bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giant Olfactory Groove Meningioma—2-Staged Approach: 2-Dimensional Operative Video
Authors: Todeschini Alexandre B , Shahein Mostafa , Montaser Alaa S , Hardesty Douglas , Otto Bradley A , Carrau Ricardo L , Prevedello Daniel M 
Published: April 2018

Abstract
A 42-yr-old female presented with an olfactory groove meningioma causing progressive vision loss and anosmia. Given the size of the tumor, we opted for a 2-stage surgery: endoscopic endonasal approach (EEA) followed by a craniotomy. Stage I surgery was a transcribriform transplanum EEA using a binostril 4-hand/2 surgeons (ENT and neuro) technique, with the patient positioned supine with the head slightly turned to the right side and tilted to the left, fixed in a 3-pin head clamp, under imaging guidance, in which we drilled out all the affected skull base bone, devascularized and debulked the tumor. Stage II surgery was done through a right frontotemporal craniotomy 2 mo later. The surgery and postoperative period was uneventful with no complications and no need for further reconstruction of the skull base. The patient's vision was normalized. Postoperative magnetic resonance imaging (MRI) confirmed a Simpson Grade 1 resection.
The rationale behind this staged approach is that we have found when using a transcranial 1-stage approach the brain edema and necessary retraction required for resection leads to brain injury, oftentimes readily identified in the diffusion-weighted imaging MRI which are associated with different degrees of cognitive impairment. The skull base bone involved is usually not removed via transcranial approaches.
Despite requiring a second surgery, this staged approach allows a true total resection (including the affected bone) and in the transcranial stage the brain is more relaxed, with less edema, reducing the need for retraction, which may lead to a better outcome.
The patient has given assent and written consent for videos, images, or clinical or genetic information to be published.
Gravitational-wave astronomy: delivering on the promises
Authors: Schutz B. F. 
Published: April 2018

Now that LIGO and Virgo have begun to detect gravitational-wave events with regularity, the field of gravitational-wave astronomy is beginning to realize its promise. Binary black holes and, very recently, binary neutron stars have been observed, and we are already learning much from them. The future, with improved sensitivity, more detectors and detectors like LISA in different frequency bands, has even more promise to open a completely hidden side of the Universe to our exploration.
This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Quasi-monolithic mirror suspensions in ground-based gravitational-wave detectors: an overview and look to the future
Authors: van Veggel Anna-Maria A. 
Published: April 2018

At the commencement of a new era in astrophysics, with added information from direct detections of gravitational-wave (GW) signals, this paper is a testament to the quasi-monolithic suspensions of the test masses of the GW detectors that have enabled the opening of a new window on the universe. The quasi-monolithic suspensions are the final stages in the seismic isolation of the test masses in GW detectors, and are specifically designed to introduce as little thermal noise as possible. The history of the development of the fused-silica quasi-monolithic suspensions, which have been so essential for the first detections of GWs, is outlined and a glimpse into the status of research towards quasi-monolithic suspensions made of sapphire and silicon is given.
This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Characterizing transient noise in the LIGO detectors
Authors: Nuttall L. K. 
Published: April 2018

Data from the LIGO detectors typically contain many non-Gaussian noise transients which arise due to instrumental and environmental conditions. These non-Gaussian transients can be an issue for the modelled and unmodelled transient gravitational-wave searches, as they can mask or mimic a true signal. Data quality can change quite rapidly, making it imperative to track and find new sources of transient noise so that data are minimally contaminated. Several examples of transient noise and the tools used to track them are presented. These instances serve to highlight the diverse range of noise sources present at the LIGO detectors during their second observing run.
This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Control of cell behaviour through nanovibrational stimulation: nanokicking
Authors: Robertson Shaun N. , Campsie Paul , Childs Peter G. , Madsen Fiona , Donnelly Hannah , Henriquez Fiona L. , Mackay William G. , Salmerón-Sánchez Manuel , Tsimbouri Monica P. , Williams Craig , Dalby Matthew J. , Reid Stuart 
Published: April 2018

Mechanical signals are ubiquitous in our everyday life and the process of converting these mechanical signals into a biological signalling response is known as mechanotransduction. Our understanding of mechanotransduction, and its contribution to vital cellular responses, is a rapidly expanding field of research involving complex processes that are still not clearly understood. The use of mechanical vibration as a stimulus of mechanotransduction, including variation of frequency and amplitude, allows an alternative method to control specific cell behaviour without chemical stimulation (e.g. growth factors). Chemical-independent control of cell behaviour could be highly advantageous for fields including drug discovery and clinical tissue engineering. In this review, a novel technique is described based on nanoscale sinusoidal vibration. Using finite-element analysis in conjunction with laser interferometry, techniques that are used within the field of gravitational wave detection, optimization of apparatus design and calibration of vibration application have been performed. We further discuss the application of nanovibrational stimulation, or ‘nanokicking’, to eukaryotic and prokaryotic cells including the differentiation of mesenchymal stem cells towards an osteoblast cell lineage. Mechanotransductive mechanisms are discussed including mediation through the Rho-A kinase signalling pathway. Optimization of this technique was first performed in two-dimensional culture using a simple vibration platform with an optimal frequency and amplitude of 1 kHz and 22 nm. A novel bioreactor was developed to scale up cell production, with recent research demonstrating that mesenchymal stem cell differentiation can be efficiently triggered in soft gel constructs. This important step provides first evidence that clinically relevant (three-dimensional) volumes of osteoblasts can be produced for the purpose of bone grafting, without complex scaffolds and/or chemical induction. Initial findings have shown that nanovibrational stimulation can also reduce biofilm formation in a number of clinically relevant bacteria. This demonstrates additional utility of the bioreactor to investigate mechanotransduction in other fields of research.This article is part of a discussion meeting issue ‘The promises of gravitational-wave astronomy’.
Electrophysiological characterization and MCH/orexin neuronal distribution in the lateral hypothalamus of naked mole-rats (Heterocephalus glaber)
Authors: Husson Zoé , Apergis-Schoute John , Smith Ewan St John 
Published: April 2018

AbstractThe lateral hypothalamus (LH) controls various homeostatic processes, including sleep-wake cycles, energy balance and thermoregulation in many mammalian species. In the LH, melanin-concentrating hormone (MCH) and hypocretin/orexin (HO) containing neurons differentially regulate these processes. Naked mole-rats (NMR) (Heterocephalus glaber) are eusocial mammals with remarkable physiological peculiarities including extreme longevity without significant weight gain and absence of thermoregulation. Altered hypothalamic function could potentially underlie the unusual NMR phenotypes, but to date electrophysiological characterization of LH NMR neurons and expression of MCH and HO is missing. Here, we performed whole-cell recordings from LH neurons in acute NMR and mouse brain slices and found that NMR and mouse neuronal basic properties and activities were comparable. Additionally, we showed that both MCH-positive and HO-positive neuronal populations exist in the NMR hypothalamus and although the majority of MCH- and HO-positive neurons are located in the LH, as previously described in rodents, significant differences exist in MCH/HO distribution in other NMR hypothalamic areas. These results indicate that NMR LH neurons are comparable to mouse neurons with respect to their electrophysiological properties, but differences in the neuronal MCH and HO populations in hypothalamic regions exist and may contribute to the adaptive changes seen in NMR homeostatic processes.
A protocol for an intercomparison of biodiversity and ecosystem services models using harmonized land-use and climate scenarios
Authors: Kim HyeJin , Rosa Isabel M.D. , Alkemade Rob , Leadley Paul , Hurtt George , Popp Alexander , van Vuuren Detlef P , Anthoni Peter , Arneth Almut , Baisero Daniele , Caton Emma , Chaplin-Kramer Rebecca , Chini Louise , De Palma Adriana , Di Fulvio Fulvio , Di Marco Moreno , Espinoza Felipe , Ferrier Simon , Fujimori Shinichiro , Gonzalez Ricardo E. , Gueguen Maya , Guerra Carlos , Harfoot Mike , Harwood Thomas D. , Hasegawa Tomoko , Haverd Vanessa , Havlík Petr , Hellweg Stefanie , Hill Samantha L. L. , Hirata Akiko , Hoskins Andrew J. , Janse Jan H. , Jetz Walter , Johnson Justin A. , Krause Andreas , Leclère David , Martins Ines S. , Matsui Tetsuya , Merow Cory , Obersteiner Michael , Ohashi Haruka , Poulter Benjamin , Purvis Andy , Quesada Benjamin , Rondinini Carlo , Schipper Aafke , Sharp Richard , Takahashi Kiyoshi , Thuiller Wilfried , Titeux Nicolas , Visconti Piero , Ware Christopher , Wolf Florian , Pereira Henrique M. 
Published: April 2018

AbstractTo support the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), the IPBES Expert Group on Scenarios and Models is carrying out an intercomparison of biodiversity and ecosystem services models using harmonized scenarios (BES-SIM). The goals of BES-SIM are (1) to project the global impacts of land use and climate change on biodiversity and ecosystem services (i.e. nature’s contributions to people) over the coming decades, compared to the 20th century, using a set of common metrics at multiple scales, and (2) to identify model uncertainties and research gaps through the comparisons of projected biodiversity and ecosystem services across models. BES-SIM uses three scenarios combining specific Shared Socio-economic Pathways (SSPs) and Representative Concentration Pathways (RCPs) to explore a wide range of land-use change and climate change futures. This paper describes the rationale for scenarios selection, the process of harmonizing input data for land use, based on the second phase of the Land Use Harmonization Project (LUH2), and climate, the biodiversity and ecosystem service models used, the core simulations carried out, the harmonization of the model output metrics, and the treatment of uncertainty. The results of this collaborative modelling project will support the ongoing global assessment of IPBES, strengthen ties between IPBES and the Intergovernmental Panel on Climate Change (IPCC) scenarios and modelling processes, advise the Convention on Biological Diversity (CBD) on its development of a post-2020 strategic plans and conservation goals, and inform the development of a new generation of nature-centred scenarios.
Evidence for a reversal of the neural information flow between object perception and object reconstruction from memory
Authors: Linde-Domingo Juan , Treder Matthias S. , Kerren Casper , Wimber Maria 
Published: April 2018

AbstractRemembering is a reconstructive process. Surprisingly little is known about how the reconstruction of a memory unfolds in time in the human brain. We used reaction times and EEG time-series decoding to test the hypothesis that the information flow is reversed when an event is reconstructed from memory, compared to when the same event is initially being perceived. Across three experiments, we found highly consistent evidence supporting such a reversed stream. When seeing an object, low-level perceptual features were discriminated faster behaviourally, and could be decoded from brain activity earlier, than high-level conceptual features. This pattern reversed during associative memory recall, with reaction times and brain activity patterns now indicating that conceptual information was reconstructed more rapidly than perceptual details. Our findings support a neurobiologically plausible model of human memory, suggesting that memory retrieval is a hierarchical, multi-layered process that prioritizes semantically meaningful information over perceptual detail.
Multimerization of HIV-1 integrase hinges on conserved SH3-docking platforms
Authors: Galilee Meytal , Alian Akram 
Published: April 2018

ABSTRACTNew anti-AIDS treatments must be continually developed in order to overcome resistance mutations including those emerging in the newest therapeutic target, the viral integrase (IN). Multimerization of IN is functionally imperative and provides a forthcoming therapeutic target. Allosteric inhibitors of IN bind to non-catalytic sites and prevent correct multimerization not only restricting viral integration but also the assembly and maturation of viral particles. Here, we report an allosteric inhibitor peptide targeting an unexploited SH3-docking platform of retroviral IN. The crystal structure of the peptide in complex with the HIV-1 IN core domain reveals a steric interference that would inhibit conserved docking of SH3-containing domain with the core domain vital for IN multimerization, providing a template for the development of novel anti-IN allosteric inhibitors.
Exogenous putrescine alleviates photoinhibition caused by salt stress through increasing cyclic electron flow in cucumber
Authors: Wu Xinyi , Shu Sheng , Wang Yu , Yuan Ruonan , Guo Shirong 
Published: April 2018

AbstractWhen plants suffer from abiotic stresses, cyclic electron flow (CEF) is induced for photoprotection. Putrescine (Put), a main polyamine in chloroplasts, plays a critical role in stress tolerance. To elucidate the mechanism of Put regulating CEF for salt-tolerance in cucumber leaves, we measured chlorophyll fluorescence, P700 redox state, ATP and NADPH accumulation and so on. The maximum photochemical efficiency of PSII (Fv/Fm) was not influenced by NaCl and/or Put, but the activity of PSI reaction center (P700) was seriously inhibited by NaCl. Salt stress induced high level of CEF, moreover, NaCl and Put treated plants exhibited much higher CEF activity and ATP accumulation than single salt-treated plants to provide adequate ATP/NADPH ratio for plants growth. Furthermore, Put decreased the trans-membrane proton gradient (ΔpH), accompanied by reducing the pH-dependent non-photochemical quenching (qE) and increasing efficient quantum yield of PSII (Y(II)). The ratio of NADP+/NADPH in salt stressed leaves was significantly increased by Put, indicating that Put relieved over-reduction pressure at PSI accepter side. Taken together, our results suggest that exogenous Put enhances CEF to supply extra ATP for PSI recovery and CO2assimilation, decreases ΔpH for electron transport related proteins staying active, and enable the non-photochemical quenching transformed into photochemical quenching.
Selection of time points for costly experiments: a comparison between human intuition and computer-aided experimental design
Authors: Ezer Daphne , Keir Joseph C. 
Published: April 2018

AbstractMotivationThe design of an experiment influences both what a researcher can measure, as well as how much confidence can be placed in the results. As such, it is vitally important that experimental design decisions do not systematically bias research outcomes. At the same time, making optimal design decisions can produce results leading to statistically stronger conclusions. Deciding where and when to sample are among the most critical aspects of many experimental designs; for example, we might have to choose the time points at which to measure some quantity in a time series experiment. Choosing times which are too far apart could result in missing short bursts of activity. On the other hand, there may be time points which provide very little information regarding the overall behaviour of the quantity in question.ResultsIn this study, we design a survey to analyse how biologists use previous research outcomes to inform their decisions about which time points to sample in subsequent experiments. We then determine how the choice of time points affects the type of perturbations in gene expression that can be observed. Finally, we present our main result: NITPicker, a computational strategy for selecting optimal time points (or spatial points along a single axis), that eliminates some of the biases caused by human decision-making while maximising information about the shape of the underlying curves, utilising ideas from the field of functional data analysis.AvailabilityNITPicker is available on GIThub (https://github.com/ezer/NITPicker).
Population level rhythms in human skin: implications for circadian medicine
Authors: Wu Gang , Ruben Marc D. , Schmidt Robert E. , Francey Lauren J. , Smith David F. , Anafi Ron C. , Hughey Jacob J. , Tasseff Ryan , Sherrill Joseph D. , Oblong John E. , Mills Kevin J. , Hogenesch John B. 
Published: April 2018

AbstractSkin is the largest organ in the body and serves important barrier, regulatory, and sensory functions. Like other tissues, skin is subject to temporal fluctuations in physiological responses under both homeostatic and stressed states. To gain insight into these fluctuations, we investigated the role of the circadian clock in the transcriptional regulation of epidermis using a hybrid experimental design, where a limited set of human subjects (n=20) were sampled throughout the 24 h cycle and a larger population (n=219) were sampled once. By looking at pairwise correlations of core clock genes in 298 skin samples, we found a robust circadian oscillator in skin at the population level. Encouraged by this, we used CYCLOPS to reconstruct the temporal order of all samples and identified hundreds of rhythmically-expressed genes at the population level in human skin. We compared these results with published time-series skin data from mouse and show strong concordance in circadian phase across species for both transcripts and pathways. Further, like blood, skin is readily accessible and a potential source of biomarkers. Using ZeitZeiger, we identified a biomarker set for human skin that is capable of reporting circadian phase to within 3 h from a single sample. In summary, we show rhythms in human skin that persist at the population scale and a path to develop robust single-sample circadian biomarkers.One Sentence SummaryHuman epidermis shows strong circadian rhythms at the population scale and provides a better source for developing robust, single-sample circadian phase biomarkers than human blood.
Assessing key decisions for transcriptomic data integration in biochemical networks
Authors: Richelle Anne , Joshi Chintan , Lewis Nathan E. 
Published: April 2018

AbstractMotivationTo gain insights into complex biological processes, genome-scale data (e.g., RNA-Seq) are often overlaid on biochemical networks. However, many networks do not have a one-to-one relationship between genes and network edges, due to the existence of isozymes and protein complexes. Therefore, decisions must be made on how to overlay data onto networks. For example, for metabolic networks, these decisions include (1) how to integrate gene expression levels using gene-protein-reaction rules, (2) the approach used for selection of thresholds on expression data to consider the associated gene as “active”, and (3) the order in which these steps are imposed. However, the influence of these decisions has not been systematically tested.ResultsWe compared 20 decision combinations using a transcriptomic dataset across 32 tissues and showed that definition of which reaction may be considered as active is mainly influenced by thresholding approach used. To determine the most appropriate decisions, we evaluated how these decisions impact the acquisition of tissue-specific active reaction lists that recapitulate organ-system tissue groups. These results will provide guidelines to improve data analyses with biochemical networks and facilitate the construction of context-specific metabolic models.Contactnlewisres@ucsd.edu
Cycle-by-cycle analysis of neural oscillations
Authors: Cole Scott , Voytek Bradley 
Published: April 2018

SummaryNeural oscillations are widely studied using methods based on the Fourier transform, which models data as sums of sinusoids. For decades these Fourier-based approaches have successfully uncovered links between oscillations and cognition or disease. However, because of the fundamental sinusoidal basis, these methods might not fully capture neural oscillatory dynamics, because neural data are both nonsinusoidal and non-stationary. Here, we present a new analysis framework, complementary to Fourier analysis, that quantifies cycle-by-cycle time-domain features. For each cycle, the amplitude, period, and waveform symmetry are measured, the latter of which is missed using conventional approaches. Additionally, oscillatory bursts are algorithmically identified, allowing us to investigate the variability of oscillatory features within and between bursts. This approach is validated on simulated noisy signals with oscillatory bursts and outperforms conventional metrics. Further, these methods are applied to real data—including hippocampal theta, motor cortical beta, and visual cortical alpha—and can differentiate behavioral conditions.
Ak-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria
Authors: Aun Erki , Brauer Age , Kisand Veljo , Tenson Tanel , Remm Maido 
Published: April 2018

AbstractWe have developed an easy-to-use and memory-efficient method called PhenotypeSeeker that (a) generates ak-mer-based statistical model for predicting a given phenotype and (b) predicts the phenotype from the sequencing data of a given bacterial isolate. The method was validated on 167Klebsiella pneumoniaeisolates (virulence), 200Pseudomonas aeruginosaisolates (ciprofloxacin resistance) and 460Clostridium difficileisolates (azithromycin resistance). The phenotype prediction models trained from these datasets performed with 88% accuracy on theK. pneumoniaetest set, 88% on theP. aeruginosatest set and 96.5% on theC. difficiletest set. Prediction accuracy was the same for assembled sequences and raw sequencing data; however, building the model from assembled genomes is significantly faster. On these datasets, the model building on a mid-range Linux server takes approximately 3 to 5 hours per phenotype if assembled genomes are used and 10 hours per phenotype if raw sequencing data are used. The phenotype prediction from assembled genomes takes less than one second per isolate. Thus, PhenotypeSeeker should be well-suited for predicting phenotypes from large sequencing datasets.PhenotypeSeeker is implemented in Python programming language, is open-source software and is available at GitHub (https://github.com/bioinfo-ut/PhenotypeSeeker/).SummaryPredicting phenotypic properties of bacterial isolates from their genomic sequences has numerous potential applications. A good example would be prediction of antimicrobial resistance and virulence phenotypes for use in medical diagnostics. We have developed a method that is able to predict phenotypes of interest from the genomic sequence of the isolate within seconds. The method uses statistical model that can be trained automatically on isolates with known phenotype. The method is implemented in Python programming language and can be run on low-end Linux server and/or on laptop computers.