bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Oats and Milk on Markers of Cardiovascular Disease
Authors: Olson Audrey , Frankenfeld Cara L. , Wallace Taylor C. , Johnson Jodee 
Published: November 2018

Background
Oat consumption has been suggested to decrease the risk of cardiovascular disease; oats are frequently co-consumed with milk, but also water and other products.

Methods
We evaluated associations of 24-hour self-reported oat and cow’s milk consumption with cardiovascular disease risk factors using National Health and Nutrition Examination Survey (1999–2014) data. Daily oat and milk consumptions were classified as (1) no oats, no milk; (2) yes oats, no milk; (3) no oats, yes milk; or (4) yes oats, yes milk. We used no oats/no milk as a reference to assess the effects of oats, milk, and oat with milk consumption on markers of cardiovascular disease (CVD). The yes oats/no milk group was then used as the reference to further determine if a relationship between oat and milk consumption on the same day existed past that of previously reported oat consumption alone.

Results
Self-reported oat intake was associated with improvements in some biomarkers of CVD risk. The prevalence of abdominal obesity measured as waist circumference was lower (odds ratio, 0.57; 95% confidence interval, 0.41–0.73), and fewer than 3+ risk factors of metabolic syndrome (odds ratio, 0.66; 95% confidence interval, 0.51–0.85) were observed in the yes oats/yes milk group as compared with nonconsumers (no oats/no milk). Similar effects were found in the yes oats/no milk group. We did not find any synergistic effects of self-reported consumption of both milk and oats during a 24-hour period on markers of CVD.

Conclusions
These results are consistent with clinical data showing oats to be associated with improvement in some biomarkers of CVD risk; however, the addition of milk does not appear to affect CVD risk factors in this cross-sectional data set.
Glymphatic Pathway of Gadolinium-Based Contrast Agents Through the Brain
Authors: Deike-Hofmann Katerina , Reuter Julia , Haase Robert , Paech Daniel , Gnirs Regula , Bickelhaupt Sebastian , Forsting Michael , Heußel Claus Peter , Schlemmer Heinz-Peter , Radbruch Alexander 
Published: November 2018

Background
The “glymphatic system” (GS), a brain-wide network of cerebrospinal fluid microcirculation, supplies a pathway through and out of the central nervous system (CNS); malfunction of the system is implicated in a variety of neurological disorders. In this exploratory study, we analyzed the potential of a new imaging approach that we coined delayed T2-weighted gadolinium-enhanced imaging to visualize the GS in vivo.

Methods
Heavily T2-weighted fluid-attenuated inversion recovery (hT2w-FLAIR) magnetic resonance imaging was obtained before, and 3 hours and 24 hours after intravenous gadolinium-based contrast agent (GBCA) application in 33 neurologically healthy patients and 7 patients with an impaired blood-brain barrier (BBB) due to cerebral metastases. Signal intensity (SI) was determined in various cerebral fluid spaces, and white matter hyperintensities were quantified by applying the Fazekas scoring system.

Findings
Delayed hT2w-FLAIR showed GBCA entry into the CNS via the choroid plexus and the ciliary body, with GBCA drainage along perineural sheaths of cranial nerves and along perivascular spaces of penetrating cortical arteries. In all patients and all sites, a significant SI increase was found for the 3 hours and 24 hours time points compared with baseline. Although no significant difference in SI was found between neurologically healthy patients and patients with an impaired BBB, a significant positive correlation between Fazekas scoring system and SI increase in the perivascular spaces 3 hours post injection was shown.

Interpretation
Delayed T2-weighted gadolinium-enhanced imaging can visualize the GBCA pathway into and through the GS. Presence of GBCAs within the GS might be regarded as part of the natural excretion process and should not be mixed up with gadolinium deposition. Rather, the correlation found between deep white matter hyperintensities, an imaging sign of vascular dementia, and GS functioning demonstrated feasibility to exploit the pathway of GBCAs through the GS for diagnostic purposes.
An Effective Simulator for Intraoral Facial Skeletal Contour Surgeries
Authors: Fu Xi , Qiao Jia , Gui Lai , Girod Sabine , Niu Feng , Liu Jianfeng , Jin Qi , Zhang Huijun , Xu Shixing , Mao Xiaoyan , Chen Ying 
Published: November 2018

Background
In East Asia, intraoral facial skeletal contour surgeries (intraoral FSCSs), including reduction gonioplasty, reduction malarplasty, and genioplasty, have become increasingly popular. Nonetheless, intraoral FSCSs are technically difficult and have a steep learning curve. An effective simulator could be beneficial for intraoral FSCS training. However, there is no intraoral FSCS simulator available. We introduced an intraoral FSCS simulator and assessed its effectiveness.

Methods
An intraoral FSCS simulator was established by covering a 3-dimensional printed skull with elastic cloth. Twenty residents were enrolled and randomly divided into experimental group A and control group B. Group A performed the intraoral FSCS on the simulator for 3 times. Group B performed the intraoral FSCS on skull model for 3 times. The intraoral FSCS simulator and trainees' performance were evaluated by a trainee-reported questionnaire before and after training, the surgical outcomes were graded by 3 senior attending physicians. All questions and the surgical outcome were scored based on a 5-point Likert scale (1 = very poor, 5 = very good). The surgical times were recorded.

Results
The intraoral FSCS simulator (4.13 ± 0.64) simulated the surgical reality significantly better than the skull (2.6 ± 0.63). In intraoral FSCS simulator training, the restriction and compliance of the facial soft tissue were vividly mimicked (4.4 ± 0.51); the intraoral approach was vividly mimicked (4.07 ± 0.59). The intraoral FSCS simulator is significantly superior to the skull in improving participants' confidence in performing intraoral FSCS, power system control, and intraoral approach adoption (<0.001). The average surgical outcome score was 3.11 ± 0.45 in group A and 3.91 ± 0.24 in group B. The average surgical time was 177.78 ± 28.38 minutes in group A and 65.26 ± 15.38 minutes in group B.

Conclusions
We developed the first intraoral FSCS simulator and proved its effectiveness preliminarily. Randomized controlled study with clinical cases is needed to further test its effectiveness.
Aesthetic Durable Forehead Contouring in Asians With Fat Grafting and Botulinum Toxin
Authors: Kang Gavin Chun-Wui , Hsiao Yen-Chang , Huang Jung-Ju , Chen Jyh-Ping , Chen Philip Kuo-Ting , Chen Yu-Ray , Chang Chun-Shin 
Published: November 2018

Background
Augmentative forehead contouring to create a full rounded smooth forehead is increasingly popular worldwide especially in East Asia where a flat and/or concave irregular forehead is considered unaesthetic. We present our outcomes performing fat transfer to the forehead in combination with botulinum toxin (Botox) corrugator-frontalis injection where indicated in East Asians.

Methods
From 2013 to 2017, 62 consecutive patients with flat and/or concave irregular unaesthetic foreheads underwent forehead fat transfer using a microautologous fat transplantation gun. Concomitant Botox injection to minimize corrugator and frontalis contraction-mediated fat displacement was indicated in 23 patients (thin forehead skin and/or excessive forehead animation or rhytides) to prevent forehead vertical crease formation. Thirty-nine subjects with a mean follow-up of 16 months (range = 3–44 months) had their pregraft and postgraft forehead contours assessed on an aesthetic grading scale. Of these 39, 17 completed forehead fat graft volumetric analysis using preoperative and postoperative 3D photography.

Results
Aesthetic results were durable at latest follow-up, and all patients were satisfied with their final appearance. The mean amount of fat transferred was 7.72 mL (range = 1.5–33 mL). One subject required a repeat fat grafting (with Botox) because of vertical crease formation after the index procedure (without Botox). Another 12 needed a second fat-grafting session to optimize the contour. All who received Botox did not develop vertical creases. The mean ± SD forehead contour grade improved from 2.29 ± 0.77 to 3.24 ± 0.67 (P < 0.001). The percentage mean ± SD retention of grafted fat was 46.71% ± 5.77% with Botox versus 39.12% ± 5.24% without Botox (P = 0.006).

Conclusions
Fat grafting to the forehead using our technique with selective Botox administration is an effective, simple, fast, inexpensive, and safe strategy for aesthetic forehead contouring especially for flat and/or concave foreheads. Forehead fat survival rate is objectively improved with simultaneous Botox injection. There is minimum downtime and long-lasting results with high patient satisfaction rates.
Detection of low-frequency mutations and removal of heat-induced artifactual mutations using Duplex Sequencing
Authors: Ahn Eun Hyun , Lee Seung Hyuk 
Published: November 2018

AbstractWe present a genome-wide comparative and comprehensive analysis of three different sequencing methods (conventional next generation sequencing (NGS), tag-based single strand sequencing (eg. SSCS), and Duplex Sequencing for investigating mitochondrial mutations in human breast epithelial cells. Duplex Sequencing produces a single strand consensus sequence (SSCS) and a duplex consensus sequence (DCS) analysis, respectively. Our study validates that although high-frequency mutations are detectable by all the three sequencing methods with the similar accuracy and reproducibility, rare (low-frequency) mutations are not accurately detectable by NGS and SSCS. Even with conservative bioinformatical modification to overcome the high error rate of NGS, the NGS frequency of rare mutations is 7.0×10−4. The frequency is reduced to 1.3×10−4with SSCS and is further reduced to 1.0×10−5using DCS. Rare mutation context spectra obtained from NGS significantly vary across independent experiments, and it is not possible to identify a dominant mutation context. In contrast, rare mutation context spectra are consistently similar in all independent DCS experiments. We have systematically identified heat-induced artifactual mutations and corrected the artifacts using Duplex Sequencing. All of these artifacts are stochastically occurring rare mutations. C>A/G>T, a signature of oxidative damage, is the most increased (170-fold) heat-induced artifactual mutation type. Our results strongly support the claim that Duplex Sequencing accurately detects low-frequency mutations and identifies and corrects artifactual mutations introduced by heating during DNA preparation.
Can you have multiple attentional templates? Large-scale replications of Van Moorselaar, Theeuwes and Olivers (2014) and Hollingworth and Beck (2016)
Authors: Frătescu Marcella , Moorselaar Dirk Van , Mathôt Sebastiaan 
Published: November 2018

AbstractStimuli that resemble the content of visual working memory (VWM) capture attention. However, theories disagree on how many VWM items can bias attention simultaneously. The multiple-state account posits a distinction between template and accessory VWM items, such that only a single template item biases attention. In contrast, homogenous-state accounts posit that all VWM items bias attention. Recently, Van Moorselaar et al. (2014) and Hollingworth and Beck (2016) tested these accounts, but obtained seemingly contradictory results. Van Moorselaar et al. (2014) found that a distractor in a visual-search task captured attention more when it matched the content of VWM (memory-driven capture). Crucially, memory-driven capture disappeared when more than one item was held in VWM, in line with the multiple-state account. In contrast, Hollingworth and Beck (2016) found memory-driven capture even when multiple items were kept in VWM, in line with a homogenous-state account. Considering these mixed results, we replicated both studies with a larger sample, and found that all key results are reliable. It is unclear to what extent these divergent results are due to paradigm differences between the studies. We conclude that is crucial to our understanding of VWM to determine the boundary conditions under which memory-driven capture occurs.
Whole plant community transplants across climates reveal structural community stability due to large shifts in species assemblage
Authors: Tomiolo Sara , Bilton Mark C. , Tielbörger Katja 
Published: November 2018

Summary(1) Climate change will decrease precipitation and increase rainfall variability in Eastern Mediterranean regions, with responses of plant communities largely uncertain. Here, we tested short-term responses of dryland plant communities to contrasting rainfall regimes using a novel experimental approach.(2) We exposed three annual plant communities to sharp changes in climatic conditions using whole community reciprocal transplants of soil and seed banks. We tested for the role of climate vs. community origin on community response and resistance. In parallel, we asked whether origin-specific climatic adaptations predict compositional shifts across climates.(3) For both community origins, the most dry-adapted species in each community increased in dry climate and the wet-adapted species increased in wet climate. Dry community origins showed large compositional shifts while maintaining stable plant density, biomass and species richness across climates. Conversely, wet communities showed smaller compositional shifts, but larger variation in biomass and richness.(4) Asynchrony in species abundances in response to rainfall variability could maintain structural community stability. This, in combination with seed dormancy, has the ability to delay extinction in response to climate change. However, increasing occurrence of extreme droughts may, in the long-term, lead to loss of wet-adapted species.
Space, time, and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate
Authors: Haworth Sarah E. , White Kevin S. , Côté Steeve D. , Shafer Aaron B.A. 
Published: November 2018

AbstractThe community of microorganisms in the gut is affected by host species, diet, and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. Here, we assayed the fecal microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified fecal microbiome diversity and composition among groups in the wild and captivity, across populations, and in a single group over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across summer months. Pairwise sample estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild group distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.SummaryThis study characterizes the microbiome of mountain goat (Oreamnos americanus) populations across populations and over summer months; we also quantified the effects of captivity to offer more insights into the health of alpine wildlife.
Mathematical Details on a Cancer Resistance Model
Authors: Greene James M. , Sanchez-Tapia Cynthia , Sontag Eduardo D. 
Published: November 2018

AbstractThe primary factor limiting the success of chemotherapy in cancer treatment is the phenomenon of drug resistance. We have recently introduced a framework for quantifying the effects of induced and non-induced resistance to cancer chemotherapy [11, 10]. In this work, we expound on the details relating to an optimal control problem outlined in [10]. The control structure is precisely characterized as a concatenation of bang-bang and path-constrained arcs via the Pontryagin Maximum Principle and differential Lie algebra techniques. A structural identifiability analysis is also presented, demonstrating that patient-specific parameters may be measured and thus utilized in the design of optimal therapies prior to the commencement of therapy. For completeness, a detailed analysis of existence results is also included.
Environmental Optimization Enables Maintenance of Quiescent Hematopoietic Stem Cells Ex Vivo
Authors: Kobayashi Hiroshi , Morikawa Takayuki , Okinaga Ayumi , Hamano Fumie , Hashidate-Yoshida Tomomi , Watanuki Shintaro , Hishikawa Daisuke , Shindou Hideo , Arai Fumio , Kabe Yasuaki , Suematsu Makoto , Shimizu Takao , Takubo Keiyo 
Published: November 2018

SUMMARYHematopoietic stem cells (HSCs) maintain lifelong hematopoiesis by remaining quiescent in the bone marrow niche. Recapitulation of a quiescent state in culture has not been achieved, as cells rapidly proliferate and differentiate in vitro. After exhaustive analysis of different environmental factor combinations and concentrations as a way to mimic physiological conditions, we were able to maintain engraftable quiescent HSCs for 1 month in culture under very low cytokine concentrations, hypoxia, and very high fatty acid levels. Exogenous fatty acids were required likely due to suppression of intrinsic fatty acid synthesis by hypoxia and low cytokine conditions. By contrast, high cytokine concentrations or normoxia induced HSC proliferation and differentiation. Our novel culture system provides a means to evaluate properties of steady state HSCs and test effects of defined factorsin vitrounder near-physiological conditions.
Chromatin profiling of the repetitive and non-repetitive genome of the human fungal pathogen Candida albicans
Authors: Price Robert Jordan , Weindling Esther , Berman Judith , Buscaino Alessia 
Published: November 2018

ABSTRACTBackgroundEukaryotic genomes are packaged into chromatin structures with pivotal roles in regulating all DNA-associated processes. Post-translational modifications of histone proteins modulate chromatin structure leading to rapid, reversible regulation of gene expression and genome stability which are key steps in environmental adaptation. Candida albicans is the leading fungal pathogen in humans, and can rapidly adapt and thrive in diverse host niches. The contribution of chromatin to C. albicans biology is largely unexplored.ResultsHere, we harnessed genome-wide sequencing approaches to generate the first comprehensive chromatin profiling of histone modifications (H3K4me3, H3K9Ac, H4K16Ac and γ-H2A) across the C. albicans genome and relate it to gene expression. We demonstrate that gene-rich non-repetitive regions are packaged in canonical euchromatin associated with histone modifications that mirror their transcriptional activity. In contrast, repetitive regions are assembled into distinct chromatin states: subtelomeric regions and the rDNA locus are assembled into canonical heterochromatin, while Major Repeat Sequences and transposons are packaged in chromatin bearing features of euchromatin and heterochromatin. Genome-wide mapping of γH2A, a marker of genome instability, allowed the identification of potential recombination-prone genomic sites. Finally, we present the first quantitative chromatin profiling in C. albicans to delineate the role of the chromatin modifiers Sir2 and Set1 in controlling chromatin structure and gene expression.ConclusionsThis study presents the first genome-wide chromatin profiling of histone modifications associated with the C. albicans genome. These epigenomic maps provide an invaluable resource to understand the contribution of chromatin to C. albicans biology.
Newly developed single-cell computational approach elucidates the stabilization of Oct4 expression in the E3.25 mouse preimplantation embryo
Authors: Gerovska Daniela , Arauzo-Bravo Marcos J. 
Published: November 2018

AbstractThe time of onset of the second cell fate decision in the mouse preimplantation embryo is still unknown. Ohnishi et al. (2014) looked for cell heterogeneity in the ICM at E3.25 that could indicate the time preceding the apparent segregation of PE and EPI at E3.5, but were not able to detect an early splitting transcriptomics event using state-of-the-art clustering techniques. We developed a new clustering algorithm, hierarchical optimal k-means (HOkM), and identified from single cell (sc) transcriptomics microarray data two groups of ICM cells during the 32 to 64 mouse embryo transition: from embryos with less than 34 cells, and more than 33 cells, corresponding to two developmental sub-stages. The genes defining these sub-stages indicate that the development of the embryo to 34 cells triggers a dramatic event as a result of which Bsg is high expressed, the canonical Wnt pathway is activated, Oct4 is stabilized to high expression and the chromatin remodeling program is initialized to establish a very early narve pluripotent state from the preceding totipotency. We characterized our HOkM partition comparing with independent scRNA-seq datasets. It was staggering to discover that from the 3.4360×1010 possible bi-partitions of the E3.25 data of Ohnishi et al. (2014), our HOkM discovered one partition that shares the biological features of the early and late 32 ICM cells of Posfai et al. (2017). We propose that the stabilization of Oct4 expression is a non-cell autonomous process that requires a minimal number of four inner cell contacts acquired during the transition from a homogeneous outer-cell environment to a heterogeneous inner/outer cell environment formed by the niche of a kernel of at least six inner cells covered by trophectoderm.
Self-assembly of polymer-encased lipid nanodiscs and membrane protein reconstitution
Authors: Sahoo Bikash R. , Genjo Takuya , Moharana Kanhu C. , Ramamoorthy Ayyalusamy 
Published: November 2018

AbstractThe absence of detergent and curvature makes nanodiscs to be excellent membrane mimetics. The lack of structural and mechanistic model of polymer-encapsulated lipid-nanodiscs limits their use to study the structure, dynamics and function of membrane proteins. In this study, we parametrized and optimized the coarse-graining (CG) bead-mapping for two differently charged and functionalized copolymers, namely styrene-maleic acid (SMAEA) and polymethacrylate (PMAQA), for the Martini force-field framework and showed nanodisc formation (< 8 nm diameter) on a time scale of tens of microseconds using molecular dynamics (MD) simulation. Structural models of ~ 2.0 or 4.8 kDa PMAQA and ~2.2 kDa SMAEA polymer based lipid-nanodiscs highlights the importance of polymer chemical structure, size and polymer:lipid molar ratio in the optimization of nanodisc structure. The ideal spatial arrangement of polymers in nanodisc, nanodisc size and thermal stability obtained from our MD simulation correlates well with the experimental observations. The polymer-nanodisc were tested for the reconstitution of single-pass or multi-pass transmembrane proteins. We expect this study to be useful in the development of novel polymer based lipid-nanodiscs and for the structural studies of membrane proteins.TOC GRAPHICS