bluuebunny/crossref_metadata_2025_split huggingface dataset:
The amplifying influence of increased ocean stratification on a future year without a summer
Authors: Fasullo J. T. , Tomas R. , Stevenson S. , Otto-Bliesner B. , Brady E. , Wahl E. 
Published: October 2017

AbstractIn 1816, the coldest summer of the past two centuries was observed over northeastern North America and western Europe. This so-called Year Without a Summer (YWAS) has been widely attributed to the 1815 eruption of Indonesia’s Mt. Tambora and was concurrent with agricultural failures and famines worldwide. To understand the potential impacts of a similar future eruption, a thorough physical understanding of the YWAS is crucial. Climate model simulations of both the 1815 Tambora eruption and a hypothetical analogous future eruption are examined, the latter occurring in 2085 assuming a business-as-usual climate scenario. Here, we show that the 1815 eruption drove strong responses in both the ocean and cryosphere that were fundamental to driving the YWAS. Through modulation of ocean stratification and near-surface winds, global warming contributes to an amplified surface climate response. Limitations in using major volcanic eruptions as a constraint on cloud feedbacks are also found.
Using a quantum work meter to test non-equilibrium fluctuation theorems
Authors: Cerisola Federico , Margalit Yair , Machluf Shimon , Roncaglia Augusto J. , Paz Juan Pablo , Folman Ron 
Published: October 2017

AbstractWork is an essential concept in classical thermodynamics, and in the quantum regime, where the notion of a trajectory is not available, its definition is not trivial. For driven (but otherwise isolated) quantum systems, work can be defined as a random variable, associated with the change in the internal energy. The probability for the different values of work captures essential information describing the behaviour of the system, both in and out of thermal equilibrium. In fact, the work probability distribution is at the core of “fluctuation theorems” in quantum thermodynamics. Here we present the design and implementation of a quantum work meter operating on an ensemble of cold atoms, which are controlled by an atom chip. Our device not only directly measures work but also directly samples its probability distribution. We demonstrate the operation of this new tool and use it to verify the validity of the quantum Jarzynksi identity.
Identifying host regulators and inhibitors of liver stage malaria infection using kinase activity profiles
Authors: Arang Nadia , Kain Heather S. , Glennon Elizabeth K. , Bello Thomas , Dudgeon Denali R. , Walter Emily N. F. , Gujral Taranjit S. , Kaushansky Alexis 
Published: October 2017

AbstractPlasmodiumparasites have extensive needs from their host hepatocytes during the obligate liver stage of infection, yet there remains sparse knowledge of specific host regulators. Here we assess 34 host-targeted kinase inhibitors for their capacity to eliminatePlasmodium yoelii-infected hepatocytes. Using pre-existing activity profiles of each inhibitor, we generate a predictive computational model that identifies host kinases, which facilitatePlasmodium yoeliiliver stage infection. We predict 47 kinases, including novel and previously described kinases that impact infection. The impact of a subset of kinases is experimentally validated, including Receptor Tyrosine Kinases, members of the MAP Kinase cascade, and WEE1. Our approach also predicts host-targeted kinase inhibitors of infection, including compounds already used in humans. Three of these compounds, VX-680, Roscovitine and Sunitinib, each eliminate >85% of infection. Our approach is well-suited to uncover key host determinants of infection in difficult model systems, including field-isolated parasites and/or emerging pathogens.
Nonlinear dynamic characterization of two-dimensional materials
Authors: Davidovikj D. , Alijani F. , Cartamil-Bueno S. J. , van der Zant H. S. J. , Amabili M. , Steeneken P. G. 
Published: October 2017

AbstractOwing to their atomic-scale thickness, the resonances of two-dimensional (2D) material membranes show signatures of nonlinearities at forces of only a few picoNewtons. Although the linear dynamics of membranes is well understood, the exact relation between the nonlinear response and the resonator’s material properties has remained elusive. Here we show a method for determining the Young’s modulus of suspended 2D material membranes from their nonlinear dynamic response. To demonstrate the method, we perform measurements on graphene and MoS2 nanodrums electrostatically driven into the nonlinear regime at multiple driving forces. We show that a set of frequency response curves can be fitted using only the cubic spring constant as a fit parameter, which we then relate to the Young’s modulus of the material using membrane theory. The presented method is fast, contactless, and provides a platform for high-frequency characterization of the mechanical properties of 2D materials.
Mapping genomic and transcriptomic alterations spatially in epithelial cells adjacent to human breast carcinoma
Authors: Abdalla Moustafa , Tran-Thanh Danh , Moreno Juan , Iakovlev Vladimir , Nair Ranju , Kanwar Nisha , Abdalla Mohamed , Lee Jennifer P. Y. , Kwan Jennifer Yin Yee , Cawthorn Thomas R. , Warren Keisha , Arneson Nona , Wang Dong-Yu , Fox Natalie S. , Youngson Bruce J. , Miller Naomi A. , Easson Alexandra M. , McCready David , Leong Wey L. , Boutros Paul C. , Done Susan J. 
Published: October 2017

AbstractAlmost all genomic studies of breast cancer have focused on well-established tumours because it is technically challenging to study the earliest mutational events occurring in human breast epithelial cells. To address this we created a unique dataset of epithelial samples ductoscopically obtained from ducts leading to breast carcinomas and matched samples from ducts on the opposite side of the nipple. Here, we demonstrate that perturbations in mRNA abundance, with increasing proximity to tumour, cannot be explained by copy number aberrations. Rather, we find a possibility of field cancerization surrounding the primary tumour by constructing a classifier that evaluates where epithelial samples were obtained relative to a tumour (cross-validated micro-averaged AUC = 0.74). We implement a spectral co-clustering algorithm to define biclusters. Relating to over-represented bicluster pathways, we further validate two genes with tissue microarrays and in vitro experiments. We highlight evidence suggesting that bicluster perturbation occurs early in tumour development.
Multifunctional nanocomposite hollow fiber membranes by solvent transfer induced phase separation
Authors: Haase Martin F. , Jeon Harim , Hough Noah , Kim Jong Hak , Stebe Kathleen J. , Lee Daeyeon 
Published: October 2017

AbstractThe decoration of porous membranes with a dense layer of nanoparticles imparts useful functionality and can enhance membrane separation and anti-fouling properties. However, manufacturing of nanoparticle-coated membranes requires multiple steps and tedious processing. Here, we introduce a facile single-step method in which bicontinuous interfacially jammed emulsions are used to form nanoparticle-functionalized hollow fiber membranes. The resulting nanocomposite membranes prepared via solvent transfer-induced phase separation and photopolymerization have exceptionally high nanoparticle loadings (up to 50 wt% silica nanoparticles) and feature densely packed nanoparticles uniformly distributed over the entire membrane surfaces. These structurally well-defined, asymmetric membranes facilitate control over membrane flux and selectivity, enable the formation of stimuli responsive hydrogel nanocomposite membranes, and can be easily modified to introduce antifouling features. This approach forms a foundation for the formation of advanced nanocomposite membranes comprising diverse building blocks with potential applications in water treatment, industrial separations and as catalytic membrane reactors.
In vivo neurochemical measurements in cerebral tissues using a droplet-based monitoring system
Authors: Petit-Pierre Guillaume , Colin Philippe , Laurer Estelle , Déglon Julien , Bertsch Arnaud , Thomas Aurélien , Schneider Bernard L. , Renaud Philippe 
Published: October 2017

AbstractDirect collection of extracellular fluid (ECF) plays a central role in the monitoring of neurological disorders. Current approaches using microdialysis catheters are however drastically limited in term of temporal resolution. Here we show a functional in vivo validation of a droplet collection system included at the tip of a neural probe. The system comprises an advanced droplet formation mechanism which enables the collection of neurochemicals present in the brain ECF at high-temporal resolution. The probe was implanted in a rat brain and could successfully collect fluid samples organized in a train of droplets. A microfabricated target plate compatible with most of the surface-based detection methods was specifically developed for sample analysis. The time-resolved brain-fluid samples are analyzed using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The results provide a time evolution picture of the cerebral tissues neurochemical composition for selected elements known for their involvement in neurodegenerative diseases.
Songbirds work around computational complexity by learning song vocabulary independently of sequence
Authors: Lipkind Dina , Zai Anja T. , Hanuschkin Alexander , Marcus Gary F. , Tchernichovski Ofer , Hahnloser Richard H. R. 
Published: October 2017

AbstractWhile acquiring motor skills, animals transform their plastic motor sequences to match desired targets. However, because both the structure and temporal position of individual gestures are adjustable, the number of possible motor transformations increases exponentially with sequence length. Identifying the optimal transformation towards a given target is therefore a computationally intractable problem. Here we show an evolutionary workaround for reducing the computational complexity of song learning in zebra finches. We prompt juveniles to modify syllable phonology and sequence in a learned song to match a newly introduced target song. Surprisingly, juveniles match each syllable to the most spectrally similar sound in the target, regardless of its temporal position, resulting in unnecessary sequence errors, that they later try to correct. Thus, zebra finches prioritize efficient learning of syllable vocabulary, at the cost of inefficient syntax learning. This strategy provides a non-optimal but computationally manageable solution to the task of vocal sequence learning.
INA complex liaises the F1Fo-ATP synthase membrane motor modules
Authors: Naumenko Nataliia , Morgenstern Marcel , Rucktäschel Robert , Warscheid Bettina , Rehling Peter 
Published: October 2017

AbstractThe F1F0-ATP synthase translates a proton flux across the inner mitochondrial membrane into a mechanical rotation, driving anhydride bond formation in the catalytic portion. The complex’s membrane-embedded motor forms a proteinaceous channel at the interface between Atp9 ring and Atp6. To prevent unrestricted proton flow dissipating the H+-gradient, channel formation is a critical and tightly controlled step during ATP synthase assembly. Here we show that the INA complex (INAC) acts at this decisive step promoting Atp9-ring association with Atp6. INAC binds to newly synthesized mitochondrial-encoded Atp6 and Atp8 in complex with maturation factors. INAC association is retained until the F1-portion is built on Atp6/8 and loss of INAC causes accumulation of the free F1. An independent complex is formed between INAC and the Atp9 ring. We conclude that INAC maintains assembly intermediates of the F1 F0-ATP synthase in a primed state for the terminal assembly step–motor module formation.
Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia
Authors: Moder Martin , Velimezi Georgia , Owusu Michel , Mazouzi Abdelghani , Wiedner Marc , Ferreira da Silva Joana , Robinson-Garcia Lydia , Schischlik Fiorella , Slavkovsky Rastislav , Kralovics Robert , Schuster Michael , Bock Christoph , Ideker Trey , Jackson Stephen P. , Menche Jörg , Loizou Joanna I. 
Published: October 2017

AbstractMaintenance of genome integrity via repair of DNA damage is a key biological process required to suppress diseases, including Fanconi anemia (FA). We generated loss-of-function human haploid cells for FA complementation group C (FANCC), a gene encoding a component of the FA core complex, and used genome-wide CRISPR libraries as well as insertional mutagenesis to identify synthetic viable (genetic suppressor) interactions for FA. Here we show that loss of the BLM helicase complex suppresses FANCC phenotypes and we confirm this interaction in cells deficient for FA complementation group I and D2 (FANCI and FANCD2) that function as part of the FA I-D2 complex, indicating that this interaction is not limited to the FA core complex, hence demonstrating that systematic genome-wide screening approaches can be used to reveal genetic viable interactions for DNA repair defects.
The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity
Authors: Santanach Alexandra , Blanco Enrique , Jiang Hua , Molloy Kelly R. , Sansó Miriam , LaCava John , Morey Lluis , Di Croce Luciano 
Published: October 2017

AbstractPolycomb group proteins (PcG) are transcriptional repressors that control cell identity and development. In mammals, five different CBX proteins associate with the core Polycomb repressive complex 1 (PRC1). In mouse embryonic stem cells (ESCs), CBX6 and CBX7 are the most highly expressed CBX family members. CBX7 has been recently characterized, but little is known regarding the function of CBX6. Here, we show that CBX6 is essential for ESC identity. Its depletion destabilizes the pluripotency network and triggers differentiation. Mechanistically, we find that CBX6 is physically and functionally associated to both canonical PRC1 (cPRC1) and non-canonical PRC1 (ncPRC1) complexes. Notably, in contrast to CBX7, CBX6 is recruited to chromatin independently of H3K27me3. Taken together, our findings reveal that CBX6 is an essential component of ESC biology that contributes to the structural and functional complexity of the PRC1 complex.
Neural activations associated with feedback and retrieval success
Authors: Wiklund-Hörnqvist Carola , Andersson Micael , Jonsson Bert , Nyberg Lars 
Published: October 2017

AbstractThere is substantial behavioral evidence for a phenomenon commonly called “the testing effect”, i.e. superior memory performance after repeated testing compared to re-study of to-be-learned materials. However, considerably less is known about the underlying neuro-cognitive processes that are involved in the initial testing phase, and thus underlies the actual testing effect. Here, we investigated functional brain activity related to test-enhanced learning with feedback. Subjects learned foreign vocabulary across three consecutive tests with correct-answer feedback. Functional brain-activity responses were analyzed in relation to retrieval and feedback events, respectively. Results revealed up-regulated activity in fronto-striatal regions during the first successful retrieval, followed by a marked reduction in activity as a function of improved learning. Whereas feedback improved behavioral performance across consecutive tests, feedback had a negligable role after the first successful retrieval for functional brain-activity modulations. It is suggested that the beneficial effects of test-enhanced learning is regulated by feedback-induced updating of memory representations, mediated via the striatum, that might underlie the stabilization of memory commonly seen in behavioral studies of the testing effect.
Application of Multimodal Navigation together with Fluorescein Angiography in Microsurgical Treatment of Cerebral Arteriovenous Malformations
Authors: Feng Shiyu , Zhang Yanyang , Sun Zhenghui , Wu Chen , Xue Zhe , Ma Yudong , Jiang Jinli 
Published: October 2017

AbstractThis study aimed to explore the clinical applications of multimodal navigation combined with indocyanine green (ICG) fluorescein angiography in microsurgical treatment of cerebral arteriovenous malformations (AVMs). We retrospectively collected 52 patients with AVMs. Assisted by anatomic image, we reestablished three-dimensional structure using preoperative functional magnetic resonance imaging (fMRI) and Diffusion tensor imaging (DTI). The operation for lesion resection was finished under the assistance of neuro-navigation. ICG fluorescein angiography was performed for 16 of the study subjects, meanwhile, FLOW800 was used to rebuild blood vessel color visual image. Brain angiography was performed 1 week after the operation to check residual malformations. The patients’ status was estimated by Modified Rankin Scale score. Of the AVMs, 92.3% (48/52) were totally removed, without severe side events. Among the patients, fluorescein angiography was carried out up to 58 times for 16 cases. All of these 16 cases were confirmed with malformations and 14 of them had draining vein. The total resection rate of these 16 cases reached 100%, and the occurrence rate of postoperative complications was not significantly increased. During the operation of lesion resection, the application of multimodal navigation could effectively protect functional cortex and conduction pathway.
Identifying stably expressed housekeeping genes in the endometrium of fertile women, women with recurrent implantation failure and recurrent miscarriages
Authors: Stocker Linden , Cagampang Felino , Cheong Ying 
Published: October 2017

AbstractHousekeeping genes (HKG) are presumed to be constitutively expressed throughout tissue types but recent studies have shown they vary with pathophysiology. Often, validation of appropriate HKG is not made. There is no consensus on which HKGs are most stably expressed in endometrial tissue so this study aimed to identify the most stable HKG in the endometrium of women with recurrent implantation failure (RIF) and recurrent miscarriages (RM). Inclusion criteria were women between 25–45 years (n = 45) suffering recurrent miscarriage (RM), recurrent implantation failure (RIF) or fertile controls. Endometrial biopsies were taken and total RNA extraction, cDNA synthesis and PCR was performed using 10 candidate HKG. The genes were arranged in terms of stability and normalisation was determined. Several HKGs not previously tested in endometrial samples were found to be more stable than those previously identified as the most stable. Of these, the 5 most stable HKG (in order of stability) werePrdm4(PR domain 4) > Ube4a(Ubiquitin-Conjugating Enzyme 4a) > Enox2(Ecto-NOX Disulfide-Thiol Exchanger 2) > Ube2d2(Ubiquitin-conjugating enzyme E2D 2) > Actb(Actin beta). We therefore recommend using at least four of the aforementioned HKG for normalisation of endometrial tissues taken from patients with RM and RIF.
Modulation of the Vault Protein-Protein Interaction for Tuning of Molecular Release
Authors: Yu Kang , Yau Yin Hoe , Sinha Ameya , Tan Tabitha , Kickhoefer Valerie A. , Rome Leonard H. , Lee Hwankyu , Shochat Susana G. , Lim Sierin 
Published: October 2017

AbstractVaults are naturally occurring ovoid nanoparticles constructed from a protein shell that is composed of multiple copies of major vault protein (MVP). The vault-interacting domain of vault poly(ADP-ribose)-polymerase (INT) has been used as a shuttle to pack biomolecular cargo in the vault lumen. However, the interaction between INT and MVP is poorly understood. It is hypothesized that the release rate of biomolecular cargo from the vault lumen is related to the interaction between MVP and INT. To tune the release of molecular cargos from the vault nanoparticles, we determined the interactions between the isolated INT-interacting MVP domains (iMVP) and wild-type INT and compared them to two structurally modified INT: 15-amino acid deletion at the C terminus (INTΔC15) and histidine substituted at the interaction surface (INT/DSA/3 H) to impart a pH-sensitive response. The apparent affinity constants determined using surface plasmon resonance (SPR) biosensor technology are 262 ± 4 nM for iMVP/INT, 1800 ± 160 nM for iMVP/INTΔC15 at pH 7.4. The INT/DSA/3 H exhibits stronger affinity to iMVP (KDapp
= 24 nM) and dissociates at a slower rate than wild-type INT at pH 6.0.
Using non-invasive transcranial stimulation to improve motor and cognitive function in Parkinson’s disease: a systematic review and meta-analysis
Authors: Goodwill Alicia M. , Lum Jarrad A. G. , Hendy Ashlee M. , Muthalib Makii , Johnson Liam , Albein-Urios Natalia , Teo Wei-Peng 
Published: October 2017

AbstractParkinson's disease (PD) is a neurodegenerative disorder affecting motor and cognitive abilities. There is no cure for PD, therefore identifying safe therapies to alleviate symptoms remains a priority. This meta-analysis quantified the effectiveness of repetitive transcranial magnetic stimulation (rTMS) and transcranial electrical stimulation (TES) to improve motor and cognitive dysfunction in PD. PubMed, EMBASE, Web of Science, Google Scholar, Scopus, Library of Congress and Cochrane library were searched. 24 rTMS and 9 TES studies (n = 33) with a sham control group were included for analyses. The Physiotherapy Evidence Database and Cochrane Risk of Bias showed high quality (7.5/10) and low bias with included studies respectively. Our results showed an overall positive effect in favour of rTMS (SMD = 0.394, CI [0.106–0.683], p = 0.007) and TES (SMD = 0.611, CI [0.188–1.035], p = 0.005) compared with sham stimulation on motor function, with no significant differences detected between rTMS and TES (Q [1] = 0.69, p = 0.406). Neither rTMS nor TES improved cognition. No effects for stimulation parameters on motor or cognitive function were observed. To enhance the clinical utility of non-invasive brain stimulation (NBS), individual prescription of stimulation parameters based upon symptomology and resting excitability state should be a priority of future research.
Prevalence and genotype distribution of human papillomavirus in 961,029 screening tests in southeastern China (Zhejiang Province) between 2011 and 2015
Authors: Chen Xiao , Xu Haiou , Xu Wanwan , Zeng Wenjie , Liu Jinwei , Wu Qing , Zhao Xiaofeng , Jiang Tang 
Published: October 2017

AbstractHuman papillomavirus infection plays a key role in the development of cervical cancer. To establish a foundation for HPV-based screening and vaccination programs, we investigated the HPV prevalence and genotypic distributions in Chinese women from Zhejiang Province. Between 2011 and 2015, a total of 961,029 samples from 2021 clinical hospitals were tested HPV genotype by a PCR-based hybridization gene chip assay, and 443,890 samples were evaluated cervical cytology by liquid-based cytology analysis. Our results showed that the positive rate for HPV was 20.54%, which ranged from 28.72% to 17.81% and varied by year of recruitment. Age-specific prevalence showed a “two-peak” pattern, with the ≤20-year-old group presenting the highest HPV infection rate, followed by 61–70-year-old group. Overall, the most prevalent genotypes were HPV16, 52 and 58. Additionally, the odds ratios for the prevalence of the HR-HPV, LR-HPV and HPV-negative groups with abnormal cytology were 12.56, 3.21 and 0.06, respectively. Among genotypes, HPV 16 has been found to have the highest OR, followed by HPV58, 18, 52. Here, we present data regarding the prevalence and type distribution of HPV infection, which can serve as valuable reference to guide nationwide cervical cancer screening and HPV vaccination programs.