bluuebunny/crossref_metadata_2025 huggingface dataset:
A general neurologist's perspective on the urgent need to apply resilience thinking to the prevention and treatment of Alzheimer's disease
Authors: Pomorska Grazyna , Ockene Judith K.
Published: August 2017

The goal of this article was to look at the problem of Alzheimer's disease (AD) through the lens of a socioecological resilience‐thinking framework to help expand our view of the prevention and treatment of AD. This serious and complex public health problem requires a holistic systems approach. We present the view that resilience thinking, a theoretical framework that offers multidisciplinary approaches in ecology and natural resource management to solve environmental problems, can be applied to the prevention and treatment of AD. Resilience thinking explains a natural process that occurs in all complex systems in response to stressful challenges. The brain is a complex system, much like an ecosystem, and AD is a disturbance (allostatic overload) within the ecosystem of the brain. Resilience thinking gives us guidance, direction, and ideas about how to comprehensively prevent and treat AD and tackle the AD epidemic.
Measuring brain synaptic vesicle protein 2A with positron emission tomography and [18F]UCB‐H
Authors: Bahri Mohamed Ali , Plenevaux Alain , Aerts Joël , Bastin Christine , Becker Guillaume , Mercier Joël , Valade Anne , Buchanan Tim , Mestdagh Nathalie , Ledoux Didier , Seret Alain , Luxen André , Salmon Eric
Published: August 2017

Introduction

Brain distribution of synaptic vesicle protein 2A was measured with fluorine‐18 UCB‐H ([18F]UCB‐H) and positron emission tomography (PET).

Methods

Images of synaptic density were acquired in healthy volunteers (two young participants and two seniors). Input function was measured by arterial blood sampling (arterial input function) and derived from PET images using carotid activity (image‐derived input function). Logan graphical analysis was used to estimate regional synaptic vesicle protein 2A distribution volume.

Results

[18F]UCB‐H uptake was ubiquitous in cortical and subcortical gray matter. Arterial input function and image‐derived input function provided regional distribution volume with a high linear relationship.

Discussion

The cerebral distribution of [18F]UCB‐H is similar to that recently observed with carbon‐11 UCB‐J ([11C]UCB‐J). An accurate [18F]UCB‐H quantification can be performed without invasive arterial blood sampling when no suitable reference region is available, using dynamic PET carotid activity. Brain synaptic density can be studied in vivo in normal and pathological aging.
HYPERELLIPTIC GRAPHS AND METRIZED COMPLEXES
Authors: LEN YOAV
Published: August 2017

We prove a version of Clifford’s theorem for metrized complexes. Namely, a metrized complex that carries a divisor of degree $2r$ and rank $r$ (for $0<r<g-1$) also carries a divisor of degree 2 and rank 1. We provide a structure theorem for hyperelliptic metrized complexes, and use it to classify divisors of degree bounded by the genus. We discuss a tropical version of Martens’ theorem for metric graphs.
National Survey of Environmental Cleaning and Disinfection in Hospitals in Thailand
Authors: Apisarnthanarak Anucha , Weber David J. , Ratz David , Saint Sanjay , Khawcharoenporn Thana , Greene M. Todd
Published: August 2017

More than 90% of Thai hospitals surveyed reported implementing environmental cleaning and disinfection (ECD) protocols. Hospital epidemiologist presence was associated with the existence of an ECD checklist (P=.01) and of ECD auditing (P=.001), while good and excellent hospital administrative support were associated with better adherence to ECD protocols (P<.001) and ECD checklists (P=.005).

Infect Control Hosp Epidemiol 2017;38:1250–1253
STRETCH Goals for I-O Psychology
Authors: Olson-Buchanan Julie B. , Allen Tammy D.
Published: August 2017

Gloss, Carr, Reichman, Abdul-Nasiru, and Oestereich (2017) present a compelling argument (or rallying call) for there being a “moral imperative for I-O psychology to overrepresent people living in the deepest forms of poverty in both science and practice” (p. 330). We agree. Our research has been dominated by a POSH perspective, and it is incumbent upon us to ensure that our science benefits those who are most affected by poverty. We believe the interest in engaging in humanitarian work psychology is growing among industrial and organizational (I-O) psychologists, yet many of us may not feel prepared to conduct such research and/or we may feel that we lack the skills to do so. Further, as Gloss et al. (2017) note, to the extent that we are unprepared to engage in research that benefits those living in poverty, in particular, we run the added risk of harming the very populations we are wanting to help. As such, the interest is there, but we may be daunted by the method. We argue that in order to heed that rallying call, without harm, we need to develop our own capabilities to engage in this important work.
From the Editor
Authors: Scott John C.
Published: August 2017

The goal of focal articles in Industrial and Organizational Psychology: Perspectives on Science and Practice is to present new ideas or different takes on existing ideas and stimulate a conversation in the form of comment articles that extend the arguments in the focal article or that present new ideas stimulated by those articles. The two focal articles in this issue stimulated a wide range of reactions and a good deal of constructive input.
Against Supersessionist Thinking: Old and New, Jews and Postcolonialism, the Ghetto and Diaspora
Authors: Cheyette Bryan
Published: August 2017

This essay focuses on the liberatory possibilities and political and disciplinary difficulties of bringing together Jewish and postcolonial studies. It begins and ends with Adorno’s critique of “actionism” in order to see what is lost when the clarity and certainty of political action is privileged over scholarly nuance and complexity (“praxis” over “theory”). This loss is surveyed through a set of related binaries (supersessionism, foundationalism, and disciplinarity), which, it is contended, reduces critical thinking to polemic and makes it all but impossible to explore interconnected Jewish and postcolonial histories. The argument is illustrated with reference to postcolonial literature and by examining the disciplining of postcolonial and memory studies in relation to the Holocaust. A way out of the binary impasse, it is suggested, is to utilize as “traveling concepts” transcultural and transnational histories (such as “diaspora” and “ghetto”) that Jewish and postcolonial studies have in common.
A multi-proxy lacustrine record of last deglacial–early Holocene environmental variability in the lower Yangtze region from the Chaohu Lake Basin, eastern China
Authors: Guan Houchun , Wu Li , Zhang Jinzhe , Shen Shihao , Chu Dongru , Li Linying
Published: August 2017

The Rb, Sr, and Ti content, Rb/Sr ratio, grain size, magnetic susceptibility, and magnetic fabric in sediments of the BZK1 core were utilized to reconstruct the evolution of the climatic environment in the Chaohu Lake Basin between the last deglacial and the early Holocene. Multi-proxy analyses indicate that lacustrine sediments in Chaohu Lake clearly record the Bølling-Allerød interstadial, the Younger Dryas event and dry-cold climate events occurring between 10.7 cal ka BP and 10.5 cal ka BP. At approximately 15.6–14.8 cal ka BP, the waters became deeper and the climate turned cool. The climate subsequently shifted to a relatively humid period and the lake was largest from 14.8 to 12.8 cal ka BP. From 12.8 to 11.7 cal ka BP, the climate abruptly turned dry and cold and the lake shrank to its lowest level. During 11.7–10.7 cal ka BP, the climate became relatively humid but, from approximately 10.7 to 10.5 cal ka BP, suddenly reverted to a dry and cold state. These climatic change records suggest that lacustrine sediments from the Chaohu Lake Basin in the lower Yangtze region responded actively to global climate changes, comparable with the environmental records from stalagmites and other lacustrine sediments in the region.
Are Parties Equally Responsive to Women and Men?
Authors: Homola Jonathan
Published: August 2017

This article explores (1) whether policy makers are equally responsive to the preferences of women and men and (2) whether the increased presence of women in parliament improves responsiveness to women’s preferences. Using a time-series cross-sectional analysis of 351 party shifts by sixty-eight different parties across twelve Western European countries, the study finds that parties respond to the preference shifts of women and men. However, parties are more responsive to the preference shifts among men than among women – a finding that is not affected by the share of female politicians in parliament. The findings question the implicit assumption that substantive political representation of women necessarily follows from their descriptive representation in legislatures.
The major types of added sugars and non-nutritive sweeteners in a sample of Australian packaged foods
Authors: Probst Yasmine C , Dengate Alexis , Jacobs Jenny , Louie Jimmy CY , Dunford Elizabeth K
Published: August 2017

Objective

Limiting the intake of added sugars in the diet remains a key focus of global dietary recommendations. To date there has been no systematic monitoring of the major types of added sugars used in the Australian food supply. The present study aimed to identify the most common added sugars and non-nutritive sweeteners in the Australian packaged food supply.

Design

Secondary analysis of data from the Australian FoodSwitch database was undertaken. Forty-six added sugars and eight non-nutritive sweetener types were extracted from the ingredient lists of 5744 foods across seventeen food categories.

Setting

Australia.

Subjects

Not applicable.

Results

Added sugar ingredients were found in 61 % of the sample of foods examined and non-nutritive sweetener ingredients were found in 69 %. Only 31 % of foods contained no added sugar or non-nutritive sweetener. Sugar (as an ingredient), glucose syrup, maple syrup, maltodextrin and glucose/dextrose were the most common sugar ingredient types identified. Most Australian packaged food products had at least one added sugar ingredient, the most common being ‘sugar’.

Conclusions

The study provides insight into the most common types of added sugars and non-nutritive sweeteners used in the Australian food supply and is a useful baseline to monitor changes in how added sugars are used in Australian packaged foods over time.
Spousal and survivor benefits in option value models of retirement: an application to Belgium
Authors: JOUSTEN ALAIN , LEFEBVRE MATHIEU
Published: August 2017

We study retirement incentives with an augmented reduced form option value model à la Stock and Wise (1990). We propose methodological extensions to better reflect the respective incentives faced by singles and couples. Our results show that a more comprehensive modeling of couples’ incentives leads to very different patterns of retirement incentives – particularly for women. We apply the new indicators to data from the Survey of Health, Ageing and retirement in Europe in Belgium and find two key results. First, contrary to several previous studies, we obtain a positive signed income effects. Second, we find very different retirement incentives for men and women, with little flexibility in the retirement decision for men and substantially more flexibility for women as a function of financial incentive and household composition.
SAMUEL HOWARD AND THE MUSIC FOR THE INSTALLATION OF THE DUKE OF GRAFTON AS CHANCELLOR OF CAMBRIDGE UNIVERSITY, 1769
Authors: HOWARD ALAN
Published: August 2017

Samuel Howard (?1710–1782) has long been a familiar inhabitant of the diligent footnotes of Handel biographers. A choirboy in the Chapel Royal, he was a member of Handel's chorus and the composer of much theatre music of his own; he later became organist of both St Bride's, Fleet Street and nearby St Clement Danes, Strand, where he was buried in 1782. His most significant and ambitious work is his fine orchestrally accompanied anthem ‘This is the day which the Lord hath made’, published posthumously in 1792 with an impressive title page detailing the performance of the work ‘at St Margaret's Church before the governors of the Westminster Infirmary, in the Two Universities, and upon many other Publick Occasions in different parts of the Kingdom’. This article confirms for the first time that this work originated as Howard's doctoral exercise; contemporary press reports and information in the University archives make clear that the composer's doctorate was linked to the provision of music for the Duke of Grafton's installation as Chancellor of Cambridge University in 1769. Surviving information about this event offers a glimpse of musical life in Cambridge on a comparable scale to the much better reported proceedings upon similar occasions in Oxford. This evidence then serves as a starting-point from which to consider Howard's later prominence as a director of high-profile public performances in London and the provinces.
Contribution of C1485T mutation in the HBx gene to human and murine hepatocarcinogenesis
Authors: Hagiwara Satoru , Nishida Naoshi , Park Ah-Mee , Komeda Yoriaki , Sakurai Toshiharu , Watanabe Tomohiro , Kudo Masatoshi
Published: August 2017

Although Hepatitis B virus (HBV) X gene mutations are frequently detected in HBV-related human hepatocellular carcinoma (HCC) patients, causative HBx mutations in the development of HCC have not yet been determined. We herein identified C1485T and C1653T mutations in the HBx gene as independent risk of HCC for HBV through the analysis using serum from chronic hepatitis B patients. We generated transgenic mice expressing wild-type (WT-HBxTg) and mutant (C1485T-HBxTg) HBx to assess the carcinogenic potential of mutated HBx. C1485T-HBxTg mice were more susceptible to diethylnitrosamine-induced hepatocarcinogenesis than WT-HBxTg mice and control non-Tg mice. The promotion of hepatocarcinogenesis in C1485T-HBxTg mice was accompanied by the activation of β-catenin and Jun N-terminal kinase (JNK) signaling pathways as well as the production of reactive oxygen species, whereas the activation of nuclear factor-kappa B in the livers of C1485T-HBxTg mice was attenuated. These results demonstrate that the HBx C1485T mutation contributes to human and murine hepatocarcinogenesis.
Ameliorative effects of melatonin on dark-induced leaf senescence in gardenia (Gardenia jasminoides Ellis): leaf morphology, anatomy, physiology and transcriptome
Authors: Zhao Daqiu , Wang Rong , Meng Jiasong , Li Zhiyuan , Wu Yanqing , Tao Jun
Published: August 2017

Cut gardenia (Gardenia jasminoides Ellis) foliage is widely used as a vase material or flower bouquet indoors; however, insufficient indoor light accelerates its senescence, which shortens its viewing time. In this study, applying melatonin to delay gardenia leaf senescence when exposed to extremely low light condition (darkness), and the results showed that 1.0 mM was the effective concentration. At this concentration, chlorophyll contents and chlorophyll fluorescence parameters (Fv/Fm, Fv/F0 and Y(II)) increased, while the carotenoid and flavonoid contents decreased. Meanwhile, stress physiological indices decreased in response to exogenous melatonin application, whereas an increase in glutamine synthetase activity, water and soluble protein contents was observed. Moreover, exogenous melatonin application also reduced leaf programmed cell death under darkness, increased the endogenous melatonin level, expression levels of tryptophan decarboxylase gene, superoxide dismutase and catalase activities and the ascorbate–glutathione cycle, and maintained more intact anatomical structures. Furthermore, transcriptome sequencing revealed that various biological processes responded to exogenous melatonin application, including carbohydrate metabolism, amino acid metabolism, lipid metabolism, plant hormone signal transduction and pigment biosynthesis. Consequently, dark-induced leaf senescence in gardenia was significantly delayed. These results provided a better understanding for improving the ornamental value of cut gardenia foliage using melatonin.
Experimental and ab initio studies of Cd5(BO3)3Cl: the first cadmium borate chlorine NLO material with isolated BO3groups
Authors: Song Yunxia , Luo Min , Liang Fei , Lin Chensheng , Ye Ning , Yan Guiyang , Lin Zheshuai
Published: August 2017

Introduction of a halogen chlorine atom into the CdO–B2O3system generates a novel nonlinear optical material Cd5(BO3)3Cl.
Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step
Authors: Lombardi Chiara , Artuso Emma , Grandi Eleonora , Lolli Marco , Spirakys Francesca , Priola Emanuele , Prandi Cristina
Published: August 2017

Structural analogues of natural strigolactones in which the butenolide D-ring has been replaced with γ-lactam. The key step was an RCM on suitably substituted amides.
Integrated catalytic sequences for catalytic upgrading of bio-derived carboxylic acids to fuels, lubricants and chemical feedstocks
Authors: Shylesh Sankaranarayanapillai , Gokhale Amit A. , Sun Keyang , Grippo Adam M. , Jadhav Deepak , Yeh Alice , Ho Christopher R. , Bell Alexis T.
Published: August 2017

We describe catalytic sequences for converting biomass-derived carboxylic acids, to fuels and lubricants that are compatible with the existing energy infrastructure.
Thermo-, photo-, and mechano-responsive liquid crystal networks enable tunable photonic crystals
Authors: Akamatsu N. , Hisano K. , Tatsumi R. , Aizawa M. , Barrett C. J. , Shishido A.
Published: August 2017

Tunable photonic crystals exhibiting optical properties that respond reversibly to external stimuli have been developed using liquid crystal networks (LCNs) and liquid crystal elastomers (LCEs).
Perceptions of Mentoring SLPs and Clinical Fellows During the Clinical Fellowship
Authors: Resendiz Maria , Summers Connie , Ruiz-Felter Roxanna , Belasco Elizabeth , Fox Katherine
Published: August 2017

The clinical fellowship (CF) is completed by speech-language pathologists (SLPs) after graduating with a master's degree. The clinical fellow is supervised by a mentoring SLP who meets the qualifications set forth by the American Speech-Language-Hearing Association (ASHA). The current study focused on differences and similarities in expectations during the CF by the mentoring SLP and clinical fellow. Participants were asked about knowledge and skills for which clinical fellows are evaluated at the end of the CF in the areas of assessment and treatment. Clinical fellows wanted more help with assessment and less assistance with treatment. Mentoring SLPs felt assistance was needed for assessment and treatment. A model is proposed at the end to aid in implementing the recommendations based on the results.
Impact of superconducting fault current limiter on the distributed energy source work
Authors: Rusiński Jacek
Published: August 2017

Globally there has been a sharp increase in the number of renewable energy sources (RESs) connected to electrical power systems (EPSs). At the same time, in many countries domestic grid codes impose strict requirements on the work of these sources in the case of a short circuit. Regulations on low‐voltage fault ride‐through (LVFRT) require that the RES support the work of the EPS during disturbances. In such cases, the RES can be damaged by prolonged duration of short circuit currents. Application of superconducting fault current limiters (SFCLs) protects the RES from the effect of short circuits and improves LVFRT capability. This study describes simulation studies showing the impact of the SFCL on the values of the short circuit current and the voltage at the RES terminals for different short circuit locations. Research results have confirmed a positive impact of the SCFL on the RES during disturbances.
Enriques surfaces in characteristic 2 with a finite group of automorphisms
Authors: Katsura Toshiyuki , Kondō Shigeyuki
Published: August 2017

Complex Enriques surfaces with a finite group of automorphisms are classified into seven types. In this paper, we determine which types of such Enriques surfaces exist in characteristic 2. In particular we give a 1-dimensional family of classical and supersingular Enriques surfaces with the automorphism group

A
u
t

(
X
)

\mathrm {Aut}(X)

isomorphic to the symmetric group

S

5

\mathfrak {S}_5

of degree 5.
An overview of multi-task learning
Authors: Zhang Yu , Yang Qiang
Published: August 2017

As a promising area in machine learning, multi-task learning (MTL) aims to improve the performance of multiple related learning tasks by leveraging useful information among them. In this paper, we give an overview of MTL by first giving a definition of MTL. Then several different settings of MTL are introduced, including multi-task supervised learning, multi-task unsupervised learning, multi-task semi-supervised learning, multi-task active learning, multi-task reinforcement learning, multi-task online learning and multi-task multi-view learning. For each setting, representative MTL models are presented. In order to speed up the learning process, parallel and distributed MTL models are introduced. Many areas, including computer vision, bioinformatics, health informatics, speech, natural language processing, web applications and ubiquitous computing, use MTL to improve the performance of the applications involved and some representative works are reviewed. Finally, recent theoretical analyses for MTL are presented.
GSimp: A Gibbs sampler based left-censored missing value imputation approach for metabolomics studies
Authors: Wei Runmin , Wang Jingye , Jia Erik , Chen Tianlu , Ni Yan , Jia Wei
Published: August 2017

Left-censored missing values commonly exist in targeted metabolomics datasets and can be considered as missing not at random (MNAR). Improper data processing procedures for missing values will cause adverse impacts on subsequent statistical analyses. However, few imputation methods have been developed and applied to the situation of MNAR in the field of metabolomics. Thus, a practical left-censored missing value imputation method is urgently needed. We have developed an iterative Gibbs sampler based left-censored missing value imputation approach (GSimp). We compared GSimp with other three imputation methods on two real-world targeted metabolomics datasets and one simulation dataset using our imputation evaluation pipeline. The results show that GSimp outperforms other imputation methods in terms of imputation accuracy, observation distribution, univariate and multivariate analyses, and statistical sensitivity. The R code for GSimp, evaluation pipeline, vignette, real-world and simulated targeted metabolomics datasets are available at:https://github.com/WandeRum/GSimp.

Author summary

Missing values caused by the limit of detection/quantification (LOD/LOQ) were widely observed in mass spectrometry (MS)-based targeted metabolomics studies and could be recognized as missing not at random (MNAR). MNAR leads to biased parameter estimations and jeopardizes following statistical analyses in different aspects, such as distorting sample distribution, impairing statistical power, etc. Although a wide range of missing value imputation methods was developed for –omics studies, a limited number of methods was designed appropriately for the situation of MNAR currently. To alleviate problems caused by MNAR and facilitate targeted metabolomics studies, we developed a Gibbs sampler based missing value imputation approach, called GSimp, which is public-accessible on GitHub. And we compared our method with existing approaches using an imputation evaluation pipeline on real-world and simulated metabolomics datasets to demonstrate the superiority of our method from different perspectives.
Enhancer connectome in primary human cells reveals target genes of disease-associated DNA elements
Authors: Mumbach Maxwell R. , Satpathy Ansuman T. , Boyle Evan A. , Dai Chao , Gowen Benjamin G. , Cho Seung Woo , Nguyen Michelle L. , Rubin Adam J. , Granja Jeffrey M. , Kazane Katelynn R. , Wei Yuning , Nguyen Trieu , Greenside Peyton G. , Corces M. Ryan , Tycko Josh , Simeonov Dimitre R. , Suliman Nabeela , Li Rui , Xu Jin , Flynn Ryan A. , Kundaje Anshul , Khavari Paul A. , Marson Alexander , Corn Jacob E. , Quertermous Thomas , Greenleaf William J. , Chang Howard Y.
Published: August 2017

The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here, we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naïve T cells to T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a four-fold increase of potential target genes for autoimmune and cardiovascular diseases.
A large, open source dataset of stroke anatomical brain images and manual lesion segmentations
Authors: Liew Sook-Lei , Anglin Julia M. , Banks Nick W. , Sondag Matt , Ito Kaori L. , Kim Hosung , Chan Jennifer , Ito Joyce , Jung Connie , Khoshab Nima , Lefebvre Stephanie , Nakamura William , Saldana David , Schmiesing Allie , Tran Cathy , Vo Danny , Ard Tyler , Heydari Panthea , Kim Bokkyu , Aziz-Zadeh Lisa , Cramer Steven C. , Liu Jingchun , Soekadar Surjo , Nordvik Jan-Egil , Westlye Lars T. , Wang Junping , Winstein Carolee , Yu Chunshui , Ai Lei , Koo Bonhwang , Craddock R. Cameron , Milham Michael , Lakich Matthew , Pienta Amy , Stroud Alison
Published: August 2017

Stroke is the leading cause of adult disability worldwide, with up to two-thirds of individuals experiencing long-term disabilities. Large-scale neuroimaging studies have shown promise in identifying robust biomarkers (e.g., measures of brain structure) of long-term stroke recovery following rehabilitation. However, analyzing large rehabilitation-related datasets is problematic due to barriers in accurate stroke lesion segmentation. Manually-traced lesions are currently the gold standard for lesion segmentation on T1-weighted MRIs, but are labor intensive and require anatomical expertise. While algorithms have been developed to automate this process, the results often lack accuracy. Newer algorithms that employ machine-learning techniques are promising, yet these require large training datasets to optimize performance. Here we present ATLAS (Anatomical Tracings of Lesions After Stroke), an open-source dataset of 304 T1-weighted MRIs with manually segmented lesions and metadata. This large, diverse dataset can be used to train and test lesion segmentation algorithms and provides a standardized dataset for comparing the performance of different segmentation methods. We hope ATLAS release 1.1 will be a useful resource to assess and improve the accuracy of current lesion segmentation methods.
Multi-reference spectral library yields almost complete coverage of heterogeneous LC-MS/MS data sets
Authors: Ammar Constantin , Berchtold Evi , Csaba Gergely , Schmidt Andreas , Imhof Axel , Zimmer Ralf
Published: August 2017

Spectral libraries play a central role in the analysis of data-independent-acquisition (DIA) proteomics experiments. A main assumption in current spectral library tools is that a single characteristic intensity pattern (CIP) suffices to describe the fragmentation of a peptide in a particular charge state (peptide charge pair). However, we find that this is often not the case. We carry out a systematic evaluation of spectral variability over public repositories and in-house datasets. We show that spectral variability is widespread and partly occurs under fixed experimental conditions. Using clustering of preprocessed spectra, we derive a limited number of Multiple Characteristic Intensity Patterns (MCIPs) for each peptide charge pair, which allow almost complete coverage of our heterogeneous dataset without affecting the false discovery rate. We show that a MCIP library derived from public repositories performs in most cases similar to a “custom-made” spectral library, which has been acquired under identical experimental conditions as the query spectra. We apply the MCIP approach to a DIA data set and observe a significant increase in peptide recognition. We propose the MCIP approach as an easy-to-implement addition to current spectral library search engines and as a new way to utilize the data stored in spectral repositories.
BBSome trains remove activated GPCRs from cilia by enabling passage through the transition zone
Authors: Ye Fan , Nager Andrew R. , Nachury Maxence V.
Published: August 2017

A diffusion barrier at the transition zone enables the compartmentalization of signaling molecules by cilia. The BBSome and the small GTPase Arl6, which triggers BBSome coat polymerization, are required for the exit of activated signaling receptors from cilia, but how diffusion barriers are crossed when membrane proteins exit cilia remains to be determined. Here we found that activation of the ciliary GPCRs Smoothened and SSTR3 drove the Arl6-dependent assembly of large, highly processive and cargo-laden retrograde BBSome trains. Single-molecule imaging revealed that the assembly of BBSome trains enables the lateral transport of ciliary GPCRs across the transition zone. Yet, the removal of activated GPCRs from cilia was inefficient because a second, periciliary diffusion barrier was infrequently crossed. We conclude that exit from cilia is a two-step process in which BBSome/Arl6 trains first moves activated GPCRs through the transition zone before a periciliary barrier can be crossed.

Upon activation, GPCRs must exit cilia for appropriate signal transduction. Using bulk imaging of BBSome and single molecule imaging of GPCRs, Ye et al. demonstrate that retrograde BBSome trains assemble on-demand upon GPCR activation and ferry GPCRs across the transition zone. Yet, ciliary exit often fails because of a second diffusion barrier.
Opposite effects of lateralised transcranial alpha versus gamma stimulation on spatial attention
Authors: Wöstmann Malte , Vosskuhl Johannes , Obleser Jonas , Herrmann Christoph S.
Published: August 2017

Spatial attention relatively increases the power of neural 10-Hz alpha oscillations in the hemisphere ipsilateral to attention. The functional roles of lateralised oscillations for attention are unclear. Here, 20 human participants performed a dichotic listening task under continuous transcranial alternating current stimulation (tACS) at alpha (10 Hz, vs sham) or gamma (47 Hz, vs sham) frequency, targeting left temporo-parietal cortex. Participants attended to four spoken numbers presented to one ear, while ignoring numbers on the other ear. As predicted, we found that alpha-tACS contralateral to the attended ear decreased recall of attended targets. Notably, gamma-tACS reversed the effect. Results provide a proof of concept that externally amplified oscillations can enhance spatial attention and facilitate attentional selection of speech. Furthermore, opposite effects of alpha versus gamma oscillations support the view that, across modalities, states of high alpha are incommensurate with active neural processing as reflected by states of high gamma.
Seamless Multiscale Modeling of Coagulation Using Dissipative Particle Dynamics
Authors: Yazdani Alireza , Li Zhen , Humphrey Jay D. , Karniadakis George Em
Published: August 2017

We propose a new multiscale framework that seamlessly integrates four key components of blood clotting namely, blood rheology, cell mechanics, coagulation kinetics and transport of species and platelet adhesive dynamics. We use transport dissipative particle dynamics (tDPD), which is the extended form of original DPD, as the base solver, while a coarse-grained representation of blood cell’s membrane accounts for its mechanics. Our results show the dominant effect of blood flow and high Peclet numbers on the reactive transport of the chemical species signifying the importance of membrane bound reactions on the surface of adhered platelets. This new multiscale particle-based methodology helps us probe synergistic mechanisms of thrombus formation, and can open new directions in addressing other biological processes from sub-cellular to macroscopic scales.
Dramatic evolution of body length due to post-embryonic changes in cell size in a newly discovered close relative ofC. elegans
Authors: Woodruff Gavin C. , Phillips Patrick C.
Published: August 2017

Understanding morphological diversity—and morphological constrainto—has been a central question in evolutionary biology since its inception. Nematodes of the genusCaenorhabditis, which contains the well-studied model systemC. elegans, display remarkable morphological consistency in the face of extensive genetic divergence. Here, we provide a description of the broad developmental patterns of a recently discovered species,C.sp. 34, which was isolated from fresh figs in Okinawa and which is among the closest known relatives ofC. elegans.C.sp. 34 displays an extremely large body size and can grow to be nearly twice as long asC. elegansand all other known members of the genus. Observations of the timing of developmental milestones reveal thatC.sp. 34 develops about twice as slowly asC. elegans. Measurements of embryo and larval size show that the size difference betweenC.sp. 34 andC. elegansis largely due to post-embryonic events, particularly during the transition from larval to adult stages. This difference in size is not attributable to differences in germ line chromosome number or the number of somatic cells. The overall difference in body size is therefore largely attributable to changes in cell size via increased cytoplasmic volume. Because of its close relationship toC. elegans, the distinctness ofC.sp. 34 provides an ideal system for the detailed analysis of evolutionary diversification. The context of over forty years ofC. elegansdevelopmental genetics also reveals clues into how natural selection and developmental constraint act jointly to promote patterns of morphological stasis and divergence in this group.
Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)
Authors: Parks Matthew , Nakov Teofil , Ruck Elizabeth , Wickett Norman J. , Alverson Andrew J.
Published: August 2017

Premise of the study

Diatoms are one of the most species-rich lineages of microbial eukaryotes. Similarities in clade age, species richness, and contributions to primary production motivate comparisons to flowering plants, whose genomes have been inordinately shaped by whole genome duplication (WGD). These events that have been linked to speciation and increased rates of lineage diversification, identifying WGDs as a principal driver of angiosperm evolution. We synthesized a relatively large but scattered body of evidence that, taken together, suggests that polyploidy may be common in diatoms.

Methods

We used data from gene counts, gene trees, and patterns of synonymous divergence to carry out the first large-scale phylogenomic analysis of genome-scale duplication histories for a phylogenetically diverse set of 37 diatom taxa.

Key results

Several methods identified WGD events of varying age across diatoms, though determining the exact number and placement of events and, more broadly, inferences of WGD at all, were greatly impacted by gene-tree uncertainty. Gene-tree reconciliations supported allopolyploidy as the predominant mode of polyploid formation, with particularly strong evidence for ancient allopolyploid events in the thalassiosiroid and pennate diatom clades.

Conclusions

Whole genome duplication appears to have been an important driver of genome evolution in diatoms. Denser taxon sampling will better pinpoint the timing of WGDs and likely reveal many more of them. We outline potential challenges in reconstructing paleopolyploid events in diatoms that, together with these results, offer a framework for understanding the evolutionary roles of genome duplication in a group that likely harbors substantial genomic diversity.
Epigenomic and 3D genome architecture in naïve and primed human embryonic stem cell states
Authors: Battle Stephanie L. , Jayavelu Naresh Doni , Azad Robert N. , Hesson Jennifer , Ahmed Faria N. , Zoller Joseph A. , Mathieu Julie , Ruohola-Baker Hannele , Ware Carol B. , David Hawkins R.
Published: August 2017

During mammalian embryogenesis changes in morphology and gene expression are concurrent with epigenomic reprogramming. Using human embryonic stem cells representing the pre-implantation blastocyst (naïve) and post-implantation epiblast (primed), our data demonstrate that a substantial portion of known human enhancers are pre-marked by H3K4me1 in naïve cells, providing an enhanced open chromatin state in naïve pluripotency. The naïve enhancer repertoire occupies nine percent of the genome, three times that of primed cells, and can exist in broad chromatin domains over fifty kilobases. Enhancer chromatin states are largely poised. Seventy-seven percent of naïve enhancers are decommissioned in a stepwise manner as cells become primed. While primed topological associated domains are unaltered upon differentiation, naïve domains expand across primed boundaries, impacting three dimensional genome architecture. Differential topological associated domain edges coincide with naïve H3K4me1 enrichment. Our results suggest that naïve-derived cells have a chromatin landscape reflective of early embryogenesis.
NMDA receptor-dependent dynamics of hippocampal place cell ensembles
Authors: Hayashi Yuichiro
Published: August 2017

Place cell activity in the hippocampus constitutes a neural representation of space. The dynamics of the place cell activity for familiar environment changes gradually over time, suggesting that this temporal dynamics enables to allocate different neural codes for spatially identical but temporally different episodes. To understand the mechanisms determining the dynamics of place cell populations, activity of hippocampal CA1 neurons was imaged during repeated performance in a spatial memory task. Comparing ensemble representations among multiple task sessions revealed that overlap rate of active place cell population was time-dependent, but independent of the number of tasks within a fixed time. This time-dependent change of hippocampal ensemble activity was suppressed by the administration of an NMDA receptor antagonist. These results suggested that the gradual change of activity pattern works as a time code, and NMDA receptor-dependent processes forms the code.
Not such silly sausages: Northern quolls exhibit aversion to toads after training with toad sausages
Authors: Indigo Naomi , Smith James , Webb Jonathan K. , Phillips Ben
Published: August 2017

The invasion of toxic cane toads (Rhinella marina) is a major threat to northern quolls (Dasyurus hallucatus) which are poisoned when they attack this novel prey item. Quolls are now endangered as a consequence of the toad invasion. Conditioned taste aversion can be used to train individual quolls to avoid toads, but we currently lack a training technique that can be used at a landscape scale to buffer entire populations from toad impact. Broad scale deployment requires a bait that can be used for training, but there is no guarantee that such a bait will ultimately elicit aversion to toads. Here we test a manufactured bait—a ‘toad sausage’—for its ability to elicit aversion to toads in northern quolls. To do this, we exposed one group of quolls to a toad sausage and another to a control sausage and compared the quolls’ predatory responses when presented with a dead adult toad. Captive quolls that consumed a single toad sausage showed substantially reduced interest in cane toads, interacting with them for less than half the time of their untrained counterparts and showing substantially reduced attack behaviour. We also quantified bait uptake in the field, by both quolls and non-target species. These field trials showed that wild quolls were the most frequent species attracted to the baits, and that approximately 61% of quolls consumed toad-aversion baits when first encountered. Between 40-68% of these animals developed aversion to further bait consumption. Our results suggest that toad-aversion sausages can be used to train wild quolls to avoid cane toads. This opens the possibility for broad-scale quoll training with toad aversion sausages: a technique that may allow wildlife managers to prevent quoll extinctions at a landscape scale.
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
Authors: Rizzetto Simone , Koppstein David NP , Samir Jerome , Singh Mandeep , Reed Joanne H. , Cai Curtis H. , Lloyd Andrew R. , Eltahla Auda A. , Goodnow Christopher C. , Luciani Fabio
Published: August 2017

The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. Cell-to-cell variability of BCR sequences due to V(D)J recombination and somatic hypermutation (SHM) necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing (scRNA-seq) presents the opportunity for simultaneous capture of the BCR sequence and transcriptomic signature for a detailed understanding of the dynamics of an immune response.

We developed VDJPuzzle 2.0, a bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains. VDJPuzzle successfully reconstructs BCRs from 98.3% (n=117) of human and 96.5% (n=200) from murine B cells. 92.0% of clonotypes and 90.3% of mutations were concordant with single-cell Sanger sequencing of the immunoglobulin chains. VDJPuzzle is available athttps://bitbucket.org/kirbyvisp/vdjpuzzle2
Behavioral and Hematological Response ofClarias gariepinusjuvenile exposed to Acute concentrations of Aqueous Extract of Siam Weed (Chloromolaena odorata) leaf as Anesthetic agent
Authors: Chidi Iheanacho Stanley , Shedrack Nworu
Published: August 2017

This experiment was carried out to investigate the effect of Siam Weed (chloromelena odorata) on the heamatology ofClarias gariepinusjuvenile. A total of one hundred and fifty (150) juvenile ofClarias gariepinuswere randomly assigned to different concentrations ofC. odorataleave aqueous extract in a completely randomize design (CRD). The concentrations were 50mg/l, 100mg/l, 150mg/l, 200mg/l. Distilled water (0.00 mg/l) was used as the control. The fish exhibited stressful behavior which was higher as the concentration ofChromolaena odorataleave extract increased. There was a gradual decrease with time until a state of calmness, which was subsequently followed by death. The effect on 96hr exposed period was recorded and blood samples collected at 24hr and 96hr interval. Result on hematological parameters revealed significant difference (P<0.05) among treatments with increase in exposure time for all the blood parameters.C. odorataat increased concentrations affected the behavior and hematology ofC. gariepinus.
Plant genetic effects on microbial hubs impact fitness across field trials
Authors: Brachi Benjamin , Filiault Daniele , Whitehurst Hannah , Darme Paul , Le Gars Pierre , Le Mentec Marine , Morton Timothy C. , Kerdaffrec Envel , Rabanal Fernando , Anastasio Alison , Box Mathew S. , Duncan Susan , Huang Feng , Leff Riley , Novikova Polina , Perisin Matthew , Tsuchimatsu Takashi , Woolley Roderick , Dean Caroline , Nordborg Magnus , Holm Svante , Bergelson Joy
Published: August 2017

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 A. thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial OTU’s. Host genetics disproportionately influenced hubs within the microbial communities, with their impact then percolating through the community, as evidenced by a decline in the heritability of particular OTUs with their distance to the nearest hub. By simultaneously measuring host performance, we found that host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants grown in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins and the immune system. Using untargeted metabolomics, we corroborate the consistent association of variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host natural variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
Authors: Ryan Corces M. , Trevino Alexandro E. , Hamilton Emily G. , Greenside Peyton G. , Sinnott-Armstrong Nicholas A. , Vesuna Sam , Satpathy Ansuman T. , Rubin Adam J. , Montine Kathleen S. , Wu Beijing , Kathiria Arwa , Cho Seung Woo , Mumbach Maxwell R. , Carter Ava C. , Kasowski Maya , Orloff Lisa A. , Risca Viviana I. , Kundaje Anshul , Khavari Paul A. , Montine Thomas J. , Greenleaf William J. , Chang Howard Y.
Published: August 2017

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol enables chromatin accessibility profiling from archival frozen tissue samples and 50 μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.