faculty mentors, (4) positive impact on clinical research skills but importance of a longitudinal program and early exposure to clinical research, and (5) challenges with executing research protocols.

Conclusion
To our knowledge, this is the first qualitative study of African clinical oncology trainees participating in a virtual clinical research training program. The lessons learned from semi-structured interviews with participants in MOZART provided valuable insights that can inform the development of similar clinical research training efforts and scale-up.
Small EPIDERMAL PATTERNING FACTOR-LIKE2 peptides regulate awn development in rice
Authors: Xiong Luling , Huang Yingyong , Liu Zupei , Li Chen , Yu Hang , Shahid Muhammad Qasim , Lin Yanhui , Qiao Xiaoyi , Xiao Junyi , Gray Julie E , Jin Jing 
Published: June 2022

Abstract
The EPIDERMAL PATTERNING FACTOR (EPF) and EPF-LIKE (EPFL) family of small secreted peptides act to regulate many aspects of plant growth and development; however, their functions are not widely characterized in rice (Oryza sativa). Here, we used clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology to individually knockout each of 11 EPF/EPFL genes in the rice cultivar Kasalath. Loss of function of most OsEPF/EPFL genes generated no obvious phenotype alteration, while disruption of OsEPFL2 in Kasalath caused a short or no awn phenotype and reduced grain size. OsEPFL2 is strongly expressed in the young panicle, consistent with a role in regulating awn and grain development. Haplotype analysis indicated that OsEPFL2 can be classified into six major haplotypes. Nucleotide diversity and genetic differentiation analyses suggested that OsEPFL2 was positively selected during the domestication of rice. Our work to systematically investigate the function of EPF/EPFL peptides demonstrates that different members of the same gene family have been independently selected for their ability to regulate a similar biological function and provides perspective on rice domestication.
Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants
Authors: Weiss Trevor , Crisp Peter A , Rai Krishan M , Song Meredith , Springer Nathan M , Zhang Feng 
Published: June 2022

Abstract
CRISPR–Cas9-mediated genome editing has been widely adopted for basic and applied biological research in eukaryotic systems. While many studies consider DNA sequences of CRISPR target sites as the primary determinant for CRISPR mutagenesis efficiency and mutation profiles, increasing evidence reveals the substantial role of chromatin context. Nonetheless, most prior studies are limited by the lack of sufficient epigenetic resources and/or by only transiently expressing CRISPR–Cas9 in a short time window. In this study, we leveraged the wealth of high-resolution epigenomic resources in Arabidopsis (Arabidopsis thaliana) to address the impact of chromatin features on CRISPR–Cas9 mutagenesis using stable transgenic plants. Our results indicated that DNA methylation and chromatin features could lead to substantial variations in mutagenesis efficiency by up to 250-fold. Low mutagenesis efficiencies were mostly associated with repressive heterochromatic features. This repressive effect appeared to persist through cell divisions but could be alleviated through substantial reduction of DNA methylation at CRISPR target sites. Moreover, specific chromatin features, such as H3K4me1, H3.3, and H3.1, appear to be associated with significant variation in CRISPR–Cas9 mutation profiles mediated by the non-homologous end joining repair pathway. Our findings provide strong evidence that specific chromatin features could have substantial and lasting impacts on both CRISPR–Cas9 mutagenesis efficiency and DNA double-strand break repair outcomes.
Subclinical atherosclerosis profiles in rheumatoid arthritis and primary Sjögren’s syndrome: the impact of BAFF genetic variations
Authors: Kintrilis Nikolaos , Gravani Fotini , Rapti Anna , Papaioannou Myrto , Flessa Christina-Maria , Nezos Adrianos , Antypa Eleni , Papadaki Ioanna , Karageorgas Τheofanis , Moutsopoulos Haralampos M , Mavragani Clio P 
Published: June 2022

Abstract

Objectives
RA and primary SS carry increased atherosclerotic risk, while B-cell activating factor holds a vital role in disease pathogenesis and atherosclerosis. We aimed to compare subclinical atherosclerosis profiles between the two clinical entities and define whether BAFF genetic variants alter atherosclerotic risk.

Methods
DNA from 166 RA, 148 primary SS patients and 200 healthy controls of similar age and sex distribution was subjected to PCR-based assay for the detection of five single nucleotide polymorphisms of the BAFF gene (rs1224141, rs12583006, rs9514828, rs1041569 and rs9514827). Genotype and haplotype frequencies were determined by SNPStats software and statistical analysis was performed by SPSS and Graphpad Software. Subclinical atherosclerosis was defined by the presence of carotid/femoral plaque formation and arterial wall thickening.

Results
Atherosclerotic plaque formation was more frequently detected in the RA vs primary SS group (80.7% vs 62.2%, P-value &lt;0.001), along with higher rates of family CVD history, current steroid dose and serum inflammatory markers. The TT genotype of the rs1224141 variant was more prevalent in RA but not primary SS patients with plaque and arterial wall thickening vs their counterparts without. Regarding the rs1014569 variant, among RA patients the TT genotype increased the risk for plaque formation while in primary SS patients the AT genotype conferred increased risk. Haplotype GTTTT was protective in the RA cohort, while TATTT and TTCTT haplotypes increased susceptibility for arterial wall thickening in the primary SS cohort.

Conclusions
Increased inflammatory burden, higher steroid doses and distinct BAFF gene variations imply chronic inflammation and B-cell hyperactivity as key contributors for the augmented atherosclerotic risk among autoimmune patients.
L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality of individuals with rheumatoid arthritis
Authors: Cai Bin , Zhou Mengmeng , Xiao Qingqing , Zou Hejian , Zhu Xiaoxia 
Published: June 2022

Abstract

Objective
We aimed to examine the relationship between serum 25-hydroxyvitamin D and all-cause, cause-specific mortality of patients with RA.

Methods
This cohort study included 1466 patients with RA from The National Health and Nutrition Examination Survey (NHANES) 2001–14. Mortality status was obtained according to death certificate records from the National Death Index. Cox proportional risk models were used to estimate hazard ratios (HR) and 95% CI for mortality. A generalized additive model, smooth curve fitting and 2-piecewise Cox proportional hazards models were established to address the nonlinearity between serum 25-hydroxyvitamin D and mortality.

Results
A total of 1466 patients [mean (s.d.) 59.89 (14.14) years old; 58.94% female] were enrolled. The weighted mean level of 25-hydroxyvitamin D was 59.26 (24.99) nmol/l and 38.95% were found with deficient (or severe deficient) vitamin D (&lt;50.00 nmol/l). During 10453 person-years of follow-up, 268 patients were documented for all-cause death, including 52 cardiovascular disease （CVD）deaths and 48 cancer deaths. Compared with patients with serum 25-hydroxyvitamin D &lt;25.00 nmol/l, patients with higher serum 25-hydroxyvitamin D were more likely to have lower rate of all-cause mortality. Nonlinear and L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality was found, and decreased serum 25-hydroxyvitamin D was significantly associated with increased risk of all-cause mortality in patients with serum 25-hydroxyvitamin D &lt;37.30 nmol/l [HR 0.95 (0.92, 0.98); P &lt; 0.01].

Conclusion
An L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality was found among patients with RA, indicating that serum 25-hydroxyvitamin D should be improved to a certain level for the prevention of premature death.
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication
Authors: Xiong Haifeng , Wang Danying , Shao Chen , Yang Xuchen , Yang Jialin , Ma Tao , Davis Charles C , Liu Liang , Xi Zhenxiang 
Published: June 2022

Abstract
Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]