bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral microbiome diversity in chimpanzees from Gombe National Park
Authors: Ozga Andrew T. , Gilby Ian , Nockerts Rebecca S. , Wilson Michael L. , Pusey Anne , Stone Anne C. 
Published: November 2019

AbstractHistoric calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.
Spontaneous eye blink rate predicts individual differences in exploration and exploitation during reinforcement learning
Authors: Van Slooten Joanne C. , Jahfari Sara , Theeuwes Jan 
Published: November 2019

AbstractSpontaneous eye blink rate (sEBR) has been linked to striatal dopamine function and to how individuals make value-based choices after a period of reinforcement learning (RL). While sEBR is thought to reflect how individuals learn from the negative outcomes of their choices, this idea has not been tested explicitly. This study assessed how individual differences in sEBR relate to learning by focusing on the cognitive processes that drive RL. Using Bayesian latent mixture modelling to quantify the mapping between RL behaviour and its underlying cognitive processes, we were able to differentiate low and high sEBR individuals at the level of these cognitive processes. Further inspection of these cognitive processes indicated that sEBR uniquely indexed explore-exploit tendencies during RL: lower sEBR predicted exploitative choices for high valued options, whereas higher sEBR predicted exploration of lower value options. This relationship was additionally supported by a network analysis where, notably, no link was observed between sEBR and how individuals learned from negative outcomes. Our findings challenge the notion that sEBR predicts learning from negative outcomes during RL, and suggest that sEBR predicts individual explore-exploit tendencies. These then influence value sensitivity during choices to support successful performance when facing uncertain reward.
A Methodology to Quantify the Geometrical Complexity of the Abdominal Aortic Aneurysm
Authors: Kyriakou Faidon , Dempster William , Nash David 
Published: November 2019

AbstractThe abdominal aortic aneurysm (AAA) anatomy influences the technical success of the endovascular aneurysm repair (EVAR), yet very few data regarding the aortic tree angles exist in the literature. This poses great limitations in the numerical analyses of endografts, constraining their design improvement as well as the identification of their operational limitations. In this study, a matrix Φ of 10 angles was constructed for the description of the pathological region and was implemented on a large dataset of anatomies. More specifically, computed tomography angiographies from 258 patients were analysed and 10 aortic angles were calculated per case, able to adequately describe the overall AAA shape. 9 dimensional variables (i.e. diameters and lengths) were also recorded. The median and extreme values of these variables were computed providing a detailed quantification of the geometrical landscape of the AAA. Moreover, statistical analysis showed that the identified angles presented no strong correlation with each other while no lateral or anterior/posterior symmetry of the AAA was identified. These findings suggest that endograft designers are free to construct any extreme case-studies with the values provided in a mix-and-match manner. This strategy can have a powerful effect in EVAR stent graft designing, as well as EVAR planning.
The type-reproduction number of sexually transmitted infections through heterosexual and vertical transmission
Authors: Ito Hiromu , Yamamoto Taro , Morita Satoru 
Published: November 2019

AbstractMultiple sexually transmitted infections (STIs) have threatened human health for centuries. Most STIs spread not only through sexual (horizontal) transmission but also through mother-to-child (vertical) transmission. In a previous work (Itoet al. 2019), we studied a simple model including heterosexual and mother-to-child transmission and proposed a formulation of the basic reproduction number over generations. In the present study, we improved the model to take into account some factors neglected in the previous work: adult mortality from infection, infant mortality caused by mother-to-child transmission, infertility or stillbirth caused by infection, and recovery with treatment. We showed that the addition of these factors has no essential effect on the theoretical formulation. To study the characteristics of the epidemic threshold, we derived analytical formulas for three type-reproduction numbers for adult men, adult women and juveniles. Our result indicates that if an efficient vaccine exists for a prevalent STI, vaccination of females is more effective for containment of the STI than vaccination of males, because the type-reproduction number for adult men is larger than that for adult women when they are larger than one.
Histone deacetylase inhibitors with high in vitro activities against Plasmodium falciparum isolates collected from Gabonese children and adults
Authors: Koehne Erik , Kreidenweiss Andrea , Zoleko Manego Rella , McCall Matthew , Mombo-Ngoma Ghyslain , Mackwitz Marcel Karl Walter , Hansen Finn K. , Held Jana 
Published: November 2019

AbstractHistone deacetylase (HDAC) enzymes are targets for the development of antimalarial drugs with a different mode of action to established antimalarials. Broad-spectrum HDAC-inhibitors show high potency against Plasmodium falciparum, but displayed some toxicity towards human cells. Inhibitors of human HDAC6 are new drug candidates with supposed reduced toxicity to human cells and favorable activities against laboratory P. falciparum strains. We investigated the potency of 12 peptoid-based HDAC-inhibitors against asexual stages of P. falciparum clinical isolates. Parasites representing different genetic backgrounds were isolated from adults and children with uncomplicated malaria in Gabon. Clinical studies on (non-HDAC-inhibitors) antimalarials, moreover, found lower drug efficacy in children, mainly attributed to acquired immunity with age in endemic areas. Therefore, we compared the in vitro sensitivity profiles of adult- and child-derived isolates to antimalarials (HDAC and standard drugs). All HDAC-inhibitors showed 50% inhibitory concentrations at nanomolar ranges with higher activities than the FDA approved reference HDAC-inhibitor SAHA. We propose peptoid-based HDAC6-inhibitors to be lead structures for further development as antimalarial chemotherapeutics. Our results further suggest no differences in activity of the tested antimalarials between P. falciparum parasites isolated from children and adults.
Multisensory integration in virtual interactions with distant objects
Authors: Kirsch Wladimir , Kunde Wilfried 
Published: November 2019

AbstractStatistically optimal integration of multimodal signals is known to take place in direct interactions with environmental objects. In the present study we tested whether the same mechanism is responsible for perceptual biases observed in a task, in which participants enclose visual objects by manually controlled visual cursors. We manipulated the relative reliability of visual object information and measured the impact of body-related information on object perception as well as the perceptual variability. The results were qualitatively consistent with statistically optimal sensory integration. However, quantitatively, the observed bias and variability measures systematically differed from the model predictions. This outcome indicates a compensatory mechanism similar to the reliability-based weighting of multisensory signals which could underlie action’s effects in visual perception reported in diverse context conditions.
Unsupervised machine-learning classification of electrophysiologically active electrodes during human cognitive task performance
Authors: Saboo Krishnakant V. , Varatharajah Yogatheesan , Berry Brent M. , Kremen Vaclav , Sperling Michael R. , Davis Kathryn A. , Jobst Barbara C. , Gross Robert E. , Lega Bradley , Sheth Sameer A. , Worrell Gregory A. , Iyer Ravishankar K. , Kucewicz Michal T. 
Published: November 2019

AbstractIdentification of active electrodes that record task-relevant neurophysiological activity is needed for clinical and industrial applications as well as for investigating brain functions. We developed an unsupervised, fully automated approach to classify active electrodes showing event-related intracranial EEG (iEEG) responses from 115 patients performing a free recall verbal memory task. Our approach employed new interpretable metrics that quantify spectral characteristics of the normalized iEEG signal based on power-in-band and synchrony measures. Unsupervised clustering of the metrics identified distinct sets of active electrodes across different subjects. In the total population of 11,869 electrodes, our method achieved 97% sensitivity and 92.9% specificity with the most efficient metric. We validated our results with anatomical localization revealing significantly greater distribution of active electrodes in brain regions that support verbal memory processing. We propose our machine-learning framework for objective and efficient classification and interpretation of electrophysiological signals of brain activities supporting memory and cognition.
Defective Proliferation and Osteogenic Potential with Altered Immunoregulatory phenotype of Native Bone marrow-Multipotential Stromal Cells in Atrophic Fracture Non-Union
Authors: El-Jawhari Jehan J. , Kleftouris George , El-Sherbiny Yasser , Saleeb Hany , West Robert M. , Jones Elena , Giannoudis Peter V. 
Published: November 2019

AbstractBone marrow-Multipotential stromal cells (BM-MSCs) are increasingly used to treat complicated fracture healing e.g., non-union. Though, the quality of these autologous cells is not well characterized. We aimed to evaluate bone healing-related capacities of non-union BM-MSCs. Iliac crest-BM was aspirated from long-bone fracture patients with normal healing (U) or non-united (NU). Uncultured (native) CD271highCD45low cells or passage-zero cultured BM-MSCs were analyzed for gene expression levels, and functional assays were conducted using culture-expanded BM-MSCs. Blood samples were analyzed for serum cytokine levels. Uncultured NU-CD271highCD45low cells significantly expressed fewer transcripts of growth factor receptors, EGFR, FGFR1, and FGRF2 than U cells. Significant fewer transcripts of alkaline phosphatase (ALPL), osteocalcin (BGLAP), osteonectin (SPARC) and osteopontin (SPP1) were detected in NU-CD271highCD45low cells. Additionally, immunoregulation-related markers were differentially expressed between NU- and U-CD271highCD45low cells. Interestingly, passage-zero NU BM-MSCs showed low expression of immunosuppressive mediators. However, culture-expanded NU and U BM-MSCs exhibited comparable proliferation, osteogenesis, and immunosuppression. Serum cytokine levels were found similar for NU and U groups. Collectively, native NU-BM-MSCs seemed to have low proliferative and osteogenic capacities; therefore, enhancing their quality should be considered for regenerative therapies. Further research on distorted immunoregulatory molecules expression in BM-MSCs could potentially benefit the prediction of complicated fracture healing.
Evolution of native defects in ZnO nanorods irradiated with hydrogen ion
Authors: Wu Tengfei , Wang Aiji , Zheng Li , Wang Guangfu , Tu Qingyun , Lv Bowen , Liu Zilin , Wu Zhenglong , Wang Yinshu 
Published: November 2019

AbstractThis work reports the study on the evolution of native defects in ZnO nanorods irradiated with hydrogen ion. ZnO nanorod arrays grown vertically on silicon substrates were irradiated by 180 keV H+ ions to a total fluence of 8.50 × 1015 ions/cm2. The X-ray diffraction spectra, photoluminescence spectra before and after irradiation and the real-time ionoluminescence spectra of the nanorod arrays during the irradiating process were measured. Formation and evolution of defects during H+ ion irradiation and effects of irradiation on the crystal structure and optical property were studied. Blue shift of exciton emission, shrink of lattice c and improvement of the crystallinity of ZnO nanorods after irradiation were observed. Simple surface passivation of the nanorods could improve the radiation resistance. Formation and evolution of the defects during H+ ion irradiation could be clarified into four stages and the related models are provided.
Lupus-like Disease in FcγRIIB−/− Mice Induces Osteopenia
Authors: Visitchanakun Peerapat , Saiworn Worasit , Jongwattanapisan Prapaporn , Leelahavanichkul Asada , Pisitkun Prapaporn , Lotinun Sutada 
Published: November 2019

AbstractOsteoporotic fracture is a major cause of morbidity in patients with systemic lupus erythematosus (SLE). Mice lacking Fc gamma receptor IIb (FcγRIIB) spontaneously develop lupus-like disease or SLE at 6-month-old. The aim of this study was to investigate whether FcγRIIB deletion induces osteopenia. μCT analysis indicated that deleting FcγRIIB did not affect cancellous bone microarchitecture in 3-month-old mice in which SLE had not yet developed. However, 6- and 10-month-old FcγRIIB−/− males that developed an SLE-like phenotype were osteopenic and FcγRIIB deletion resulted in decreased cancellous bone volume. Histomorphometry confirmed a significant decrease in cancellous bone volume in 6- and 10-month-old FcγRIIB−/− males. The osteoclast number was increased without any change in osteoblast number. In vitro assays indicated that deleting FcγRIIB increased osteoclast differentiation while alkaline phosphatase activity and mineralization were unaltered. These changes were associated with increases in steady-state mRNA levels for the osteoclast marker genes Trap and Ctsk. Moreover, FcγRIIB−/− mice had higher level of serum TNFα, a proinflammatory cytokine. A soluble TNFα receptor, etanercept, prevented cancellous bone loss in FcγRIIB−/− mice. Our results indicate that FcγRIIB indirectly regulates cancellous bone homeostasis following SLE development. FcγRIIB deletion induces inflammatory bone loss due to increased TNFα-mediated bone resorption without any change in bone formation in mice with SLE-like syndrome.
An Early Intestinal Cancer Prediction Algorithm Based on Deep Belief Network
Authors: Wan Jing-Jing , Chen Bo-Lun , Kong Yi-Xiu , Ma Xing-Gang , Yu Yong-Tao 
Published: November 2019

AbstractThe incidence of colorectal cancer (colorectal cancer, CRC) in China has increased in recent years, and its mortality rate has become one of the highest among all cancers. CRC also increasingly affects people’s health and quality of life, and the workloads of medical doctors have further increased due to the lack of sufficient medical resources in China. The goal of this study was to construct an automated expert system using a deep learning technique to predict the probability of early stage CRC based on the patient’s case report and the patient’s attributes. Compared with previous prediction methods, which are either based on sophisticated examinations or have high computational complexity, this method is shown to provide valuable information such as suggesting potentially important early signs to assist in early diagnosis, early treatment and prevention of CRC, hence helping medical doctors reduce the workloads of endoscopies and other treatments.
Bone marrow adipose tissue does not express UCP1 during development or adrenergic-induced remodeling
Authors: Craft Clarissa S. , Robles Hero , Lorenz Madelyn R. , Hilker Eric D. , Magee Kristann L. , Andersen Thomas L. , Cawthorn William P. , MacDougald Ormond A. , Harris Charles A. , Scheller Erica L. 
Published: November 2019

AbstractAdipocytes within the skeleton are collectively termed bone marrow adipose tissue (BMAT). BMAT contributes to peripheral and local metabolism, however, its capacity for cell-autonomous expression of uncoupling protein 1 (UCP1), a biomarker of beige and brown adipogenesis, remains unclear. To overcome this, Ucp1-Cre was used to drive diphtheria toxin expression in cells expressing UCP1 (Ucp1Cre+/DTA+). Despite loss of brown adipose tissue, BMAT volume was not reduced in Ucp1Cre+/DTA+ mice. Comparably, in mTmG reporter mice (Ucp1Cre+/mTmG+), Ucp1-Cre expression was absent from BMAT in young (3-weeks) and mature (16-weeks) male and female mice. Further, β3-agonist stimulation failed to induce Ucp1-Cre expression in BMAT. This demonstrates that BMAT adipocytes are not UCP1-expressing beige/brown adipocytes. Thus, to identify novel and emerging roles for BMAT adipocytes in skeletal and whole-body homeostasis, we performed gene enrichment analysis of microarray data from adipose tissues of adult rabbits. Pathway analysis revealed genetic evidence for differences in BMAT including insulin resistance, decreased fatty acid metabolism, and enhanced contributions to local processes including bone mineral density through candidate genes such as osteopontin. In sum, this supports a paradigm by which BMAT adipocytes are a unique subpopulation that is specialized to support cells within the skeletal and hematopoietic niche.
Deterministic and time resolved thermo-magnetic switching in a nickel nanowire
Authors: Proenca M. P. , Muñoz M. , Villaverde I. , Migliorini A. , Raposo V. , Lopez-Diaz L. , Martinez E. , Prieto J. L. 
Published: November 2019

AbstractHeating a ferromagnetic material is often perceived as detrimental for most applications. This is indeed the case for modern nano-scaled spintronic devices which are operated solely (at least ideally) by an electric current. Heat is a by-product of the current-driven operation and it deteriorates many functionalities of the device. A large scientific and technological effort is devoted these days to avoid heat in modern magnetic nano devices. Here we show that heat can be used to provide an additional and useful degree of freedom in the control of the local magnetization at the nanoscale. In a ferromagnetic nanowire, temperature is used to induce a magnetic switching through a perfectly deterministic mechanism. The nucleation of the magnetic domain walls that triggers the switching can be achieved at a field considerably smaller than the nucleation field and, importantly, the exact moment of the magnetic switching can be pre-determined with nanosecond precision by controlling the power delivered locally to the switching area. With the help of micromagnetic simulations and a theoretical model, we provide an accurate explanation of how this deterministic thermo-magnetic switching operates. The concepts described in this work may lead to an increased functionality in magnetic nano-devices based on magnetic domain walls.
Better monsoon precipitation in coupled climate models due to bias compensation
Authors: Yang Ben , Zhang Yaocun , Qian Yun , Song Fengfei , Leung L. Ruby , Wu Peili , Guo Zhun , Lu Yixiong , Huang Anning 
Published: November 2019

AbstractMonsoon precipitation is a dominant driver of floods and droughts over East Asia, which affect billions of people. The lack of air-sea coupling has been blamed for the poor East Asian monsoon precipitation simulations in atmosphere-only models because coupled models generally do better. Based on analysis of simulations from 18 pairs of atmosphere-only and coupled models from the Coupled Model Intercomparison Project phase 5, we show that the improved monsoon precipitation in coupled models is largely due to compensation from sea surface temperature (SST) biases that originate from atmosphere model biases. Such bias compensation is demonstrated using surface energy budgets and a process chain to improve both the climatological mean and interannual precipitation patterns in coupled models. Models with larger atmosphere model errors benefit more from coupling and models with smaller errors benefit less. Hence the key to simultaneously improving the simulations of East Asian monsoon precipitation and SST is a better atmosphere model.
Many-body effects in doped WS2 monolayer quantum disks at room temperature
Authors: Lin T. N. , Santiago S. R. M. , Caigas S. P. , Yuan C. T. , Lin T. Y. , Shen J. L. , Chen Y. F. 
Published: November 2019

AbstractDue to strong Coulomb interactions, reduced screening effects, and quantum confinement, transition-metal dichalcogenide (TMD) monolayer quantum disks (MQDs) are expected to exhibit large exciton binding energy, which is beneficial for the investigation of many-body physics at room temperature. Here, we report the first observations of room-temperature many-body effects in tungsten disulfide (WS2) MQDs by both optical measurements and theoretical studies. The band-gap renormalization in WS2 MQDs was about 250 ± 15 meV as the carrier density was increased from 0.6(±0.2) × 1012 to 8.3(±0.2) × 1012 cm−2. We observed a striking exciton binding energy as large as 990 ± 30 meV at the lowest carrier density, which is larger than that in WS2 monolayers. The huge exciton binding energy in WS2 MQDs is attributed to the extra quantum confinement in the lateral dimension. The band-gap renormalization and exciton binding energies are explained using efficient reduced screening. On the basis of the Debye screening formula, the Mott density in WS2 MQDs was estimated to be ~3.95 × 1013 cm−2. Understanding and manipulation of the many-body effects in two-dimensional materials may open up new possibilities for developing exciton-based optoelectronic devices.