bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Improved Multiplex Polymerase Chain Reaction (PCR) Assay for the Identification of Mosquito (Diptera: Culicidae) Blood Meals
Authors: Field Eleanor N , Gehrke Ella J , Ruden Rachel M , Adelman James S , Smith Ryan C 
Published: October 2019

AbstractThe analysis of vertebrate blood meals serves as an integral component of vector incrimination studies where feeding preferences and host associations influence vector-borne disease transmission. Diagnostic polymerase chain reaction (PCR)-based techniques have been widely used to determine host associations, yet applications for Culex (Diptera: Culicidae), which feed primarily on bird populations, have been limited by multistep PCR techniques that approach each potential host species singly. As a result, we have developed a multiplexed primer set targeting mitochondrial cytochrome b sequences that can distinguish human, bird, and mammalian host blood meals in a single PCR reaction, an improvement over previous analyses relying on single primers or other multiplex primer approaches through the inclusion of avian primers. To validate this new methodology, we demonstrate its application on blood samples as well as field-collected Culex samples. Although designed for applications with mosquito vectors, this multiplex PCR assay is not mosquito-specific, and should serve as a valuable tool for identifying the blood meals of other blood-feeding arthropods, contributing greatly to the study of vector-borne disease.
Impact of Overweight and Obesity on US Papillary Thyroid Cancer Incidence Trends (1995–2015)
Authors: Kitahara Cari M , Pfeiffer Ruth M , Sosa Julie A , Shiels Meredith S 
Published: October 2019

Abstract

Background
Since the early 1980s, papillary thyroid cancer (PTC) incidence rates and the prevalence of obesity, a risk factor for PTC, have increased substantially in the United States. We estimated the proportion of PTC incidence in the United States attributable to overweight and obesity during 1995–2015.

Methods
National Institutes of Health-AARP Diet and Health Study cohort data (n = 457 331 participants, 50–71 years and cancer-free at baseline) were used to estimate multivariable-adjusted hazard ratios (HRs) for PTC across body mass index categories. Population attributable fractions (PAFs) were calculated using estimated hazard ratios and annual overweight and obesity prevalence estimates from the National Health Interview Survey. PAF estimates were combined with Surveillance, Epidemiology, and End Results-13 data to calculate annual percent changes in PTC incidence rates attributable (and unrelated) to overweight and obesity.

Results
Overweight (25.0–29.0 kg/m2) and obesity (≥30.0 kg/m2) were associated with 1.26-fold (95% confidence interval [CI] = 1.05- to 1.52-fold) and 1.30-fold (95% CI = 1.05- to 1.62-fold) increased risks of PTC, respectively, and nearly threefold (HR = 2.93, 95% CI = 1.25 to 6.87) and greater than fivefold (HR = 5.42, 95% CI = 2.24 to 13.1) increased risks of large (&gt;4 cm) PTCs compared with normal weight (18.5–24.9 kg/m2). During 1995–2015, PAF estimates for overweight and obesity increased from 11.4% to 16.2% for all PTCs and from 51.4% to 63.2% for large PTCs. Overweight or obesity accounted for 13.6% and 57.8% of the annual percent changes in total (5.9%/y) and large (4.5%/y) PTC incidence rates, respectively, during 1995–2015.

Conclusions
Overweight and obesity may have contributed importantly to the rapid rise in PTC incidence during 1995–2015. By 2015, we estimate that one of every six PTCs diagnosed among adults 60 years or older, including nearly two-thirds of large PTCs, were attributable to overweight and obesity.
Diverse trajectories of plastome degradation in holoparasitic Cistanche and genomic location of the lost plastid genes
Authors: Liu Xiaoqing , Fu Weirui , Tang Yiwei , Zhang Wenju , Song Zhiping , Li Linfeng , Yang Ji , Ma Hong , Yang Jianhua , Zhou Chan , Davis Charles C , Wang Yuguo 
Published: October 2019

Abstract
The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.
Positive root pressure is critical for whole-plant desiccation recovery in two species of terrestrial resurrection ferns
Authors: Holmlund Helen I , Davis Stephen D , Ewers Frank W , Aguirre Natalie M , Sapes Gerard , Sala Anna , Pittermann Jarmila 
Published: October 2019

AbstractDesiccation-tolerant (DT) organisms can lose nearly all their water without dying. Desiccation tolerance allows organisms to survive in a nearly completely dehydrated, dormant state. At the cellular level, sugars and proteins stabilize cellular components and protect them from oxidative damage. However, there are few studies of the dynamics and drivers of whole-plant recovery in vascular DT plants. In vascular DT plants, whole-plant desiccation recovery (resurrection) depends not only on cellular rehydration, but also on the recovery of organs with unequal access to water. In this study, in situ natural and artificial irrigation experiments revealed the dynamics of desiccation recovery in two DT fern species. Organ-specific irrigation experiments revealed that the entire plant resurrected when water was supplied to roots, but leaf hydration alone (foliar water uptake) was insufficient to rehydrate the stele and roots. In both species, pressure applied to petioles of excised desiccated fronds resurrected distal leaf tissue, while capillarity alone was insufficient to resurrect distal pinnules. Upon rehydration, sucrose levels in the rhizome and stele dropped dramatically as starch levels rose, consistent with the role of accumulated sucrose as a desiccation protectant. These findings provide insight into traits that facilitate desiccation recovery in dryland ferns associated with chaparral vegetation of southern California.
miR156-targeted SPL10 controls Arabidopsis root meristem activity and root-derived de novo shoot regeneration via cytokinin responses
Authors: Barrera-Rojas Carlos Hernán , Rocha Gabriel Henrique Braga , Polverari Laura , Pinheiro Brito Diego Armando , Batista Diego Silva , Notini Marcela M , da Cruz Ana Claudia Ferreira , Morea Edna Gicela Ortiz , Sabatini Sabrina , Otoni Wagner Campos , Nogueira Fabio Tebaldi Silveira 
Published: October 2019

AbstractRoot growth is modulated by different factors, including phytohormones, transcription factors, and microRNAs (miRNAs). MicroRNA156 and its targets, the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes, define an age-dependent pathway that controls several developmental processes, including lateral root emergence. However, it remains unclear whether miR156-regulated SPLs control root meristem activity and root-derived de novo shoot regeneration. Here, we show that MIR156 and SPL genes have opposing expression patterns during the progression of primary root (PR) growth in Arabidopsis, suggesting that age cues may modulate root development. Plants with high miR156 levels display reduced meristem size, resulting in shorter primary root (PRs). Conversely, plants with reduced miR156 levels show higher meristem activity. Importantly, loss of function of SPL10 decreases meristem activity, while SPL10 de-repression increases it. Meristem activity is regulated by SPL10 probably through the reduction of cytokinin responses, via the modulation of type-B ARABIDOPSIS RESPONSE REGULATOR1(ARR1) expression. We also show that SPL10 de-repression in the PRs abolishes de novo shoot regenerative capacity by attenuating cytokinin responses. Our results reveal a cooperative regulation of root meristem activity and root-derived de novo shoot regeneration by integrating age cues with cytokinin responses via miR156-targeted SPL10.
Enhanced Carrier Screening for Spinal Muscular Atrophy: Detection of Silent (SMN1: 2 + 0) Carriers Utilizing a Novel TaqMan Genotyping Method
Authors: Azad Abul Kalam , Huang Chih-Kang , Jin Hong , Zou Hongwei , Yanakakis Lindsay , Du Juan , Fiddler Morry , Naeem Rizwan , Goldstein Yitz 
Published: October 2019

Abstract

Background
Individuals whose copies of the survival motor neuron 1 (SMN1) gene exist on the same chromosome are considered silent carriers for spinal muscular atrophy (SMA). Conventional screening for SMA only determines SMN1 copy number without any information regarding how those copies are arranged. A single nucleotide variant (SNV) rs143838139 is highly linked with the silent carrier genotype, so testing for this SNV can more accurately assess risk to a patient of having an affected child.

Methods
Using a custom-designed SNV-specific Taqman genotyping assay, we determined and validated a model for silent-carrier detection in the laboratory.

Results
An initial cohort of 21 pilot specimens demonstrated results that were 100% concordant with a reference laboratory method; this cohort was utilized to define the reportable range. An additional 177 specimens were utilized for a broader evaluation of clinical validity and reproducibility. Allelic-discrimination analysis demonstrated tight clustering of genotype groupings and excellent reproducibility, with a coefficient of variation for all genotypes ranging from 1% to 4%.

Conclusion
The custom-developed Taqman SNV genotyping assay we tested provides a rapid, accurate, and cost-effective method for routine SMA silent-carrier screening and considerably improves detection rates of residual risk for SMA carriers.
Detecting the halo heating from AGN feedback with ALMA
Authors: Brownson S , Maiolino R , Tazzari M , Carniani S , Henden N 
Published: October 2019

ABSTRACT
The Sunyaev–Zel’dovich (SZ) effect can potentially be used to investigate the heating of the circumgalactic medium and subsequent suppression of cold gas accretion on to the host galaxy caused by quasar feedback. We use a deep ALMA observation of HE0515-4414 in band 4, the most luminous quasar known at the peak of cosmic star formation (z = 1.7), to search for the SZ signal tracing the heating of the galaxy’s halo. ALMA’s sensitivity to a broad range of spatial scales enables us to disentangle emitting compact sources from the negative, extended SZ signal. We obtain a marginal SZ detection (∼3.3σ) on scales of about 300 kpc (30–40 arcsec), at the 0.2 mJy level, 0.5 mJy after applying a correction factor for primary beam attenuation and flux that is resolved out by the array. We show that our result is consistent with a simulated ALMA observation of a similar quasar in the fable cosmological simulations. We emphasize that detecting an SZ signal is more easily achieved in the visibility plane than in the (inferred) images. We also confirm a marginal detection (3.2σ) of a potential SZ dip on smaller scales (<100 kpc) already claimed by other authors, possibly highlighting the complex structure of the halo heating. Finally, we use SZ maps from the fable cosmological simulations, convolved with ALMA simulations, to illustrate that band 3 observations are much more effective in detecting the SZ signal with higher significance, and discuss the optimal observing strategy.
3D hydrodynamic simulations of C ingestion into a convective O shell
Authors: Andrassy R , Herwig F , Woodward P , Ritter C 
Published: October 2019

ABSTRACT
Interactions between convective shells in evolved massive stars have been linked to supernova impostors, to the production of the odd-Z elements Cl, K, and Sc, and they might also help generate the large-scale asphericities that are known to facilitate shock revival in supernova explosion models. We investigate the process of ingestion of C-shell material into a convective O-burning shell, including the hydrodynamic feedback from the nuclear burning of the ingested material. Our 3D hydrodynamic simulations span almost 3 dex in the total luminosity Ltot. All but one of the simulations reach a quasi-stationary state with the entrainment rate and convective velocity proportional to Ltot and $L_\mathrm{tot}^{1/3}$, respectively. Carbon burning provides $14\!-\!33{{\ \rm per\ cent}}$ of the total luminosity, depending on the set of reactions considered. Equivalent simulations done on 7683 and 11523 grids are in excellent quantitative agreement. The flow is dominated by a few large-scale convective cells. An instability leading to large-scale oscillations with Mach numbers in excess of 0.2 develops in an experimental run with the energy yield from C burning increased by a factor of 10. This run represents most closely the conditions expected in a violent O–C shell merger, which is a potential production site for odd-Z elements such as K and Sc and which may seed asymmetries in the supernova progenitor. 1D simulations may underestimate the energy generation from the burning of ingested material by as much as a factor 2 owing to their missing the effect of clumpiness of entrained material on the nuclear reaction rate.
The 2016 January eruption of recurrent Nova LMC 1968
Authors: Kuin N P M , Page K L , Mróz P , Darnley M J , Shore S N , Osborne J P , Walter F , Di Mille F , Morrell N , Munari U , Bohlsen T , Evans A , Gehrz R D , Starrfield S , Henze M , Williams S C , Schwarz G J , Udalski A , Szymański M K , Poleski R , Soszyński I , Ribeiro V A R M , Angeloni R , Breeveld A A , Beardmore A P , Skowron J 
Published: October 2019

ABSTRACTWe present a comprehensive review of all observations of the eclipsing recurrent Nova LMC 1968 in the Large Magellanic Cloud which was previously observed in eruption in 1968, 1990, 2002, 2010, and most recently in 2016. We derive a probable recurrence time of 6.2 ± 1.2 yr and provide the ephemerides of the eclipse. In the ultraviolet–optical–IR photometry the light curve shows high variability right from the first observation around 2 d after eruption. Therefore no colour changes can be substantiated. Outburst spectra from 2016 and 1990 are very similar and are dominated by H and He lines longward of 2000 Å. Interstellar reddening is found to be E(B − V) = 0.07 ± 0.01. The super soft X-ray luminosity is lower than the Eddington luminosity and the X-ray spectra suggest the mass of the white dwarf (WD) is larger than 1.3 M⊙. Eclipses in the light curve suggest that the system is at high orbital inclination. On day 4 after the eruption a recombination wave was observed in Fe ii ultraviolet absorption lines. Narrow-line components are seen after day 6 and explained as being due to reionization of ejecta from a previous eruption. The UV spectrum varies with orbital phase, in particular a component of the He ii 1640 Å emission line, which leads us to propose that early-on the inner WD Roche lobe might be filled with a bound opaque medium prior to the re-formation of an accretion disc. Both this medium and the ejecta can cause the delay in the appearance of the soft X-ray source.
Ultra-diffuse galaxies in the Auriga simulations
Authors: Liao Shihong , Gao Liang , Frenk Carlos S , Grand Robert J J , Guo Qi , Gómez Facundo A , Marinacci Federico , Pakmor Rüdiger , Shao Shi , Springel Volker 
Published: October 2019

ABSTRACT
We investigate the formation of ultra-diffuse galaxies (UDGs) using the Auriga high-resolution cosmological magnetohydrodynamical simulations of Milky Way–sized galaxies. We identify a sample of 92 UDGs in the simulations that match a wide range of observables such as sizes, central surface brightness, Sérsic indices, colours, spatial distribution, and abundance. Auriga UDGs have dynamical masses similar to normal dwarfs. In the field, the key to their origin is a strong correlation present in low-mass dark matter haloes between galaxy size and halo spin parameter. Field UDGs form in dark matter haloes with larger spins compared to normal dwarfs in the field, in agreement with previous semi-analytical models. Satellite UDGs, on the other hand, have two different origins: ${\sim}55{{\ \rm per\ cent}}$ of them formed as field UDGs before they were accreted; the remaining ${\sim}45{{\ \rm per\ cent}}$ were normal field dwarfs that subsequently turned into UDGs as a result of tidal interactions.
CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies
Authors: Wang Jianhua , Huang Dandan , Zhou Yao , Yao Hongcheng , Liu Huanhuan , Zhai Sinan , Wu Chengwei , Zheng Zhanye , Zhao Ke , Wang Zhao , Yi Xianfu , Zhang Shijie , Liu Xiaorong , Liu Zipeng , Chen Kexin , Yu Ying , Sham Pak Chung , Li Mulin Jun 
Published: October 2019

AbstractGenome-wide association studies (GWASs) have revolutionized the field of complex trait genetics over the past decade, yet for most of the significant genotype-phenotype associations the true causal variants remain unknown. Identifying and interpreting how causal genetic variants confer disease susceptibility is still a big challenge. Herein we introduce a new database, CAUSALdb, to integrate the most comprehensive GWAS summary statistics to date and identify credible sets of potential causal variants using uniformly processed fine-mapping. The database has six major features: it (i) curates 3052 high-quality, fine-mappable GWAS summary statistics across five human super-populations and 2629 unique traits; (ii) estimates causal probabilities of all genetic variants in GWAS significant loci using three state-of-the-art fine-mapping tools; (iii) maps the reported traits to a powerful ontology MeSH, making it simple for users to browse studies on the trait tree; (iv) incorporates highly interactive Manhattan and LocusZoom-like plots to allow visualization of credible sets in a single web page more efficiently; (v) enables online comparison of causal relations on variant-, gene- and trait-levels among studies with different sample sizes or populations and (vi) offers comprehensive variant annotations by integrating massive base-wise and allele-specific functional annotations. CAUSALdb is freely available at http://mulinlab.org/causaldb.
Ambulation on Postoperative Day #0 Is Associated With Decreased Morbidity and Adverse Events After Elective Lumbar Spine Surgery: Analysis From the Michigan Spine Surgery Improvement Collaborative (MSSIC)
Authors: Zakaria Hesham Mostafa , Bazydlo Michael , Schultz Lonni , Abdulhak Muwaffak , Nerenz David R , Chang Victor , Schwalb Jason M 
Published: October 2019

Abstract

BACKGROUND
While consistently recommended, the significance of early ambulation after surgery has not been definitively studied.

OBJECTIVE
To identify the relationship between ambulation on the day of surgery (postoperative day (POD)#0) and 90-d adverse events after lumbar surgery.

METHODS
The Michigan Spine Surgery Improvement Collaborative (MSSIC) is a prospective multicenter registry of spine surgery patients. As part of routine postoperative care, patients either ambulated on POD#0 or did not. The 90-d adverse events of length of stay (LOS), urinary retention (UR), urinary tract infection (UTI), ileus, readmission, surgical site infection (SSI), pulmonary embolism/deep vein thrombosis (PE/DVT), and disposition to a rehab facility were measured.

RESULTS
A total of 23 295 lumbar surgery patients were analyzed. POD#0 ambulation was associated with decreased LOS (relative LOS 0.83, P < .001), rehab discharge (odds ratio [OR] 0.52, P < .001), 30-d (OR 0.85, P = .044) and 90-d (OR 0.86, P = .014) readmission, UR (OR 0.73, P = 10), UTI (OR 73, P = .001), and ileus (OR 0.52, P < .001) for all patients. Significant improvements in LOS, rehab discharge, readmission, UR, UTI, and ileus were observed in subset analysis of single-level decompressions (4698 pts), multilevel decompressions (4079 pts), single-level fusions (4846 pts), and multilevel fusions (4413 pts). No change in rate of SSI or DVT/PE was observed for patients who ambulated POD#0.

CONCLUSION
POD#0 ambulation is associated with a significantly decreased risk for several key adverse events after lumbar spine surgery. Decreasing the incidence of these outcomes would be associated with significant cost savings. As ambulation POD#0 is a modifiable factor in any patient's postoperative care following most spine surgery, it should be encouraged and incorporated into spine-related, enhanced-recovery-after-surgery programs.
Stagnant Venous Outflow Predicts Brain Arteriovenous Malformation Obliteration After Gamma Knife Radiosurgery Without Prior Intervention
Authors: Hu Yong-Sin , Lee Cheng-Chia , Wu Hsiu-Mei , Yang Huai-Che , Lin Te-Ming , Luo Chao-Bao , Guo Wan-Yuo , Chung Wen-Yuh , Lin Chung-Jung 
Published: October 2019

Abstract

BACKGROUND
Gamma Knife radiosurgery (GKRS) obliterates 65% to 82% of brain arteriovenous malformations (BAVMs).

OBJECTIVE
To explore the impact of hemodynamics on GKRS outcomes.

METHODS
We retrospectively (2011-2017) included 98 patients with BAVMs who had received GKRS alone. Two evaluators, blinded to the outcomes, analyzed the pre-GKRS angiography and magnetic resonance images to obtain the morphological characteristics and quantitative digital subtraction angiography (QDSA) parameters. The venous stasis index was defined as the inflow gradient divided by the absolute value of the outflow gradient. Patients’ follow-up magnetic resonance or digital subtraction angiography images were evaluated for the presence of complete obliteration (CO). Cox regression and Kaplan–Meier analyses were conducted to determine the correlations between the parameters and outcomes.

RESULTS
Among the 98 patients, 63 (63.4%) achieved CO after GKRS at a median latency period of 31 mo. In multivariable analyses with adjustments for age and sex, increased BAVM volume (hazard ratio (HR) 0.949, P = .022) was an independent characteristic predictor, and venous stenosis (HR 2.595, P = .009), venous rerouting (HR 0.375, P = .022), and larger stasis index (HR 1.227, P = .025) were independent angiographic predictors of CO. BAVMs with a stasis index of >1.71 had a higher 36-mo probability of CO than those with a stasis index of ≤1.71 (61.1% vs 26.7%, P < .001).

CONCLUSION
BAVMs with a larger stasis index, indicating more stagnant venous outflow, may predict obliteration after GKRS. QDSA analysis may help in predicting BAVM treatment outcomes and making therapeutic decisions.