bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways
Authors: Heinz Leonard P. , Kopec Wojciech , de Groot Bert L. , Fink Rainer H. A. 
Published: April 2018

AbstractThe ryanodine receptor 1 is a large calcium ion channel found in mammalian skeletal muscle. The ion channel gained a lot of attention recently, after multiple independent authors published near-atomic cryo electron microscopy data. Taking advantage of the unprecedented quality of structural data, we performed molecular dynamics simulations on the entire ion channel as well as on a reduced model. We calculated potentials of mean force for Ba2+, Ca2+, Mg2+, K+, Na+and Cl−ions using umbrella sampling to identify the key residues involved in ion permeation. We found two main binding sites for the cations, whereas the channel is strongly repulsive for chloride ions. Furthermore, the data is consistent with the model that the receptor achieves its ion selectivity by over-affinity for divalent cations in a calcium-block-like fashion. We reproduced the experimental conductance for potassium ions in permeation simulations with applied voltage. The analysis of the permeation paths shows that ions exit the pore via multiple pathways, which we suggest to be related to the experimental observation of different subconducting states.
Namib Desert primary productivity is driven by cryptic microbial community N-fixation
Authors: Ramond Jean-Baptiste , Woodborne Stephan , Hall Grant , Seely Mary , Cowan Don A. 
Published: April 2018

AbstractCarbon exchange in drylands is typically low, but during significant rainfall events (wet anomalies) drylands act as a C sink. During these anomalies the limitation on C uptake switches from water to nitrogen. In the Namib Desert of southern Africa, the N inventory in soil organic matter available for mineralisation is insufficient to support the observed increase in primary productivity. The C4 grasses that flourish after rainfall events are not capable of N fixation, and so there is no clear mechanism for adequate N fixation in dryland ecosystems to support rapid C uptake. Here we demonstrate that N fixation by photoautotrophic hypolithic communities forms the basis for the N budget for plant productivity events in the Namib Desert. Stable N isotope (δ15N) values of Namib Desert hypolithic biomass, and surface and subsurface soils were measured over 3 years across dune and gravel plain biotopes. Hypoliths showed significantly higher biomass and lower δ15N values than soil organic matter. The δ15N values of hypoliths approach the theoretical values for nitrogen fixation. Our results are strongly indicative that hypolithic communities are the foundation of productivity after rain events in the Namib Desert and are likely to play similar roles in other arid environments.
Monitoring voltage fluctuations of intracellular membranes
Authors: Sepehri Rad Masoud , Cohen Lawrence B. , Braubach Oliver , Baker Bradley J. 
Published: April 2018

AbstractIn eukaryotic cells, the endoplasmic reticulum (ER) is the largest continuous membrane-enclosed network which surrounds a single lumen. Using a new genetically encoded voltage indicator (GEVI), we applied the patch clamp technique to cultured HEK293 cells and neurons and found that there is a very fast electrical interaction between the plasma membrane and internal membrane(s). This discovery suggests a novel mechanism for interaction between the external membrane and internal membranes as well as mechanisms for interactions between the various internal membranes. The ER may transfer electrical signals between the plasma membrane and other internal organelles. The internal membrane optical signal is reversed in polarity but has a time course similar to that of the plasma membrane signal. The optical signal of the GEVI in the plasma membrane is consistent from trial to trial. However, the internal signal decreases in size with repeated trials suggesting that the electrical coupling is degrading and/or the resistance of the internal membrane is decaying.
The stage of seed development influences iron bioavailability in pea (Pisum sativum L.)
Authors: Moore Katie L. , Rodríguez-Ramiro Ildefonso , Jones Eleanor R. , Jones Emily J. , Rodríguez-Celma Jorge , Halsey Kirstie , Domoney Claire , Shewry Peter R. , Fairweather-Tait Susan , Balk Janneke 
Published: April 2018

AbstractPea seeds are widely consumed in their immature form, known as garden peas and petit pois, mostly after preservation by freezing or canning. Mature dry peas are rich in iron in the form of ferritin, but little is known about the content, form or bioavailability of iron in immature stages of seed development. Using specific antibodies and in-gel iron staining, we show that ferritin loaded with iron accumulated gradually during seed development. Immunolocalization and high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that iron-loaded ferritin was located at the surface of starch-containing plastids. Standard cooking procedures destabilized monomeric ferritin and the iron-loaded form. Iron uptake studies using Caco-2 cells showed that the iron in microwaved immature peas was more bioavailable than in boiled mature peas, despite similar levels of soluble iron in the digestates. By manipulating the levels of phytic acid in the digestates we demonstrate that phytic acid is the main inhibitor of iron uptake from mature peas in vitro. Taken together, our data show that immature peas and mature dry peas contain similar levels of ferritin-iron, which is destabilized during cooking. However, iron from immature peas is more bioavailable because of lower phytic acid levels compared to mature peas.
Elevated leptin and decreased adiponectin independently predict the post-thrombotic syndrome in obese and non-obese patients
Authors: Mrozinska Sandra , Cieslik Joanna , Broniatowska Elżbieta , Undas Anetta 
Published: April 2018

AbstractPost-thrombotic syndrome (PTS) is a common complication of deep vein thrombosis (DVT). Little is known about the involvement of adipokines in the pathogenesis of DVT. We evaluated whether adipokines can predict PTS. In a prospective cohort study, 320 DVT patients aged 70 years or less were enrolled. Serum adiponectin, leptin and resistin levels were measured three months since the index first-ever DVT. After 2 years’ follow-up PTS was diagnosed in 83 of 309 available patients (26.9%) who had 13.9% lower adiponectin and 16% higher leptin levels compared with the remainder (both p < 0.0001). No PTS-associated differences in C-reactive protein, fibrinogen, D-dimer, plasminogen activator inhibitor-1 and resistin were observed. The multivariable logistic regression adjusted for age, sex, obesity and tissue plasminogen activator (tPa) showed that lower adiponectin (odds ratio [OR], 0.42; 95% confidence interval [CI], 0.31–0.56) and higher leptin levels (OR, 1.49; 95% CI, 1.31–1.69) are independent predictors for PTS. Obesity-stratified logistic regression analysis confirmed that lower adiponectin (OR, 0.49; 95% CI, 0.38–0.64) and higher leptin (OR, 1.41; 95% Cl, 1.25–1.58) levels predicted PTS. Our findings showed that lower adiponectin and higher leptin measured 3 months after DVT, regardless of obesity, can independently predict PTS, which suggests novel links between adipokines and thrombosis.
Recurrent complex spinal tuberculosis accompanied by sinus tract formation: causes of recurrence and clinical treatments
Authors: Wang Biao , Kong Lingbo , Zhu Ziqi , Gao Wenjie , Guo Hua , Wang Xiaodong , Li Hui , Zhao Qinpeng , Zhang Haiping , Hao Dingjun 
Published: April 2018

AbstractRecurrent complex spinal tuberculosis accompanied by sinus tract formation is one of the most common and complex types of recurrent tuberculosis. To date, only very few studies have reported the strategies and effectiveness of surgical treatments on postoperative recurrent spinal tuberculosis accompanied by sinus tract formation. In this study, 21 recurrent patients out of 87 patients with complex spinal tuberculosis were reviewed. The data of the patients, including age, gender, existence of drug-resistant mycobacterium tuberculosis, postoperative standard chemotherapy, completeness of lesion debridement, reconstruction of the spinal stability, nutritional status, accompaniment by tuberculosis in other regions, timing of the operations, and areas of the lesions, were collected for single- and multiple-factor analyses. The clinical outcomes were evaluated by long-term follow-ups. The results showed that 7 factors were significantly associated with postoperative recurrence of complex spinal tuberculosis accompanied by sinus tract formation. This suggested that when we treat complex spinal tuberculosis, we should pay more attention to these seven indicators to avoid postoperative recurrence, and our clinical outcomes suggested that it is difficult to treat recurrent complicated spinal tuberculosis combined with sinus tract formation. The key for successful surgical treatment includes effective chemotherapy, radical debridement and proper reconstruction of spinal stability.
The behavioral and neural binding phenomena during visuomotor integration of angry facial expressions
Authors: Coll Sélim Yahia , Ceravolo Leonardo , Frühholz Sascha , Grandjean Didier 
Published: April 2018

AbstractDifferent parts of our brain code the perceptual features and actions related to an object, causing a binding problem, in which the brain has to integrate information related to an event without any interference regarding the features and actions involved in other concurrently processed events. Using a paradigm similar to Hommel, who revealed perception-action bindings, we showed that emotion could bind with motor actions when relevant, and in specific conditions, irrelevant for the task. By adapting our protocol to a functional Magnetic Resonance Imaging paradigm we investigated, in the present study, the neural bases of the emotion-action binding with task-relevant angry faces. Our results showed that emotion bound with motor responses. This integration revealed increased activity in distributed brain areas involved in: (i) memory, including the hippocampi; (ii) motor actions with the precentral gyri; (iii) and emotion processing with the insula. Interestingly, increased activations in the cingulate gyri and putamen, highlighted their potential key role in the emotion-action binding, due to their involvement in emotion processing, motor actions, and memory. The present study confirmed our previous results and point out for the first time the functional brain activity related to the emotion-action association.
Si Nanocrystal-Embedded SiO
x
nanofoils: Two-Dimensional Nanotechnology-Enabled High Performance Li Storage Materials
Authors: Yoo Hyundong , Park Eunjun , Bae Juhye , Lee Jaewoo , Chung Dong Jae , Jo Yong Nam , Park Min-Sik , Kim Jung Ho , Dou Shi Xue , Kim Young-Jun , Kim Hansu 
Published: April 2018

AbstractSilicon (Si) based materials are highly desirable to replace currently used graphite anode for lithium ion batteries. Nevertheless, its usage is still a big challenge due to poor battery performance and scale-up issue. In addition, two-dimensional (2D) architectures, which remain unresolved so far, would give them more interesting and unexpected properties. Herein, we report a facile, cost-effective, and scalable approach to synthesize Si nanocrystals embedded 2D SiO
x
nanofoils for next-generation lithium ion batteries through a solution-evaporation-induced interfacial sol-gel reaction of hydrogen silsesquioxane (HSiO1.5, HSQ). The unique nature of the thus-prepared centimeter scale 2D nanofoil with a large surface area enables ultrafast Li+ insertion and extraction, with a reversible capacity of more than 650 mAh g−1, even at a high current density of 50 C (50 A g−1). Moreover, the 2D nanostructured Si/SiO
x
nanofoils show excellent cycling performance up to 200 cycles and maintain their initial dimensional stability. This superior performance stems from the peculiar nanoarchitecture of 2D Si/SiO
x
nanofoils, which provides short diffusion paths for lithium ions and abundant free space to effectively accommodate the huge volume changes of Si during cycling.
Mineral dust as a driver of carbon accumulation in northern latitudes
Authors: Kylander Malin E. , Martínez-Cortizas A. , Bindler Richard , Kaal Joeri , Sjöström Jenny K. , Hansson Sophia V. , Silva-Sánchez Noemí , Greenwood Sarah L. , Gallagher Kerry , Rydberg Johan , Mörth Carl-Magnus , Rauch Sebastien 
Published: April 2018

AbstractPeatlands in northern latitudes sequester one third of the world’s soil organic carbon. Mineral dusts can affect the primary productivity of terrestrial systems through nutrient transport but this process has not yet been documented in these peat-rich regions. Here we analysed organic and inorganic fractions of an 8900-year-old sequence from Store Mosse (the “Great Bog”) in southern Sweden. Between 5420 and 4550 cal yr BP, we observe a seven-fold increase in net peat-accumulation rates corresponding to a maximum carbon-burial rate of 150 g C m−2 yr−1 – more than six times the global average. This high peat accumulation event occurs in parallel with a distinct change in the character of the dust deposited on the bog, which moves from being dominated by clay minerals to less weathered, phosphate and feldspar minerals. We hypothesize that this shift boosted nutrient input to the bog and stimulated ecosystem productivity. This study shows that diffuse sources and dust dynamics in northern temperate latitudes, often overlooked by the dust community in favour of arid and semi-arid regions, can be important drivers of peatland carbon accumulation and by extension, global climate, warranting further consideration in predictions of future climate variability.
Concurrent micro- to macro-cardiac electrophysiology in myocyte cultures and human heart slices
Authors: Chowdhury Rasheda A. , Tzortzis Konstantinos N. , Dupont Emmanuel , Selvadurai Shaun , Perbellini Filippo , Cantwell Chris D. , Ng Fu Siong , Simon Andre R. , Terracciano Cesare M. , Peters Nicholas S. 
Published: April 2018

AbstractThe contact cardiac electrogram is derived from the extracellular manifestation of cellular action potentials and cell-to-cell communication. It is used to guide catheter based clinical procedures. Theoretically, the contact electrogram and the cellular action potential are directly related, and should change in conjunction with each other during arrhythmogenesis, however there is currently no methodology by which to concurrently record both electrograms and action potentials in the same preparation for direct validation of their relationships and their direct mechanistic links. We report a novel dual modality apparatus for concurrent electrogram and cellular action potential recording at a single cell level within multicellular preparations. We further demonstrate the capabilities of this system to validate the direct link between these two modalities of voltage recordings.
EAAC1 gene deletion reduces adult hippocampal neurogenesis after transient cerebral ischemia
Authors: Choi Bo Young , Won Seok Joon , Kim Jin Hee , Sohn Min , Song Hong Ki , Chung Tae Nyoung , Kim Tae Yul , Suh Sang Won 
Published: April 2018

AbstractSeveral studies have demonstrated that excitatory amino acid carrier-1 (EAAC1) gene deletion exacerbates hippocampal and cortical neuronal death after ischemia. However, presently there are no studies investigating the role of EAAC1 in hippocampal neurogenesis. In this study, we tested the hypothesis that reduced cysteine transport into neurons by EAAC1 knockout negatively affects adult hippocampal neurogenesis under physiological or pathological states. This study used young mice (aged 3–5 months) and aged mice (aged 11–15 months) of either the wild-type (WT) or EAAC1
−/−
genotype. Ischemia was induced through the occlusion of bilateral common carotid arteries for 30 minutes. Histological analysis was performed at 7 or 30 days after ischemia. We found that both young and aged mice with loss of the EAAC1 displayed unaltered cell proliferation and neuronal differentiation, as compared to age-matched WT mice under ischemia-free conditions. However, neurons generated from EAAC1
−/−
mice showed poor survival outcomes in both young and aged mice. In addition, deletion of EAAC1 reduced the overall level of neurogenesis, including cell proliferation, differentiation, and survival after ischemia. The present study demonstrates that EAAC1 is important for the survival of newly generated neurons in the adult brain under physiological and pathological conditions. Therefore, this study suggests that EAAC1 plays an essential role in modulating hippocampal neurogenesis.
Electrochemical detection of NGF using a reduced graphene oxide- titanium nitride nanocomposite
Authors: Wei Zheng , Wang Yanchun , Zhang Junping 
Published: April 2018

AbstractThere is a correlation between the severity of neurological impairment in patients that have suffered a cerebrovascular accident and the nerve growth factor (NGF) level. This study addressed the fabrication of a titanium nitride (TiN) and reduced graphene oxide (RGO)-based composite with remarkable electrocatalytic activity towards NGF oxidation in a phosphate buffer solution (PB, 0.1 M). The proposed electrochemical sensor was linearly related to the NGF concentration in the range of 10 nM-5 μM with a detection limit of 2.6 nM.
Chalcogen passivation: an in-situ method to manipulate the morphology and electrical property of GaAs nanowires
Authors: Yang Zai-xing , Yin Yanxue , Sun Jiamin , Bian Luozhen , Han Ning , Zhou Ziyao , Shu Lei , Wang Fengyun , Chen Yunfa , Song Aimin , Ho Johnny C. 
Published: April 2018

AbstractRecently, owing to the large surface-area-to-volume ratio of nanowires (NWs), manipulation of their surface states becomes technologically important and being investigated for various applications. Here, an in-situ surfactant-assisted chemical vapor deposition is developed with various chalcogens (e.g. S, Se and Te) as the passivators to enhance the NW growth and to manipulate the controllable p-n conductivity switching of fabricated NW devices. Due to the optimal size effect and electronegativity matching, Se is observed to provide the best NW surface passivation in diminishing the space charge depletion effect induced by the oxide shell and yielding the less p-type (i.e. inversion) or even insulating conductivity, as compared with S delivering the intense p-type conductivity for thin NWs with the diameter of ~30 nm. Te does not only provide the surface passivation, but also dopes the NW surface into n-type conductivity by donating electrons. All of the results can be extended to other kinds of NWs with similar surface effects, resulting in careful device design considerations with appropriate surface passivation for achieving the optimal NW device performances.
Explicit size distributions of failure cascades redefine systemic risk on finite networks
Authors: Burkholz Rebekka , Herrmann Hans J. , Schweitzer Frank 
Published: April 2018

AbstractHow big is the risk that a few initial failures of nodes in a network amplify to large cascades that span a substantial share of all nodes? Predicting the final cascade size is critical to ensure the functioning of a system as a whole. Yet, this task is hampered by uncertain and missing information. In infinitely large networks, the average cascade size can often be estimated by approaches building on local tree and mean field approximations. Yet, as we demonstrate, in finite networks, this average does not need to be a likely outcome. Instead, we find broad and even bimodal cascade size distributions. This phenomenon persists for system sizes up to 107 and different cascade models, i.e. it is relevant for most real systems. To show this, we derive explicit closed-form solutions for the full probability distribution of the final cascade size. We focus on two topological limit cases, the complete network representing a dense network with a very narrow degree distribution, and the star network representing a sparse network with a inhomogeneous degree distribution. Those topologies are of great interest, as they either minimize or maximize the average cascade size and are common motifs in many real world networks.
Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)
Authors: Beermann Jan , Westbury Michael V. , Hofreiter Michael , Hilgers Leon , Deister Fabian , Neumann Hermann , Raupach Michael J. 
Published: April 2018

AbstractTaxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of ‘taxonomics’. Here, we describe the cryptic speciesEpimeria frankeisp. nov. from the North Sea, and also redescribe its sister species,Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
Inherent flexibility of CLIC6 revealed by crystallographic and solution studies
Authors: Ferofontov Alisa , Strulovich Roi , Marom Milit , Giladi Moshe , Haitin Yoni 
Published: April 2018

AbstractChloride intracellular channels (CLICs) are a family of unique proteins, that were suggested to adopt both soluble and membrane-associated forms. Moreover, following this unusual metamorphic change, CLICs were shown to incorporate into membranes and mediate ion conductionin vitro, suggesting multimerization upon membrane insertion. Here, we present a 1.8 Å resolution crystal structure of the CLIC domain of mouse CLIC6 (mCLIC6). The structure reveals a monomeric arrangement and shows a high degree of structural conservation with other CLICs. Small-angle X-ray scattering (SAXS) analysis of mCLIC6 demonstrated that the overall solution structure is similar to the crystallographic conformation. Strikingly, further analysis of the SAXS data using ensemble optimization method unveiled additional elongated conformations, elucidating high structural plasticity as an inherent property of the protein. Moreover, structure-guided perturbation of the inter-domain interface by mutagenesis resulted in a population shift towards elongated conformations of mCLIC6. Additionally, we demonstrate that oxidative conditions induce an increase in mCLIC6 hydrophobicity along with mild oligomerization, which was enhanced by the presence of membrane mimetics. Together, these results provide mechanistic insights into the metamorphic nature of mCLIC6.