bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hill number as a bacterial diversity measure framework with high-throughput sequence data
Authors: Kang Sanghoon , Rodrigues Jorge L. M. , Ng Justin P. , Gentry Terry J. 
Published: November 2016

AbstractBacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (Na), to control the variability associated with rare taxa by differentially weighing them. Here, we investigated Hill number as a framework for microbial diversity measure using a taxa-accmulation curve (TAC) with soil bacterial community data from two distinct studies by 454 pyrosequencing. The reliable biodiversity estimation was obtained when an increase in Hill number arose as the coverage became stable in TACs for a ≥ 1. In silico analysis also indicated that a certain level of sampling depth was desirable for reliable biodiversity estimation. Thus, in order to attain bacterial diversity from second generation sequencing, Hill number can be a good diversity framework with given sequencing depth, that is, until technology is further advanced and able to overcome the under- and random-sampling issues of the current sequencing approaches.
Maternal high-fat diet prevents developmental programming by early-life stress
Authors: Rincel M , Lépinay A L , Delage P , Fioramonti J , Théodorou V S , Layé S , Darnaudéry M 
Published: November 2016

AbstractAnxiety disorders and depression are well-documented in subjects exposed to adverse childhood events. Recently, maternal obesity and/or maternal consumption of high-fat diets (HFD) have been also proposed as risk factors for offspring mental health. Here using an animal model in rats, we explored the combinatorial effects of a maternal HFD (40% of energy from fat without impact on maternal weight; during gestation and lactation) and maternal separation (MS) in offspring. In the prefrontal cortex (PFC) of pups, MS led to changes in the expression of several genes such asBdnf(brain derived neurotrophic factor),5HT-r1a(serotonin receptor 1a) andRest4(neuron-restrictive silencer element, repressor element 1, silencing transcription factor (Rest), splicing variant 4). Surprisingly, perinatal HFD strongly attenuated the developmental alterations induced by MS. Furthermore, maternal HFD totally prevented the endophenotypes (anxiety, spatial memory, social behavior, hypothalamic–pituitary–adrenal (HPA) axis response to stress, hippocampal neurogenesis and visceral pain) associated with MS at adulthood. Finally, we also demonstrated that HFD intake reduced anxiety and enhanced maternal care in stressed dams. Overall, our data suggest that a HFD restricted to gestation and lactation, which did not lead to overweight in dams, had limited effects in unstressed offspring, highlighting the role of maternal obesity, rather than fat exposureper se,on brain vulnerability during development.
Towards designing new nano-scale protein architectures
Authors: Aupič Jana , Lapenta Fabio , Strmšek Žiga , Jerala Roman 
Published: November 2016

The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design. This review offers an overview on rational and computational design approaches focusing on the main achievements of novel protein nanostructure design.
Isoflurane-Associated Mydriasis Mimicking Blown Pupils in a Patient Treated in a Neurointensive Care Unit
Authors: Korf Eva , Tronnier Volker , Gliemroth Jan , Küchler Jan 
Published: November 2016

AbstractWe report a misinterpretation of bilateral mydriasis as blown pupils related to elevated intracranial pressure (ICP) under volatile sedation with isoflurane (Anesthetic Conserving Device [AnaConDa], Hudson RCI, Uppland Vasby, Sweden) in a 59-year-old patient with a severe traumatic brain injury with frontal contusion. The patient showed bilateral mydriasis and a missing light reflex 8 hours after changing sedation from intravenous treatment with midazolam and esketamine to volatile administration of isoflurane. Because cranial computed tomography ruled out signs of cerebral herniation, we assumed the bilateral mydriasis was caused by isoflurane and reduced the isoflurane supply. Upon this reduction the mydriasis regressed, suggesting the observed mydriasis was related to an overdose of isoflurane. Intensivists should be aware of the reported phenomenon to avoid unnecessary diagnostic investigations that might harm the patient. We recommend careful control of the isoflurane dose when fixed and dilated pupils appear in patients without other signs of elevated ICP.
EGFR signaling is critical for maintaining the superficial layer of articular cartilage and preventing osteoarthritis initiation
Authors: Jia Haoruo , Ma Xiaoyuan , Tong Wei , Doyran Basak , Sun Zeyang , Wang Luqiang , Zhang Xianrong , Zhou Yilu , Badar Farid , Chandra Abhishek , Lu X. Lucas , Xia Yang , Han Lin , Enomoto-Iwamoto Motomi , Qin Ling 
Published: November 2016

SignificanceThe uppermost superficial zone of articular cartilage plays multifaceted roles in maintaining cartilage structure, function, and mechanical properties and in preventing cartilage degeneration during osteoarthritis initiation. However, its regulation by growth factors and hormones is still largely unknown. Here we report that EGFR signaling is an important growth factor pathway that maintains superficial chondrocyte number, promotes boundary lubricant secretion and cartilage surface lubrication, and stimulates mechanical strength of articular cartilage. Reduction in EGFR activity leads to structurally, functionally, and mechanically compromised articular cartilage during development and drastically accelerates cartilage degeneration under normal and surgically induced osteoarthritis conditions. Thus, our studies strongly suggest that targeting cartilage surface EGFR signaling should be considered as a novel direction for osteoarthritis treatment.
β-Arrestin mediates the Frank–Starling mechanism of cardiac contractility
Authors: Abraham Dennis M. , Davis Robert T. , Warren Chad M. , Mao Lan , Wolska Beata M. , Solaro R. John , Rockman Howard A. 
Published: November 2016

Significance
The Frank–Starling law of the heart describes the heart’s ability to enhance contractility in response to increased cardiac filling. This property is fundamental to how humans maintain cardiovascular function in response to changes in circulating blood volume, and is regulated by enhanced calcium sensitivity of myofilaments with biomechanical stretch. The mechanism of how biomechanical stretch leads to changes in the myofilament calcium sensitivity remains poorly understood. Using genetic and pharmacologic approaches, we show that β-arrestin and the angiotensin II type I receptor act as crucial molecular regulators of the Frank–Starling law of the heart. This work identifies β-arrestins as important regulators of this fundamental principle of cardiac contractility.
Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants
Authors: Yue Kan , Huang Mingjun , Marson Ryan L. , He Jinlin , Huang Jiahao , Zhou Zhe , Wang Jing , Liu Chang , Yan Xuesheng , Wu Kan , Guo Zaihong , Liu Hao , Zhang Wei , Ni Peihong , Wesdemiotis Chrys , Zhang Wen-Bin , Glotzer Sharon C. , Cheng Stephen Z. D. 
Published: November 2016

Significance
How far can we push self-assembly toward unusual nanostructures? Frank–Kasper and quasicrystal phases represent unconventional phases of ordered spheroids originally identified in metal alloys. We report that Frank–Kasper and quasicrystal phases and their transition sequence are observed in one-component giant surfactants by introducing variations in molecular geometry. Both X-ray scattering and electron microscopy techniques are used to identify the self-assembled nanostructures. Combining molecular dynamics simulations, we attribute the appearance of these phases to molecular geometry as a result of tail number variation. Our findings lay the foundation for rational design of unconventional soft-matter phases and for exploiting them for unusual properties and functions.
Stretchable multichannel antennas in soft wireless optoelectronic implants for optogenetics
Authors: Park Sung Il , Shin Gunchul , McCall Jordan G. , Al-Hasani Ream , Norris Aaron , Xia Li , Brenner Daniel S. , Noh Kyung Nim , Bang Sang Yun , Bhatti Dionnet L. , Jang Kyung-In , Kang Seung-Kyun , Mickle Aaron D. , Dussor Gregory , Price Theodore J. , Gereau Robert W. , Bruchas Michael R. , Rogers John A. 
Published: November 2016

Significance
Soft, multichannel antennas enable wireless, battery-free operation of fully implantable optoelectronic systems designed for use in studies of brain function. These systems support independent, remote control of multiple light-emitting diodes that inject into targeted regions of the deep brain, where they separately stimulate activity in genetically and spatially discrete neural circuits, via the use of the techniques of optogenetics. These capabilities represent significant advancements over alternative technology approaches for this important branch of neuroscience research. In vivo studies using optimized systems demonstrate wireless control of two different brain regions and distinct activation of subpopulations of neurons using separately activated light sources associated with these subdermal devices.
TNFα-stimulated gene-6 (TSG6) activates macrophage phenotype transition to prevent inflammatory lung injury
Authors: Mittal Manish , Tiruppathi Chinnaswamy , Nepal Saroj , Zhao You-Yang , Grzych Dagmara , Soni Dheeraj , Prockop Darwin J. , Malik Asrar B. 
Published: November 2016

SignificanceWe found that TNFα-stimulated gene-6 (TSG6), a secreted 30-kDa immunomodulatory protein, resolved LPS-induced inflammatory lung injury by shifting macrophages from a proinflammatory to an anti-inflammatory phenotype. Macrophages from mice genetically deficient in TSG6 failed to transition, demonstrating the essential role of TSG6 in mediating macrophage plasticity. The finding that TSG6 induced the marked transition in anti-inflammatory macrophages lays the foundation for its therapeutic application.
Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity
Authors: Charlop-Powers Zachary , Pregitzer Clara C. , Lemetre Christophe , Ternei Melinda A. , Maniko Jeffrey , Hover Bradley M. , Calle Paula Y. , McGuire Krista L. , Garbarino Jeanne , Forgione Helen M. , Charlop-Powers Sarah , Brady Sean F. 
Published: November 2016

Significance
Bacterial natural products (NPs) have served as inspiration for many therapeutics. The hunt for new bioactive NPs has led to a global search for natural ecosystems from which bacteria can be cultured. Here, we used NP-focused metagenome sequencing to explore biosynthetic diversity in urban park soil of New York City. Our analyses reveal rich biosynthetic diversity in these microbiomes and predict that gene clusters encoding many clinically approved NPs families discovered using bacteria cultured from around the world are actually present in the soil microbiomes of a single city. Contrary to traditional NP discovery efforts that involve shallow explorations of diverse environments, our data suggest that a deeper exploration of local microbiomes may prove equally, if not, more productive.
Tau prions from Alzheimer’s disease and chronic traumatic encephalopathy patients propagate in cultured cells
Authors: Woerman Amanda L. , Aoyagi Atsushi , Patel Smita , Kazmi Sabeen A. , Lobach Iryna , Grinberg Lea T. , McKee Ann C. , Seeley William W. , Olson Steven H. , Prusiner Stanley B. 
Published: November 2016

Significance
The progressive nature of neurodegenerative diseases is due to the spread of prions, misfolded infectious proteins, in the brain. In tauopathies, the protein tau misfolds, causing several diseases, including Alzheimer’s disease (AD) and chronic traumatic encephalopathy (CTE). Here we created a panel of mammalian cell lines expressing a fragment of tau fused to yellow fluorescent protein. Each cell line selectively detects tau prions that are misfolded into self-propagating conformations; such cells permit identification of minute differences among tauopathies. For example, tau prions in AD and CTE are distinct from prions in other tauopathies such as Pick’s disease and progressive supranuclear palsy. These insights are likely to contribute to the development of future therapeutics.
Supramolecular PEGylation of biopharmaceuticals
Authors: Webber Matthew J. , Appel Eric A. , Vinciguerra Brittany , Cortinas Abel B. , Thapa Lavanya S. , Jhunjhunwala Siddharth , Isaacs Lyle , Langer Robert , Anderson Daniel G. 
Published: November 2016

Significance
Pharmaceutical practice has transitioned away from small-molecule drugs to the use of biomolecules (peptides, proteins, and antibodies). Where formulation of small molecules focused primarily on solubility, biopharmaceuticals introduced an array of complications due to their more complex secondary and tertiary structures, contributing to concerns surrounding aggregation and denaturation over time in formulation. Here, we outline an approach using noncovalent supramolecular affinity to endow biopharmaceuticals with a polymer known to inhibit protein aggregation and improve solubility. This method stands in contrast to similar approaches to covalently graft the same polymer onto the protein, instead offering a broadly useful and modular formulation excipient that can be combined with authentic unmodified protein drugs to extend shelf life.
Zika virus cell tropism in the developing human brain and inhibition by azithromycin
Authors: Retallack Hanna , Di Lullo Elizabeth , Arias Carolina , Knopp Kristeene A. , Laurie Matthew T. , Sandoval-Espinosa Carmen , Mancia Leon Walter R. , Krencik Robert , Ullian Erik M. , Spatazza Julien , Pollen Alex A. , Mandel-Brehm Caleigh , Nowakowski Tomasz J. , Kriegstein Arnold R. , DeRisi Joseph L. 
Published: November 2016

Significance
Zika virus (ZIKV) is a mosquito-borne flavivirus that has rapidly spread through the Americas and has been associated with fetal abnormalities, including microcephaly. To understand how microcephaly develops, it is important to identify which cell types of the developing brain are susceptible to infection. We use primary human tissue to show that radial glia and astrocytes are more susceptible to infection than neurons, a pattern that correlates with expression of a putative viral entry receptor, AXL. We also perform a screen of Food and Drug Administration-approved compounds, with an emphasis on drugs known to be safe in pregnancy. We identify an antibiotic, azithromycin, that reduces viral proliferation in glial cells, and compare its activity with daptomycin and sofosbuvir, two additional drugs with anti-ZIKV activity.
Adaptation of the short version of the Psychological Capital Questionnaire (PCQ-12) into Spanish / Adaptación al español de la versión reducida del Cuestionario de Capital Psicológico (PCQ-12)
Authors: León-Pérez José M. , Antino Mirko , León-Rubio José M. 
Published: November 2016

Psychological capital (PsyCap) has been a topic of increasing interest in the last decade. However, there is a lack of validated instruments in Spanish to map PsyCap and its consequences for individuals’ well-being. Consequently, the goal of this study is to adapt the 12-item short version of the Psychological Capital Questionnaire (PCQ-12) to the Spanish context by analysing its internal consistency and reliability, factor solution and external validity. Results indicated that the PCQ-12 exhibited good Cronbach’s alpha (.87) and omega coefficient (.93) values in a sample from a vehicle inspection company ( n = 798). As expected, results also revealed that a second-order factor structure provided the best fit. Moreover, PsyCap is associated with increased job engagement (β = .579; R 2 adjusted = .333), decreased job burnout (β = −.409; R 2 adjusted = .166), and lower psychological distress (β = −.349; R 2 adjusted = .121) (all p < .01), which provided additional support for using the PCQ-12 in the Spanish context. Implications for theory and practice are discussed.
Quantitation using a stable isotope dilution assay (SIDA) and thresholds of taste-active pyroglutamyl decapeptide ethyl esters (PGDPEs) in sake
Authors: Hashizume Katsumi , Ito Toshiko , Igarashi Shinya 
Published: November 2016

Abstract
A stable isotope dilution assay (SIDA) for two taste-active pyroglutamyl decapeptide ethyl esters (PGDPE1; (pGlu)LFGPNVNPWCOOC2H5, PGDPE2; (pGlu)LFNPSTNPWCOOC2H5) in sake was developed using deuterated isotopes and high-resolution mass spectrometry. Recognition thresholds of PGDPEs in sake were estimated as 3.8 μg/L for PGDPE1 and 8.1 μg/L for PGDPE2, evaluated using 11 student panelists aged in their twenties. Quantitated concentrations in 18 commercial sake samples ranged from 0 to 27 μg/L for PGDPE1 and from 0 to 202 μg/L for PGDPE2. The maximum levels of PGDPE1 and PGDPE2 in the sake samples were approximately 8 and 25 times higher than the estimated recognition thresholds, respectively. The results indicated that PGDPEs may play significant sensory roles in the sake. The level of PGDPEs in unpasteurized sake samples decreased during storage for 50 days at 6 °C, suggesting PGDPEs may be enzymatically decomposed.
Exile and Petrarch’s Reinvention of Authorship
Authors: Hooper Laurence E. 
Published: November 2016

AbstractThis article demonstrates a systematic connection between the novelty of Petrarch’s authorship and his self-definition as an exile. Petrarch employs the unusual termexilium/esilioto substantiate his unprecedented claim that literature is a legally validofficium(civic role). Following Dante, Petrarch grounds his exilic authorship in the Christian discourse ofperegrinatio:life as pilgrimage through exile. But Petrarch’s newofficiumallows him a measure of control over literary creation that no prior Italian writer had enjoyed. This is especially true of the “Canzoniere,” Petrarch’s compilation of his vernacular lyrics, whose singularity functions as a proxy for its author’s selfhood.
Civic Piety and Patriotism: Patrician Humanists and Jews in Venice and Its Empire
Authors: Bowd Stephen 
Published: November 2016

AbstractThis article focuses on the contribution of anti-Jewish themes to political ideals and reality in the works of two leading Venetian patrician humanists — Ludovico Foscarini and Paolo Morosini. The article demonstrates that their literary attacks on Jews were shaped by classical, patristic, medieval, and humanist texts, and by the experience of service to the state. It also demonstrates that their work contributed to debates about the toleration of Jews in Venetian territory and can be linked to the humanist engagement with Judaism at a critical point for both phenomena in the fifteenth century.
Projecting Power: Cathedral Chapters and Public Rituals in Portugal, 1564–1650
Authors: Silva Hugo Ribeiro da 
Published: November 2016

AbstractIn the post-Tridentine period, conflicts in cathedrals revealed social dynamics that extended beyond the cathedral walls. Cathedral chapters had to deal with the competition of ecclesiastic as well as secular institutions, involving bishops, Inquisition officials, monks, and members of lay confraternities and city councils. All of them competed to preserve or advance their privileged place in a society of orders, and these rivalries often emerged in public ceremonies. Rituals thus provided a promising setting for power struggles. More than merely local episodes, these conflicts illustrate the rebalance of power in the sixteenth and seventeenth centuries that characterized the early modern state.
Acoustofluidic bacteria separation
Authors: Li Sixing , Ma Fen , Bachman Hunter , Cameron Craig E , Zeng Xiangqun , Huang Tony Jun 
Published: November 2016

Abstract
Bacterial separation from human blood samples can help with the identification of pathogenic bacteria for sepsis diagnosis. In this work, we report an acoustofluidic device for label-free bacterial separation from human blood samples. In particular, we exploit the acoustic radiation force generated from a tilted-angle standing surface acoustic wave (taSSAW) field to separate Escherichia coli from human blood cells based on their size difference. Flow cytometry analysis of the E. coli separated from red blood cells shows a purity of more than 96%. Moreover, the label-free electrochemical detection of the separated E. coli displays reduced non-specific signals due to the removal of blood cells. Our acoustofluidic bacterial separation platform has advantages such as label-free separation, high biocompatibility, flexibility, low cost, miniaturization, automation, and ease of in-line integration. The platform can be incorporated with an on-chip sensor to realize a point-of-care sepsis diagnostic device.