1,557 research outputs found
VI-Band Follow-Up Observations of Ultra-Long-Period Cepheid Candidates in M31
The ultra-long period Cepheids (ULPCs) are classical Cepheids with pulsation
periods exceeding days. The intrinsic brightness of ULPCs are ~1
to ~3 mag brighter than their shorter period counterparts. This makes them
attractive in future distance scale work to derive distances beyond the limit
set by the shorter period Cepheids. We have initiated a program to search for
ULPCs in M31, using the single-band data taken from the Palomar Transient
Factory, and identified eight possible candidates. In this work, we presented
the VI-band follow-up observations of these eight candidates. Based on our
VI-band light curves of these candidates and their locations in the
color-magnitude diagram and the Period-Wesenheit diagram, we verify two
candidates as being truly ULPCs. The six other candidates are most likely other
kinds of long-period variables. With the two confirmed M31 ULPCs, we tested the
applicability of ULPCs in distance scale work by deriving the distance modulus
of M31. It was found to be mag. The large error
in the derived distance modulus, together with the large intrinsic dispersion
of the Period-Wesenheit (PW) relation and the small number of ULPCs in a given
host galaxy, means that the question of the suitability of ULPCs as standard
candles is still open. Further work is needed to enlarge the sample of
calibrating ULPCs and reduce the intrinsic dispersion of the PW relation before
re-considering ULPCs as suitable distance indicators.Comment: 13 pages, with 14 Figures and 4 Tables (one online table). AJ
accepte
Long-term Periodicities of Cataclysmic Variables with Synoptic Surveys
A systematic study on the long-term periodicities of known Galactic
cataclysmic variables (CVs) was conducted. Among 1580 known CVs, 344 sources
were matched and extracted from the Palomar Transient Factory (PTF) data
repository. The PTF light curves were combined with the Catalina Real-Time
Transient Survey (CRTS) light curves and analyzed. Ten targets were found to
exhibit long-term periodic variability, which is not frequently observed in the
CV systems. These long-term variations are possibly caused by various
mechanisms, such as the precession of the accretion disk, hierarchical triple
star system, magnetic field change of the companion star, and other possible
mechanisms. We discuss the possible mechanisms in this study. If the long-term
period is less than several tens of days, the disk precession period scenario
is favored. However, the hierarchical triple star system or the variations in
magnetic field strengths are most likely the predominant mechanisms for longer
periods.Comment: 33 pages, 9 figures (manuscript form), Accepted for publication in
PAS
Simple non-invasive scoring systems and histological scores in predicting mortality in patients with non-alcoholic fatty liver disease: A systematic review and meta-analysis
[Background and Aim] There is debate among the hepatology community regarding the simple non-invasive scoring systems and histological scores (even it was developed for histological classification) in predicting clinical outcomes in patients with non-alcoholic fatty liver disease (NAFLD). This study aimed to determine whether the presence of simple non-invasive scoring systems and histological scores could predict all-cause mortality, liver-related mortality, and liver disease decompensation (liver failure, cirrhosis, hepatocellular carcinoma, or decompensated liver disease).[Methods] The pooled hazard ratio of prognostic factors and incidence rate per 1000 person-years in patients with NAFLD was calculated and further adjusted by two different models of handling the duplicated data.[Results] A total of 19 longitudinal studies were included. Most simple non-invasive scoring systems (Fibrosis-4 Score, BARD, and aspartate aminotransferase-to-platelet ratio index ) and histological scores (NAFLD activity score, Brunt, and "steatosis, activity, and fibrosis" ) failed in predicting mortality, and only the NAFLD fibrosis score > 0.676 showed prognostic ability to all-cause mortality (four studies, 7564 patients, 118 352 person-years followed up, pooled hazard ratio 1.44, 95% confidence interval [CI] 1.05â1.96). The incidence rate per 1000 person-years of all-cause mortality, liver-related mortality, cardiovascular-related mortality, and liver disease decompensation resulted in a pooled incidence rate per 1000 person-years of 22.65 (14 studies, 95% CI 9.62â53.31), 3.19 (7 studies, 95% CI 1.14â8.93), 6.02 (6 studies, 95% CI 4.69â7.74), and 11.46 (4 studies, 95% CI 5.33â24.63), respectively.[Conclusion] Non-alcoholic fatty liver disease fibrosis score showed promising prognostic value to all-cause mortality. Most present simple non-invasive scoring systems and histological scores failed to predict clinical outcomes.Peer reviewe
Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing
Background: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. Results: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). Conclusions: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level
SN 2021zny: an early flux excess combined with late-time oxygen emission suggests a double white dwarf merger event
We present a photometric and spectroscopic analysis of the ultra-luminous and
slowly evolving 03fg-like Type Ia SN 2021zny. Our observational campaign starts
from hours after explosion (making SN 2021zny one of the earliest
observed members of its class), with dense multi-wavelength coverage from a
variety of ground- and space-based telescopes, and is concluded with a nebular
spectrum months after peak brightness. SN 2021zny displayed several
characteristics of its class, such as the peak brightness ( mag),
the slow decline ( mag), the blue early-time colours,
the low ejecta velocities and the presence of significant unburned material
above the photosphere. However, a flux excess for the first days
after explosion is observed in four photometric bands, making SN 2021zny the
third 03fg-like event with this distinct behavior, while its d spectrum
shows prominent [O I] lines, a very unusual characteristic of thermonuclear
SNe. The early flux excess can be explained as the outcome of the interaction
of the ejecta with of H/He-poor circumstellar
material at a distance of cm, while the low ionization state of
the late-time spectrum reveals low abundances of stable iron-peak elements. All
our observations are in accordance with a progenitor system of two
carbon/oxygen white dwarfs that undergo a merger event, with the disrupted
white dwarf ejecting carbon-rich circumstellar material prior to the primary
white dwarf detonation.Comment: 19 pages, 16 figures, accepted for publication in MNRA
Genetic determinants of co-accessible chromatin regions in activated T cells across humans.
Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment
The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in
operation since July 2014. This paper describes the second data release from
this phase, and the fourteenth from SDSS overall (making this, Data Release
Fourteen or DR14). This release makes public data taken by SDSS-IV in its first
two years of operation (July 2014-2016). Like all previous SDSS releases, DR14
is cumulative, including the most recent reductions and calibrations of all
data taken by SDSS since the first phase began operations in 2000. New in DR14
is the first public release of data from the extended Baryon Oscillation
Spectroscopic Survey (eBOSS); the first data from the second phase of the
Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2),
including stellar parameter estimates from an innovative data driven machine
learning algorithm known as "The Cannon"; and almost twice as many data cubes
from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous
release (N = 2812 in total). This paper describes the location and format of
the publicly available data from SDSS-IV surveys. We provide references to the
important technical papers describing how these data have been taken (both
targeting and observation details) and processed for scientific use. The SDSS
website (www.sdss.org) has been updated for this release, and provides links to
data downloads, as well as tutorials and examples of data use. SDSS-IV is
planning to continue to collect astronomical data until 2020, and will be
followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14
happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov
2017 (this is the "post-print" and "post-proofs" version; minor corrections
only from v1, and most of errors found in proofs corrected
Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes
Stratification of women according to their risk of breast cancer based on polygenic risk scores (PRSs) could improve screening and prevention strategies. Our aim was to develop PRSs, optimized for prediction of estrogen receptor (ER)-specific disease, from the largest available genome-wide association dataset and to empirically validate the PRSs in prospective studies. The development dataset comprised 94,075 case subjects and 75,017 control subjects of European ancestry from 69 studies, divided into training and validation sets. Samples were genotyped using genome-wide arrays, and single-nucleotide polymorphisms (SNPs) were selected by stepwise regression or lasso penalized regression. The best performing PRSs were validated in an independent test set comprising 11,428 case subjects and 18,323 control subjects from 10 prospective studies and 190,040 women from UK Biobank (3,215 incident breast cancers). For the best PRSs (313 SNPs), the odds ratio for overall disease per 1 standard deviation in ten prospective studies was 1.61 (95%CI: 1.57-1.65) with area under receiver-operator curve (AUC) = 0.630 (95%CI: 0.628-0.651). The lifetime risk of overall breast cancer in the top centile of the PRSs was 32.6%. Compared with women in the middle quintile, those in the highest 1% of risk had 4.37- and 2.78-fold risks, and those in the lowest 1% of risk had 0.16- and 0.27-fold risks, of developing ER-positive and ER-negative disease, respectively. Goodness-of-fit tests indicated that this PRS was well calibrated and predicts disease risk accurately in the tails of the distribution. This PRS is a powerful and reliable predictor of breast cancer risk that may improve breast cancer prevention programs.NovartisEli Lilly and CompanyAstraZenecaAbbViePfizer UKCelgeneEisaiGenentechMerck Sharp and DohmeRocheCancer Research UKGovernment of CanadaArray BioPharmaGenome CanadaNational Institutes of HealthEuropean CommissionMinistĂšre de l'Ăconomie, de lâInnovation et des Exportations du QuĂ©becSeventh Framework ProgrammeCanadian Institutes of Health Researc
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