bluuebunny/crossref_metadata_2025_split huggingface dataset:
STEPS: an efficient prospective likelihood approach to genetic association analyses of secondary traits in extreme phenotype sequencing
Authors: Bi Wenjian , Li Yun , Smeltzer Matthew P , Gao Guimin , Zhao Shengli , Kang Guolian 
Published: June 2018

Summary
It has been well acknowledged that methods for secondary trait (ST) association analyses under a case–control design (ST$_{\text{CC}}$) should carefully consider the sampling process to avoid biased risk estimates. A similar situation also exists in the extreme phenotype sequencing (EPS) designs, which is to select subjects with extreme values of continuous primary phenotype for sequencing. EPS designs are commonly used in modern epidemiological and clinical studies such as the well-known National Heart, Lung, and Blood Institute Exome Sequencing Project. Although naïve generalized regression or ST$_{\text{CC}}$ method could be applied, their validity is questionable due to difference in statistical designs. Herein, we propose a general prospective likelihood framework to perform association testing for binary and continuous STs under EPS designs (STEPS), which can also incorporate covariates and interaction terms. We provide a computationally efficient and robust algorithm to obtain the maximum likelihood estimates. We also present two empirical mathematical formulas for power/sample size calculations to facilitate planning of binary/continuous STs association analyses under EPS designs. Extensive simulations and application to a genome-wide association study of benign ethnic neutropenia under an EPS design demonstrate the superiority of STEPS over all its alternatives above.
Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly
Authors: Yin Dongmei , Ji Changmian , Ma Xingli , Li Hang , Zhang Wanke , Li Song , Liu Fuyan , Zhao Kunkun , Li Fapeng , Li Ke , Ning Longlong , He Jialin , Wang Yuejun , Zhao Fei , Xie Yilin , Zheng Hongkun , Zhang Xingguo , Zhang Yijing , Zhang Jinsong 
Published: June 2018

Abstract
Arachis monticola (2n = 4x = 40) is the only allotetraploid wild peanut within the Arachis genus and section, with an AABB-type genome of ~2.7 Gb in size. The AA-type subgenome is derived from diploid wild peanut Arachis duranensis, and the BB-type subgenome is derived from diploid wild peanut Arachis ipaensis. A. monticola is regarded either as the direct progenitor of the cultivated peanut or as an introgressive derivative between the cultivated peanut and wild species. The large polyploidy genome structure and enormous nearly identical regions of the genome make the assembly of chromosomal pseudomolecules very challenging. Here we report the first reference quality assembly of the A. monticola genome, using a series of advanced technologies. The final whole genome of A. monticola is ~2.62 Gb and has a contig N50 and scaffold N50 of 106.66 Kb and 124.92 Mb, respectively. The vast majority (91.83%) of the assembled sequence was anchored onto the 20 pseudo-chromosomes, and 96.07% of assemblies were accurately separated into AA- and BB- subgenomes. We demonstrated efficiency of the current state of the strategy for de novo assembly of the highly complex allotetraploid species, wild peanut (A. monticola), based on whole-genome shotgun sequencing, single molecule real-time sequencing, high-throughput chromosome conformation capture technology, and BioNano optical genome maps. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within the Arachis genus and among legume crops.
YAMP: a containerized workflow enabling reproducibility in metagenomics research
Authors: Visconti Alessia , Martin Tiphaine C , Falchi Mario 
Published: June 2018

Abstract
YAMP ("Yet Another Metagenomics Pipeline") is a user-friendly workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. Although YAMP was developed to be ready to use by nonexperts, bioinformaticians will appreciate its flexibility, modularization, and simple customization.
Binning enables efficient host genome reconstruction in cnidarian holobionts
Authors: Celis Juan Sebastián , Wibberg Daniel , Ramírez-Portilla Catalina , Rupp Oliver , Sczyrba Alexander , Winkler Anika , Kalinowski Jörn , Wilke Thomas 
Published: June 2018

Abstract

Background
Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities—together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.

Results
Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.

Conclusions
Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.
A Boussinesq slurry model of the F-layer at the base of Earth’s outer core
Authors: Wong Jenny , Davies Christopher J , Jones Chris A 
Published: June 2018

SUMMARY
Seismic observations suggest that a stably stratified layer, known as the F-layer, 150–300 km thick exists at the bottom of Earth’s liquid outer core. These observations contrast with the density inferred from the Preliminary Reference Earth Model (PREM), which assumes an outer core that is well-mixed and adiabatic throughout. The liquid core is composed primarily of iron alloyed with a light component. A thermal boundary layer produces the opposite effect on the density profile compared with the observations, and single phase, thermochemical models do not provide a sufficient dynamic description of how light element is transported across the F-layer into the overlying liquid outer core. We therefore propose that the layer can be explained by a slurry on the liquidus, whereby solid particles of iron crystallize from the liquid alloy throughout the layer. The slurry model provides a dynamic explanation of how light element can be transported across a stable layer. We make two key assumptions, the first of which is fast-melting where the timescale of freezing is considered short compared to other processes. The second assumption is that we consider a binary alloy where the light element is purely composed of oxygen, which is expelled entirely into the liquid during freezing. We present a steady state 1-D box model of a slurry formulated in a reference frame moving at the speed of inner core growth. We ascertain temperature, light element concentration and solid flux profiles by varying the layer thickness, inner core heat flux and thermal conductivity, since there is some uncertainty in these estimates. Our solutions demonstrate that the steady state slurry can satisfy the geophysical constraints on the density jump across the layer and the core–mantle boundary heat flux.
Pediatric Inflammatory Bowel Disease Clinical Innovations Meeting of the Crohn’s & Colitis Foundation: Charting the Future of Pediatric IBD
Authors: Picoraro Joseph A , Lee Dale , Heller Caren A , Weaver Alandra , Hyams Jeffrey S , Conklin Laurie S , Otley Anthony , Ziring David , Kugathasan Subra , Rosh Joel R , Mulberg Andrew , Denson Lee A , Kappelman Michael D , Grossman Andrew B , Bousvaros Athos , Park K T 
Published: June 2018

AbstractThe Crohn’s & Colitis Foundation has facilitated transformational research in pediatric inflammatory bowel disease (IBD), through the RISK and PROTECT studies, that has laid the groundwork for a comprehensive understanding of molecular mechanisms of disease and predictors of therapeutic response in children. Despite these advances, children have lacked timely and informed access to the latest therapeutic advancements in IBD. The Crohn's & Colitis Foundation convened a Pediatric Resource Organization for Kids with Inflammatory Intestinal Diseases (PRO-KIIDS) Clinical Innovations Meeting at the inaugural Crohn's and Colitis Congress in January 2018 to devise how to advance the care of children with IBD. The working group selected 2 priorities: (1) accelerating therapies to children with IBD and (2) stimulating investigator-initiated research while fostering sustainable collaboration; and proposed 2 actions: (a) the convening of a task force to specifically address how to accelerate pharmacotherapies to children with IBD and (b) the funding of a multicenter clinical and translational research study that incorporates the building of critical research infrastructure.10.1093/ibd/izy205_video1 izy205.video1 5799266615001
New insights into behavioural ecology of European seabass off the West Coast of France: implications at local and population scales
Authors: de Pontual Hélène , Lalire Maxime , Fablet Ronan , Laspougeas Claire , Garren François , Martin Stéphane , Drogou Mickael , Woillez Mathieu 
Published: June 2018

AbstractFrom 2010 to 2012, 246 data storage tags were deployed on European seabass in the Iroise Natural Marine Park, a marine protected area (MPA) off west Brittany, France. A return rate of 14.6% associated with long time series of data provided new information on fish ecology (e.g. maximum experienced depth greater than 225 m, temperature range 6.80–21.87°C). Depth and temperature series were used to infer individual migration using an innovative hidden Markov model (HMM) especially developed for seabass geolocation. Reconstructed fish tracks revealed that seabass is a partially migratory species, as individuals exhibited either long-distance migrations towards the Bay of Biscay or the Celtic Sea, or residency behaviour in the Iroise Sea. Fidelity to summer feeding areas and to winter spawing areas was demonstrated. These results suggest that the population is spatially structured. The Iroise Sea is likely a mixing zone for different stocks or sub-populations, and may also shelter a resident population. At the population scale, such findings may impact ICES stock assessment and the resulting decisions from EU managers. At the local scale, conservation action could be taken by MPA managers. Besides, this study demonstrates the high potential of archival tags for investigating multi-year behavioural patterns such as site fidelity to offshore spawning areas.
Classification of Toric Manifolds over an n-Cube with One Vertex Cut
Authors: Hasui Sho , Kuwata Hideya , Masuda Mikiya , Park Seonjeong 
Published: June 2018

AbstractA complete nonsingular toric variety (called a toric manifold) is over $P$ if its quotient by the compact torus is homeomorphic to $P$ as a manifold with corners. Bott manifolds are toric manifolds over an $n$-cube $I^n$ and blowing them up at a fixed point produces toric manifolds over $\operatorname{vc}(I^n)$ an $n$-cube with one vertex cut. They are all projective. On the other hand, Oda’s three-fold, the simplest non-projective toric manifold, is over $\operatorname{vc}(I^3)$. In this paper, we classify toric manifolds over $\operatorname{vc}(I^n)$$(n\ge 3)$ as varieties and as smooth manifolds. It consequently turns out that there are many non-projective toric manifolds over $\operatorname{vc}(I^n)$ but they are all diffeomorphic, and toric manifolds over $\operatorname{vc}(I^n)$ in some class are determined by their cohomology rings as varieties.
5-Aminolevulinic Acid-Induced Fluorescence in Focal Cortical Dysplasia: Report of 3 Cases
Authors: Roberts David W , Bravo Jaime J , Olson Jonathan D , Hickey William F , Harris Brent T , Nguyen Lananh N , Hong Jennifer , Evans Linton T , Fan Xiaoyao , Wirth Dennis , Wilson Brian C , Paulsen Keith D 
Published: June 2018

Abstract

BACKGROUND
Three patients enrolled in a clinical trial of 5-aminolevulinic-acid (5-ALA)-induced fluorescence-guidance, which has been demonstrated to facilitate intracranial tumor resection, were found on neuropathological examination to have focal cortical dysplasia (FCD).

OBJECTIVE
To evaluate in this case series visible fluorescence and quantitative levels of protoporphyrin IX (PpIX) during surgery and correlate these findings with preoperative magnetic resonance imaging (MRI) and histopathology.

METHODS
Patients were administered 5-ALA (20 mg/kg) approximately 3 h prior to surgery and underwent image-guided, microsurgical resection of their MRI- and electrophysiologically identified lesions. Intraoperative visible fluorescence was evaluated using an operating microscope adapted with a commercially available blue light module. Quantitative PpIX levels were assessed using a handheld fiber-optic probe and a wide-field imaging spectrometer. Sites of fluorescence measurements were co-registered with both preoperative MRI and histopathological analysis.

RESULTS
Three patients with a pathologically confirmed diagnosis of FCD (Types 1b, 2a, and 2b) underwent surgery. All patients demonstrated some degree of visible fluorescence (faint or moderate), and all patients had quantitatively elevated concentrations of PpIX. No evidence of neoplasia was identified on histopathology, and in 1 patient, the highest concentrations of PpIX were found at a tissue site with marked gliosis but no typical histological features of FCD.

CONCLUSION
FCD has been found to be associated with intraoperative 5-ALA-induced visible fluorescence and quantitatively confirmed elevated concentrations of the fluorophore PpIX in 3 patients. This finding suggests that there may be a role for fluorescence-guidance during surgical intervention for epilepsy-associated FCD.
The role of family absolute and relative income in suicide among Chinese rural young adults: mediation effects of social support and coping strain
Authors: Zhou Qin , Zhang Jie , Hennessy Dwight A 
Published: June 2018

Abstract

Background
suicide is a major public health issue in China. However, research on the impact of absolute and relative economic stats on suicide is scarce among the Chinese population, particularly rural young adults. Using a case-control psychological autopsy study design, we aimed to investigate the effect of family absolute and relative income on suicide among Chinese rural young adults and to further explore the potential mediating mechanism under these associations.

Method
the information of 393 suicide cases and 416 community living controls were collected for this study. A Binary Choice Model was used to analyze the association between family absolute and relative income and suicide risk, as well as potential mediating factors for these associations.

Results
a much stronger association was found between relative income and suicide than between absolute income and suicide. Social support was a dominant mediator for the association between family relative income and suicide among both female and male young adults. Coping strain emerged as a mediating factor within the link between absolute income and suicide for males.

Conclusions
public health interventions to reduce suicide should pay more attention to relative income in addition to absolute income as potential targets for intervention, and how social support and coping strain act as mediating factors.
Hypoxic‐stabilized EPAS1 proteins transactivate DNMT1 and cause promoter hypermethylation and transcription inhibition of EPAS1 in non‐small cell lung cancer
Authors: Xu Xiang‐Hong , Bao Yang , Wang Xiaotian , Yan Fengyang , Guo Shicheng , Ma Yanyun , Xu Dong , Jin Li , Xu Jibin , Wang Jiucun 
Published: June 2018

ABSTRACTNon‐small cell lung cancer (NSCLC) is the leading cause of cancer mortality globally. Although cigarette smoking is by far the most important risk factor for lung cancer, the aberrant expression of oncogenes and tumor suppressor genes contributes a great deal to tumorigenesis. Here, we reveal that aberrant expression of endothelial PAS domain‐containing protein 1 (EPAS1) gene, which encodes hypoxia inducible factor 2a, has a critical role in NSCLC. Our results showed EPAS1 mRNA was down‐regulated in 82.5% of NSCLC tissues, and a new region of EPAS1 promoter was found to be highly methylated in lung cancer cell lines and NSCLC tissues. Moreover, the methylation rates were negatively correlated to EPAS1 mRNA expression in lung tissues. Further, demethylation analysis demonstrated EPAS1 was regulated by DNA methyltransferases (DNMTs) in NSCLC. In contrast, DNMT1was verified as an EPAS1 target gene by chromatin immunoprecipitation assay and could be transactivated by stabilized EPAS1 proteins in hypoxic lung cells, thereby decreasing EPAS1 mRNA expression by methylation regulation. Collectively, our study suggests there might be a mechanism of negative‐feedback regulation for EPAS1in NSCLC. That is, hypoxic‐stabilized EPAS1 proteins transactivated ΌΝΜΤΊ, which further promoted the hypermethylation of EPAS1 promoter and decreased EPAS1 mRNA expression levels in NSCLC.—Xu, X.‐H., Bao, Y., Wang, X., Yan, F., Guo, S., Ma, Y., Xu, D., Jin, L., Xu, J., Wang, J. Hypoxic‐stabilized EPAS1 proteins transactivate DNMT1 and cause promoter hypermethylation and transcription inhibition of EPAS1 in non‐small cell lung cancer. FASEB J. 32, 6694–6705 (2018). www.fasebj.org
Topical application of anthranilate derivatives ameliorates psoriatic inflammation in a mouse model by inhibiting keratinocyte‐derived chemokine expression and neutrophil infiltration
Authors: Lin Zih‐Chan , Hsieh Pei‐Wen , Hwang Tsong‐Long , Chen Chi‐Yuan , Sung Calvin T. , Fang Jia‐You 
Published: June 2018

ABSTRACTPsoriasis is an inflammatory autoimmune skin disorder possessing a complex etiology related to genetic and environmental triggers. Keratinocytes show a potential role for the origin of psoriasis. In this study, we estimated the efficiency of 2 anthranilate derivatives—(E)‐4‐(N‐{2‐[1‐(hydroxyimino)ethyl]phenyl}sulfamoyl)phenyl pivalate (HFP031) and butyl 2‐[2‐(2‐fluorophenyl)acetamido]benzoate (HFP034)—on psoriasis amelioration in a mouse model. The results showed that topical treatment with both compounds could attenuate epidermal thickness and scaling in an imiquimod (IMQ)‐induced psoriasis mouse model via decreased expression of cytokines and chemokines [C‐X‐C chemokine ligand (CXCL)1 and CXCL2], leading to the reduction of neutrophilic abscess in the skin. The in vivo cutaneous absorption of HFP034 was 7.6‐fold greater than that of HFP031. Both compounds caused negligible irritation on healthy mouse skin. In addition, we examined the effect of the anthranilate derivatives on chemokine expression in IMQ‐treated HaCaT keratinocytes. Our results elucidated a mechanism for anti‐inflammatory activity of HFP034 that involved the elevation of intracellular cAMP concentration, suppression of NF‐κB activity, and attenuation of neutrophil chemoattractant expression. These results suggest that HFP034 could increase the cutaneous concentration of cAMP to suppress neutrophil infiltration into the skin. Topically applied HFP034 may demonstrate a potential for future clinical application as a novel therapy for psoriasis treatment.—Lin, Z.‐C., Hsieh, P.‐W., Hwang, T.‐L., Chen, C.‐Y., Sung, C. T., Fang, J.‐Y. Topical application of anthranilate derivatives ameliorates psoriatic inflammation in a mouse model by inhibiting keratinocyte‐derived chemokine expression and neutrophil infiltration. FASEB J. 32, 6783–6795 (2018). www.fasebj.org
Percutaneous Transiliac–Transsacral Screw Fixation of Sacral Fragility Fractures Improves Pain, Ambulation, and Rate of Disposition to Home
Authors: Walker J. Brock , Mitchell Sean M. , Karr Sean D. , Lowe Jason A. , Jones Clifford B. 
Published: June 2018

Objective:
To determine whether percutaneous transiliac–transsacral screw fixation improves pain, ambulation, length of stay, and the rate of disposition to home in patients with sacral fragility fractures.

Design:
Retrospective cohort study.

Setting:
Single academic Level 1 trauma center.

Patients/Participants:
Elderly patients who presented with an isolated sacral fragility fracture between August 2015 and August 2017. Of the 41 patients included in the study, 16 were treated operatively and 25 were treated nonoperatively.

Intervention:
Percutaneous transiliac–transsacral screw fixation.

Main Outcome Measurements:
Pain, ambulation, length of stay, complications, and disposition.

Results:
Patients treated operatively reported a greater improvement in pain as measured by the visual analog scale (3.9 vs. 0.6 points, P < 0.001). At the time of discharge, 100% of surgically treated patients were able to ambulate compared with 72% in the nonoperative group (P = 0.03). Average distance ambulating at the time of discharge was higher in the operative group (95 vs. 35 ft, P < 0.01). Length of stay was similar between the 2 groups (3.6 days in operative group vs. 4.2 days in nonoperative group, P = 0.5). Of the patients treated operatively, 75% were discharged to home compared with only 20% in the nonoperative group (P < 0.001). There were no complications related to surgery.

Conclusions:
Percutaneous transiliac–transsacral screw fixation of sacral fragility fractures lessens pain, improves ambulation, and increases the rate of disposition to home. Further investigation is needed to determine if surgical fixation provides benefit regarding medium- and long-term outcome variables.

Level of Evidence:
Therapeutic Level III. See Instructions for Authors for a complete description of levels of evidence.