bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into global planktonic diatom diversity: The importance of comparisons between phylogenetically equivalent units that account for time
Authors: Nakov Teofil , Beaulieu Jeremy M , Alverson Andrew J 
Published: July 2018

Abstract
Metabarcoding has offered unprecedented insights into microbial diversity. In many studies, short DNA sequences are binned into consecutively lower Linnaean ranks, and ranked groups (e.g., genera) are the units of biodiversity analyses. These analyses assume that Linnaean ranks are biologically meaningful and that identically ranked groups are comparable. We used a metabarcode dataset for marine planktonic diatoms to illustrate the limits of this approach. We found that the 20 most abundant marine planktonic diatom genera ranged in age from 4 to 134 million years, indicating the non-equivalence of genera because some have had more time to diversify than others. However, species richness was largely independent of genus age, suggesting that disparities in species richness among genera were better explained by variation in rates of speciation and extinction. Taxonomic classifications often do not reflect phylogeny, so genus-level analyses can include phylogenetically nested genera, further confounding rank-based analyses. These results underscore the indispensable role of phylogeny in understanding patterns of microbial diversity.
Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a
Authors: Xiao Dongchang , Liu Xiaoning , Zhang Min , Zou Min , Deng Qinqin , Sun Dayu , Bian Xuting , Cai Yulong , Guo Yanan , Liu Shuting , Li Shengguo , Shiang Evelyn , Zhong Hongyu , Cheng Lin , Xu Haiwei , Jin Kangxin , Xiang Mengqing 
Published: July 2018

AbstractInduced neural stem cells (iNSCs) reprogrammed from somatic cells have great potentials in cell replacement therapies and in vitro modeling of neural diseases. Direct conversion of fibroblasts into iNSCs has been shown to depend on a couple of key neural progenitor transcription factors (TFs), raising the question of whether such direct reprogramming can be achieved by non-neural progenitor TFs. Here we report that the non-neural progenitor TF Ptf1a alone is sufficient to directly reprogram mouse and human fibroblasts into self-renewable iNSCs capable of differentiating into functional neurons, astrocytes and oligodendrocytes, and improving cognitive dysfunction of Alzheimer’s disease mouse models when transplanted. The reprogramming activity of Ptf1a depends on its Notch-independent interaction with Rbpj which leads to subsequent activation of expression of TF genes and Notch signaling required for NSC specification, self-renewal, and homeostasis. Together, our data identify a non-canonical and safer approach to establish iNSCs for research and therapeutic purposes.
How nanoscale protein interactions determine the mesoscale dynamic organisation of bacterial outer membrane proteins
Authors: Chavent Matthieu , Duncan Anna L. , Rassam Patrice , Birkholz Oliver , Hélie Jean , Reddy Tyler , Beliaev Dmitry , Hambly Ben , Piehler Jacob , Kleanthous Colin , Sansom Mark S. P. 
Published: July 2018

AbstractThe spatiotemporal organisation of membranes is often characterised by the formation of large protein clusters. In Escherichia coli, outer membrane protein (OMP) clustering leads to OMP islands, the formation of which underpins OMP turnover and drives organisation across the cell envelope. Modelling how OMP islands form in order to understand their origin and outer membrane behaviour has been confounded by the inherent difficulties of simulating large numbers of OMPs over meaningful timescales. Here, we overcome these problems by training a mesoscale model incorporating thousands of OMPs on coarse-grained molecular dynamics simulations. We achieve simulations over timescales that allow direct comparison to experimental data of OMP behaviour. We show that specific interaction surfaces between OMPs are key to the formation of OMP clusters, that OMP clusters present a mesh of moving barriers that confine newly inserted proteins within islands, and that mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.
Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism
Authors: Zarrinpar Amir , Chaix Amandine , Xu Zhenjiang Z. , Chang Max W. , Marotz Clarisse A. , Saghatelian Alan , Knight Rob , Panda Satchidananda 
Published: July 2018

AbstractAntibiotic-induced microbiome depletion (AIMD) has been used frequently to study the role of the gut microbiome in pathological conditions. However, unlike germ-free mice, the effects of AIMD on host metabolism remain incompletely understood. Here we show the effects of AIMD to elucidate its effects on gut homeostasis, luminal signaling, and metabolism. We demonstrate that AIMD, which decreases luminal Firmicutes and Bacteroidetes species, decreases baseline serum glucose levels, reduces glucose surge in a tolerance test, and improves insulin sensitivity without altering adiposity. These changes occur in the setting of decreased luminal short-chain fatty acids (SCFAs), especially butyrate, and the secondary bile acid pool, which affects whole-body bile acid metabolism. In mice, AIMD alters cecal gene expression and gut glucagon-like peptide 1 signaling. Extensive tissue remodeling and decreased availability of SCFAs shift colonocyte metabolism toward glucose utilization. We suggest that AIMD alters glucose homeostasis by potentially shifting colonocyte energy utilization from SCFAs to glucose.
Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease
Authors: Zhang Xu , Deeke Shelley A. , Ning Zhibin , Starr Amanda E. , Butcher James , Li Jennifer , Mayne Janice , Cheng Kai , Liao Bo , Li Leyuan , Singleton Ruth , Mack David , Stintzi Alain , Figeys Daniel 
Published: July 2018

AbstractAlterations in gut microbiota have been implicated in the pathogenesis of inflammatory bowel disease (IBD), however factors that mediate the host–microbiota interactions remain largely unknown. Here we collected mucosal-luminal interface samples from a pediatric IBD inception cohort and characterized both the human and microbiota proteins using metaproteomics. We show that microbial proteins related to oxidative stress responses are upregulated in IBD cases compared to controls. In particular, we demonstrate that the expression of human proteins related to oxidative antimicrobial activities is increased in IBD cases and correlates with the alteration of microbial functions. Additionally, we reveal that many of these human proteins are present and show altered abundance in isolated free extracellular vesicles (EVs). Therefore, our study suggests that the alteration of intestinal EV proteomes is associated with the aberrant host–microbiota interactions in IBD.
Non-collinear spin states in bottom-up fabricated atomic chains
Authors: Steinbrecher Manuel , Rausch Roman , That Khai Ton , Hermenau Jan , Khajetoorians Alexander A. , Potthoff Michael , Wiesendanger Roland , Wiebe Jens 
Published: July 2018

AbstractNon-collinear spin states with unique rotational sense, such as chiral spin-spirals, are recently heavily investigated because of advantages for future applications in spintronics and information technology and as potential hosts for Majorana Fermions when coupled to a superconductor. Tuning the properties of such spin states, e.g., the rotational period and sense, is a highly desirable yet difficult task. Here, we experimentally demonstrate the bottom-up assembly of a spin-spiral derived from a chain of iron atoms on a platinum substrate using the magnetic tip of a scanning tunneling microscope as a tool. We show that the spin-spiral is induced by the interplay of the Heisenberg and Dzyaloshinskii-Moriya components of the Ruderman-Kittel-Kasuya-Yosida interaction between the iron atoms. The relative strengths and signs of these two components can be adjusted by the interatomic iron distance, which enables tailoring of the rotational period and sense of the spin-spiral.
Evidence for excessive osteoclast activation in SIRT6 null mice
Authors: Zhang Demao , Jing Junjun , Lou Feng , Li Ruimin , Ping Yilin , Yu Fanyuan , Wu Fanzi , Yang Xiao , Xu Ruoshi , Li Feifei , Wang Ke , Bai Mingru , Pi Caixia , Xie Jing , Zheng Liwei , Ye Ling , Zhou Xuedong 
Published: July 2018

AbstractSIRT6 is a NAD-dependent histone 3 deacetylase. SIRT6 null mice have been reported suffering osteopenia. However, the role of SIRT6 in bone resorption is still not well understood. In this study, we focused on the role of SIRT6 in osteoclast. We performed histological analysis on the femur, spine, alveolar bone and even tail of mutant mice, and found the bone mass is sharply decreased while the osteoclast activity is significantly increased. These phenotypes were further demonstrated by the osteoclast differentiation in cell-cultures with TRAP staining and Pit Resorption Assay. We next found the proliferation activity of mutant osteoclast precursors was increased, which might account for the enhanced osteoclast formation. The concentration of tartrate-resistant acid phosphatase 5b, a marker of osteoclast differentiation, was significantly higher in the mutant mice than control. Besides, the osteoclastogenic and NF-κB signaling related genes were significantly up-regulated. Moreover, osteoblast/osteoclast co-culture demonstrated that SIRT6 regulated osteoclast mainly through osteoblast paracrine manner, rather than osteoclast-autonomous behavior. Together, the enhanced osteoclast activation in SIRT6 null mice might be regulated by the hyperactive NF-κB signaling and the enhanced proliferation activity of osteoclast precursors through osteoblast paracrine manner at the cellular level.
Prevascularization of dermal substitutes with adipose tissue-derived microvascular fragments enhances early skin grafting
Authors: Frueh Florian S. , Später Thomas , Körbel Christina , Scheuer Claudia , Simson Anna C. , Lindenblatt Nicole , Giovanoli Pietro , Menger Michael D. , Laschke Matthias W. 
Published: July 2018

AbstractSplit-thickness skin grafts (STSG) are still the gold standard for the treatment of most skin defects. Hence, there is an ongoing need to improve this procedure. For this purpose, we herein analyzed dermal matrices seeded with adipose tissue-derived microvascular fragments (ad-MVF) in a bradythrophic wound model. In additional experiments, the matrices were covered with autologous STSG 10 days after implantation. Green fluorescence protein (GFP)+ ad-MVF were isolated from C57BL/6-Tg(CAG-EGFP)1Osb/J mice and seeded onto collagen-glycosaminoglycan matrices. Non-seeded and prevascularized matrices were implanted into full-thickness skin defects on the skull of CD1 nu/nu mice for 21 days. Vascularization, lymphangiogenesis and incorporation of the matrices were analyzed using photo-acoustic imaging, trans-illumination stereomicroscopy, histology, and immunohistochemistry. The survival rate of STSG was assessed by planimetry. After 21 days, the density of microvascular and lymphatic networks was significantly higher in prevascularized matrices when compared to controls. This was associated with an improved implant integration. Moreover, prevascularization with ad-MVF allowed successful autologous skin grafting already at day 10, while coverage of non-seeded controls at day 10 resulted in STSG necrosis. In conclusion, ad-MVF represent powerful vascularization units. Seeded on dermal substitutes, they accelerate and enhance the healing of full-thickness skin defects and allow early coverage with STSG.
Analysis of the influence of imaging-related uncertainties on cerebral aneurysm deformation quantification using a no-deformation physical flow phantom
Authors: Schetelig Daniel , Sedlacik Jan , Fiehler Jens , Frölich Andreas , Knopp Tobias , Sothmann Thilo , Waschkewitz Jonathan , Werner René 
Published: July 2018

AbstractCardiac-cycle related pulsatile aneurysm motion and deformation is assumed to provide valuable information for assessing cerebral aneurysm rupture risk. Accordingly, numerous studies addressed quantification of cerebral aneurysm wall motion and deformation. Most of them utilized in vivo imaging data, but image-based aneurysm deformation quantification is subject to pronounced uncertainties: unknown ground-truth deformation; image resolution in the order of the expected deformation; direct interplay between contrast agent inflow and image intensity. To analyze the impact of the uncertainties on deformation quantification, a multi-imaging modality ground-truth phantom study is performed. A physical flow phantom was designed that allowed simulating pulsatile flow through a variety of modeled cerebral vascular structures. The phantom was imaged using different modalities [MRI, CT, 3D-RA] and mimicking physiologically realistic flow conditions. Resulting image data was analyzed by an established registration-based approach for automated wall motion quantification. The data reveals severe dependency between contrast media inflow-related image intensity changes and the extent of estimated wall deformation. The study illustrates that imaging-related uncertainties affect the accuracy of cerebral aneurysm deformation quantification, suggesting that in vivo imaging studies have to be accompanied by ground-truth phantom experiments to foster data interpretation and to prove plausibility of the applied image analysis algorithms.
Force field adaptation does not alter space representation
Authors: Michel Carine , Bonnetain Lucie , Amoura Sarah , White Olivier 
Published: July 2018

AbstractPrism adaptation is a well-known model to study sensorimotor adaptive processes. It has been shown that following prism exposure, after-effects are not only restricted to the sensorimotor level but extend as well to spatial cognition. The main purpose of the present study was to investigate in healthy individuals whether expansion to spatial cognition is restricted to adaptive processes peculiar to prism adaptation or whether it occurs as well following other forms of adaptive process such as adaptation to a novel dynamic environment during pointing movements. Representational after-effects were assessed by the perceptual line bisection task before and after adaptation to a leftward or a rightward force field. The main results showed that adaptation developed at sensorimotor level but did not influence space representation. Our results have therefore a strong methodological impact for prospective investigations focusing on sensorimotor plasticity while sparing space cognition. These methodological considerations will be particulary relevant when addressing sensorimotor plasticity in patients with specific representational feature to preserve. The discussion highlights the differences between prism and dynamic adaptation that could explain the lack of after-effect on space representation following force field adaptation.
Sympathetic inputs regulate adaptive thermogenesis in brown adipose tissue through cAMP-Salt inducible kinase axis
Authors: Paulo Esther , Wu Dongmei , Wang Yangmeng , Zhang Yun , Wu Yixuan , Swaney Danielle L. , Soucheray Margaret , Jimenez-Morales David , Chawla Ajay , Krogan Nevan J. , Wang Biao 
Published: July 2018

AbstractVarious physiological stimuli, such as cold environment, diet, and hormones, trigger brown adipose tissue (BAT) to produce heat through sympathetic nervous system (SNS)- and β-adrenergic receptors (βARs). The βAR stimulation increases intracellular cAMP levels through heterotrimeric G proteins and adenylate cyclases, but the processes by which cAMP modulates brown adipocyte function are not fully understood. Here we described that specific ablation of cAMP production in brown adipocytes led to reduced lipolysis, mitochondrial biogenesis, uncoupling protein 1 (Ucp1) expression, and consequently defective adaptive thermogenesis. Elevated cAMP signaling by sympathetic activation inhibited Salt-inducible kinase 2 (Sik2) through protein kinase A (PKA)-mediated phosphorylation in brown adipose tissue. Inhibition of SIKs enhanced Ucp1 expression in differentiated brown adipocytes and Sik2 knockout mice exhibited enhanced adaptive thermogenesis at thermoneutrality in an Ucp1-dependent manner. Taken together, our data indicate that suppressing Sik2 by PKA-mediated phosphorylation is a requisite for SNS-induced Ucp1 expression and adaptive thermogenesis in BAT, and targeting Sik2 may present a novel therapeutic strategy to ramp up BAT thermogenic activity in humans.
Sequential Effects in SNARC
Authors: Gökaydin Dinis , Brugger Peter , Loetscher Tobias 
Published: July 2018

AbstractSmall and large numbers are typically associated with the left and right side of space, respectively. We conducted an online version of the classical Spatial-Numerical Association of Response Codes (SNARC) paradigm in 604 subjects in order to analyse how previous trials and responses affect SNARC. Our results point to a strong inversion of number-space associations (left/large and right/small) when the last trial was incoherent - i.e. when a response with the left hand was made to a large number or vice-versa. In addition, we demonstrate that the congruency of trials beyond just the last two can influence SNARC, providing empirical support for an important assumption of a working memory account of spatial-numerical associations. Finally, we show that sequential effects in SNARC can be captured by a simple exponential filter, known to underpin sequential effects across a range of stimuli detection and perceptual two-alternative forced choice decision tasks. Our findings point to universal mechanisms responsible for the processing of sequences from perception to cognition.
Cellular-resolution 3D virtual histology of human coronary arteries using x-ray phase tomography
Authors: Vågberg William , Persson Jonas , Szekely Laszlo , Hertz Hans M. 
Published: July 2018

AbstractHigh-spatial-resolution histology of coronary artery autopsy samples play an important role for understanding heart disease such as myocardial infarction. Unfortunately, classical histology is often destructive, has thick slicing, requires extensive sample preparation, and is time-consuming. X-ray micro-CT provides fast nondestructive 3D imaging but absorption contrast is often insufficient, especially for observing soft-tissue features with high resolution. Here we show that propagation-based x-ray phase-contrast tomography has the resolution and contrast to image clinically relevant soft-tissue features in intact coronary artery autopsy samples with cellular resolution. We observe microscopic lipid-rich plaques, individual adipose cells, ensembles of few foam cells, and the thin fibrous cap. The method relies on a small-spot laboratory x-ray microfocus source, and provides high-spatial resolution in all three dimensions, fast data acquisition, minimum sample distortion and requires no sample preparation.
Relative fat mass (RFM) as a new estimator of whole-body fat percentage ─ A cross-sectional study in American adult individuals
Authors: Woolcott Orison O. , Bergman Richard N. 
Published: July 2018

AbstractHigh whole-body fat percentage is independently associated with increased mortality. We aimed to identify a simple anthropometric linear equation that is more accurate than the body mass index (BMI) to estimate whole-body fat percentage among adult individuals. National Health and Nutrition Examination Survey (NHANES) 1999–2004 data (n = 12,581) were used for model development and NHANES 2005–2006 data (n = 3,456) were used for model validation. From the 365 anthropometric indices generated, the final selected equation was as follows: 64 − (20 × height/waist circumference) + (12 × sex), named as the relative fat mass (RFM); sex = 0 for men and 1 for women. In the validation dataset, compared with BMI, RFM better predicted whole-body fat percentage, measured by dual energy X-ray absorptiometry (DXA), among women and men. RFM showed better accuracy than the BMI and had fewer false negative cases of body fat-defined obesity among women and men. RFM reduced total obesity misclassification among all women and all men and, overall, among Mexican-Americans, European-Americans and African-Americans. In the population studied, the suggested RFM was more accurate than BMI to estimate whole-body fat percentage among women and men and improved body fat-defined obesity misclassification among American adult individuals of Mexican, European or African ethnicity.
Genetic diversity and selection signatures of the beef ‘Charolais de Cuba’ breed
Authors: Rodriguez-Valera Yoel , Renand Gilles , Naves Michel , Fonseca-Jiménez Yidix , Moreno-Probance Teresa Inés , Ramos-Onsins Sebastian , Rocha Dominique , Ramayo-Caldas Yuliaxis 
Published: July 2018

AbstractIn this study, we used BovineSNP50 Genotyping BeadChip data to estimate the structure, putative ancestral origin as well as to identify regions with selective sweeps that may have had an important role in the adaptation to tropical conditions of the ‘Charolais de Cuba’ (CHCU) breed. According to a principal component analysis, CHCU samples cluster together with taurine breeds with an estimated 93% oftaurusancestral alleles. Despite the short period since importation, we detected differentiation (Fst = 0.049) between the French Charolaise (CHA) and CHCU. However, CHA breed was the closest breed to CHCU followed by other hybrids breed with a clear CHA origin. Linkage disequilibrium (r2) decay tends to be lower in CHCU compared to CHA probably due to a less intense artificial selection programs of CHCU. Signals of recent adaptation to tropical conditions between CHCU and CHA were identified. Genes mapping within those regions reflect different functions related to immunity, metabolic changes and heat tolerance (CHCU) and muscle development and meat quality (CHA) that may have had an important role in the phenotypic differentiation of these breeds. Further studies will expand our knowledge on the molecular basis of adaptation of cattle to tropical conditions and molecular process associated with meat quality traits.