bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glomerulocapillary miRNA response to HLA-class I antibody in vitro and in vivo
Authors: Heinemann Falko M. , Jindra Peter T. , Bockmeyer Clemens L. , Zeuschner Philip , Wittig Juliane , Höflich Heike , Eßer Marc , Abbas Mahmoud , Dieplinger Georg , Stolle Katharina , Vester Udo , Hoyer Peter F. , Immenschuh Stephan , Heinold Andreas , Horn Peter A. , Li Wentian , Eisenberger Ute , Becker Jan U. 
Published: October 2017

AbstractChanges in miRNA expression of glomerular capillaries during antibody-mediated rejection (ABMR) are poorly understood and could contribute to the deleterious inflammation and fibrosis of ABMR via suppression of target genes. A better understanding could lead to novel diagnostic tools and reveal novel therapeutic targets. We explored deregulated miRNAs in an glomeruloendothelialin vitromodel of ABMR due to class I human leukocyte antigen (HLA) with and without complement activation. We studied a set of 16 promising candidate miRNAs in microdissected glomeruli a confirmation set of 20 human transplant biopsies (DSA+) compared to 10 matched controls without evidence for ABMR. Twelve out of these 16 glomerulocapillary miRNAs could successfully be confirmed as dysregulatedin vivowith 10 upregulated (let-7c-5p, miR-28-3p, miR-30d-5p, miR-99b-5p, miR-125a-5p, miR-195-5p, miR-374b-3p, miR-484, miR-501-3p, miR-520e) and 2 downregulated (miR29b-3p, miR-885-5p) in DSA+ vs. controls. A random forest analysis based on glomerular miRNAs identified 18/20 DSA+ and 8/10 controls correctly. This glomerulocapillary miRNA signature associated with HLA class I-DSA could improve our understanding of ABMR and be useful for diagnostic or therapeutic purposes.
A digital microfluidic system for loop-mediated isothermal amplification and sequence specific pathogen detection
Authors: Wan Liang , Chen Tianlan , Gao Jie , Dong Cheng , Wong Ada Hang-Heng , Jia Yanwei , Mak Pui-In , Deng Chu-Xia , Martins Rui P. 
Published: October 2017

AbstractA digital microfluidic (DMF) system has been developed for loop-mediated isothermal amplification (LAMP)-based pathogen nucleic acid detection using specific low melting temperature (Tm) Molecular Beacon DNA probes. A positive-temperature-coefficient heater with a temperature sensor for real-time thermal regulation was integrated into the control unit, which generated actuation signals for droplet manipulation. To enhance the specificity of the LAMP reaction, low-Tm Molecular Beacon probes were designed within the single-stranded loop structures on the LAMP reaction products. In the experiments, only 1 μL of LAMP reaction samples containing purified Trypanosoma brucei DNA were required, which represented over a 10x reduction of reagent consumption when comparing with the conventional off-chip LAMP. On-chip LAMP for unknown sample detection could be accomplished in 40 min with a detection limit of 10 copies/reaction. Also, we accomplished an on-chip melting curve analysis of the Molecular Beacon probe from 30 to 75 °C within 5 min, which was 3x faster than using a commercial qPCR machine. Discrimination of non-specific amplification and lower risk of aerosol contamination for on-chip LAMP also highlight the potential utilization of this system in clinical applications. The entire platform is open for further integration with sample preparation and fluorescence detection towards a total-micro-analysis system.
New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter
Authors: Huang Yuhong , Yi Zhuolin , Jin Yanling , Zhao Yonggui , He Kaize , Liu Dayu , Zhao Dong , He Hui , Luo Huibo , Zhang Wenxue , Fang Yang , Zhao Hai 
Published: October 2017

AbstractTraditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively. The relatively high diversity was observed when the temperature increased to 70 and 62 °C for Jiang- and Nong-flavor liquor starter, respectively. Some thermophilic fungi have already been isolated. Microbial communities that might contribute to ethanol fermentation, saccharification and flavor development were identified and shown to be core communities in correlation-based network analysis. The predictively functional profile of bacterial communities showed significant difference in energy, carbohydrate and amino acid metabolism and the degradation of aromatic compounds between the two kinds of liquor starters. Here we report these liquor starters as a new functionally microbial resource, which can be used for discovering thermophilic and aerobic enzymes and for food and feed preservation.
The Correlation of Pirani and Dimeglio Scoring Systems for Ponseti Management at Different Levels of Deformity Severity
Authors: Fan Hua , Liu Yubin , Zhao Li , Chu Caiting , An Yongyu , Wang Tingting , Li Wenhua 
Published: October 2017

AbstractThe Pirani and Dimeglio scoring systems both have excellent inter-observer and intra-observer reliability, but no research has been conducted to determine their inter-observer reliability and their relationship at different levels of deformity. A total of 173 idiopathic clubfoot cases were reviewed using Pirani and Dimeglio scoring systems, and the number of casts needed was also recorded. For clubfeet with a cast number equal to 2 or 7 and 8, the inter-observer reliability of the two scoring systems was poor or moderate, and there was no correlation between the two scoring systems. There was also no correlation between the Dimeglio scoring score with the number of casts for grade II or IV clubfeet. A binary regression of the number of casts on initial Pirani or Dimeglio scores showed that there was a Quadratic or Cubic relation between the scores and the cast numbers. In conclusion, in the case of mild and very severe clubfoot deformity, the interobserver reliability and its ability to predict the number of casts needed for clubfoot deformity correction was poor. A more objective evaluation system may be required.
Bipolar configuration with twisted loop defect in chiral nematic droplets under homeotropic surface anchoring
Authors: Krakhalev Mikhail N. , Gardymova Anna P. , Prishchepa Oxana O. , Rudyak Vladimir Yu. , Emelyanenko Alexander V. , Liu Jui-Hsiang , Zyryanov Victor Ya. 
Published: October 2017

AbstractOptical textures and appropriate orientational structures have been studied within droplets of chiral nematic dispersed in polymer assigning the homeotropic anchoring. The helix axis of the chiral structure inside droplets forms the bipolar configuration. The optical droplet textures were analysed in the unpolarised light, analyser switching-off scheme and in crossed polarisers. The twisted loop defect reveals itself convincingly in all schemes. Its appearance at the optical patterns of the chiral nematic droplets has been examined depending on their size and the aspect direction. The existence of the defect has been verified by the structural and optical calculations. The effect of an electric field on both the defect line shape and the orientational structure of chiral nematic has been studied.
Protein profiling identified key chemokines that regulate the maintenance of human pluripotent stem cells
Authors: Jiang Zongmin , Li Yonggang , Ji Xinglai , Tang Yiyuli , Yu Haijing , Ding Lei , Yu Min , Cui Qinghua , Zhang Ming , Ma Yanping , Li Meizhang 
Published: October 2017

AbstractMicroenvironment (or niche)-providing chemokines regulate many important biological functions of tissue-specific stem cells. However, to what extent chemokines influence human pluripotent stem cells (hPSCs) is not yet completely understood. In this study, we applied protein array to screen chemokines found within the cytokine pool in the culture supernatant of hPSCs. Our results showed that chemokines were the predominant supernatant components, and came from three sources: hPSCs, feeder cells, and culture media. Chemotaxis analysis of IL-8, SDF-1α, and IP-10 suggested that chemokines function as uniform chemoattractants to mediate in vitro migration of the hPSCs. Chemokines mediate both differentiated and undifferentiated states of hPSCs. However, balanced chemokine signaling tends to enhance their stemness in vitro. These results indicate that chemokines secreted from both stem cells and feeder cells are essential to mobilize hPSCs and maintain their stemness.
Interactive phenotyping of large-scale histology imaging data with HistomicsML
Authors: Nalisnik Michael , Amgad Mohamed , Lee Sanghoon , Halani Sameer H. , Velazquez Vega Jose Enrique , Brat Daniel J. , Gutman David A. , Cooper Lee A. D. 
Published: October 2017

AbstractWhole-slide imaging of histologic sections captures tissue microenvironments and cytologic details in expansive high-resolution images. These images can be mined to extract quantitative features that describe tissues, yielding measurements for hundreds of millions of histologic objects. A central challenge in utilizing this data is enabling investigators to train and evaluate classification rules for identifying objects related to processes like angiogenesis or immune response. In this paper we describe HistomicsML, an interactive machine-learning system for digital pathology imaging datasets. This framework uses active learning to direct user feedback, making classifier training efficient and scalable in datasets containing 108+ histologic objects. We demonstrate how this system can be used to phenotype microvascular structures in gliomas to predict survival, and to explore the molecular pathways associated with these phenotypes. Our approach enables researchers to unlock phenotypic information from digital pathology datasets to investigate prognostic image biomarkers and genotype-phenotype associations.
Modulating medial septal cholinergic activity reduces medial entorhinal theta frequency without affecting speed or grid coding
Authors: Carpenter Francis , Burgess Neil , Barry Caswell 
Published: October 2017

AbstractMedial septal inputs to the hippocampal system are crucial for aspects of temporal and spatial processing, such as theta oscillations and grid cell firing. However, the precise contributions of the medial septum’s cholinergic neurones to these functions remain unknown. Here, we recorded neuronal firing and local field potentials from the medial entorhinal cortex of freely foraging mice, while modulating the excitability of medial septal cholinergic neurones. Alteration of cholinergic activity produced a reduction in the frequency of theta oscillations, without affecting the slope of the non-linear theta frequency vs running speed relationship observed. Modifying septal cholinergic tone in this way also led mice to exhibit behaviours associated with novelty or anxiety. However, grid cell firing patterns were unaffected, concordant with an absence of change in the slopes of the theta frequency and firing rate speed signals thought to be used by grid cells.
Metal Solidification Imaging Process by Magnetic Induction Tomography
Authors: Ma Lu , Spagnul Stefano , Soleimani Manuchehr 
Published: October 2017

AbstractThere are growing number of important applications that require a contactless method for monitoring an object surrounded inside a metallic enclosure. Imaging metal solidification is a great example for which there is no real time monitoring technique at present. This paper introduces a technique - magnetic induction tomography - for the real time in-situ imaging of the metal solidification process. Rigorous experimental verifications are presented. Firstly, a single inductive coil is placed on the top of a melting wood alloy to examine the changes of its inductance during solidification process. Secondly, an array of magnetic induction coils are designed to investigate the feasibility of a tomographic approach, i.e., when one coil is driven by an alternating current as a transmitter and a vector of phase changes are measured from the remaining of the coils as receivers. Phase changes are observed when the wood alloy state changes from liquid to solid. Thirdly, a series of static cold phantoms are created to represent various liquid/solid interfaces to verify the system performance. Finally, a powerful temporal reconstruction method is applied to realise real time in-situ visualisation of the solidification and the measurement of solidified shell thickness, a first report of its kind.
Serial-omics of P53−/−, Brca1−/− Mouse Breast Tumor and Normal Mammary Gland
Authors: Breitkopf Susanne B. , Taveira Mateus De Oliveira , Yuan Min , Wulf Gerburg M. , Asara John M. 
Published: October 2017

AbstractThis study demonstrates a liquid-liquid extraction for the sequential tandem mass spectrometry (LC-MS/MS) analysis of non-polar lipids, polar metabolites, proteins and phosphorylation sites from a single piece of tissue. Extraction of 10 mg BRCA−/−, p53−/− breast tumor tissue or normal mammary gland tissue with methyl-tert-butyl ether (MTBE) results in three phases: an upper non-polar phase containing 1,382 lipids, a lower polar phase with 805 metabolites and a precipitated protein pellet with 4,792 proteins with 1,072 phosphorylation sites. Comparative analysis revealed an activated AKT-mTOR pathway in tumors. Tumors also showed a reduction of phosphorylation sites involved in transcription and RNA splicing and decreased abundance of enzymes in lipid synthesis. Analysis of polar metabolites revealed a reduction in glycolysis, pentose phosphate pathway, polyamines and nucleotides, but an increase in TCA and urea cycle intermediates. Analysis of lipids revealed a shift from high triglycerides in mammary gland to high phospholipid levels in tumors. The data were integrated into a model showing breast tumors exhibit features on the proteomic, lipidomic and metabolomic level that are distinct from normal breast tissue. Our integrative technique lends itself to samples such as tumor biopsies, dried blood spots and fluids including urine and CSF to develop biomarkers of disease.
3d-4f coupling and multiferroicity in frustrated Cairo Pentagonal oxide DyMn2O5
Authors: Chattopadhyay S. , Petit S. , Ressouche E. , Raymond S. , Balédent V. , Yahia G. , Peng W. , Robert J. , Lepetit M.-B. , Greenblatt M. , Foury-Leylekian P. 
Published: October 2017

AbstractIn solid state science, multifunctional materials and especially multiferroics have attracted a great deal of attention, as they open the possibility for next generation spintronic and data storage devices. Interestingly, while many of them host coexisting 3d and 4f elements, the role of the coupling between these two magnetic entities has remained elusive. By means of single crystal neutron diffraction and inelastic neutron scattering experiments we shed light on this issue in the particular case of the multiferroic oxide DyMn2O5. This compound undergoes a first order magnetic transition from a high temperature incommensurate phase to a low temperature commensurate one. Our investigation reveals that although these two phases have very different magnetic structures, the spin excitations are quite similar indicating a fragile low temperature ground state with respect to the high temperature one. Such a rare scenario is argued to be a manifestation of the competition between the exchange interaction and 4f magnetic anisotropy present in the system. It is concluded that the magnetic structure, hence the ferroelectricity, can be finely tuned depending on the anisotropy of the rare earth.
Natural history of Helicobacter pylori VacA toxin in human gastric epithelium in vivo: vacuoles and beyond
Authors: Necchi Vittorio , Sommi Patrizia , Vanoli Alessandro , Fiocca Roberto , Ricci Vittorio , Solcia Enrico 
Published: October 2017

AbstractUptake, intracellular trafficking and pathologic effects of VacA toxin from Helicobacter pylori have been widely investigated in vitro. However, no systematic analysis investigated VacA intracellular distribution and fate in H. pylori-infected human gastric epithelium in vivo, using ultrastructural immunocytochemistry that combines precise toxin localization with analysis of the overall cell ultrastructure and intercompartimental/interorganellar relationships. By immunogold procedure, in this study we investigated gastric biopsies taken from dyspeptic patients to characterize the overall toxin’s journey inside human gastric epithelial cells in vivo. Endocytic pits were found to take up VacA at sites of bacterial adhesion, leading to a population of peripheral endosomes, which in deeper (juxtanuclear) cytoplasm enlarged and fused each other to form large VacA-containing vacuoles (VCVs). These directly opened into endoplasmic reticulum (ER) cisternae, which in turn enveloped mitochondria and contacted the Golgi apparatus. In all such organelles we found toxin molecules, often coupled with structural damage. These findings suggest direct toxin transfer from VCVs to other target organelles such as ER/Golgi and mitochondria. VacA-induced cytotoxic changes were associated with the appearance of auto(phago)lysosomes containing VacA, polyubiquitinated proteins, p62/SQSTM1 protein, cathepsin D, damaged mitochondria and bacterial remnants, thus leading to persistent cell accumulation of degradative products.
Hf/Sb co-doping induced a high thermoelectric performance of ZrNiSn: First-principles calculation
Authors: Zhang Ju , Zhang Xiwen , Wang Yuanxu 
Published: October 2017

AbstractPrevious experiments showed that Hf/Sb co-doping in ZrNiSn impressively improved the electrical conductivity (σ). To explore the physical reasons for this improvement, the electronic structures of HfxZr1−xNiSn1−ySby (x = 0, 0.25, 0.5; y = 0, 0.02) have been systematically investigated by using the first-principles method and semiclassical Boltzmann transport theory. 50% Hf doping at Zr site in ZrNiSn simultaneously increases the degeneracy and dispersion of energy bands near the conduction band edge, which are helpful to optimizing Seebeck coefficient and slightly improving σ. Furthermore, 2% Sb co-doping at Sn site in Hf0.5Zr0.5NiSn not only increases total density of states near the Fermi energy but also retains high mobility, and N
v
reaches eleven at the conduction band minimum, thereby inducing a large improvement in σ. Additionally, the Bader charge analysis shows the reason why Sb co-doping supplies more electrons. It is most likely derived from that Sb loses more electrons and Sb-Ni has a stronger hybridization than Sn-Ni. Moreover, we predict that the ZT of Hf0.5Zr0.5NiSn0.98Sb0.02 at 1000 K can reach 1.37 with the carrier concentration of 7.56 × 1018 cm−3, indicating that Hf/Sb co-doping may be an effective approach in optimizing thermoelectric properties of ZrNiSn alloy compounds.
Enhanced Attentional Bias Variability in Post-Traumatic Stress Disorder and its Relationship to More General Impairments in Cognitive Control
Authors: Swick Diane , Ashley Victoria 
Published: October 2017

AbstractHypervigilance towards threat is one of the defining features of post-traumatic stress disorder (PTSD). This symptom predicts that individuals with PTSD will be biased to attend to potential dangers in the environment. However, cognitive tasks designed to assess visual-spatial attentional biases have shown mixed results. A newer proposal suggests that attentional bias is not a static phenomenon, but rather is characterized by fluctuations towards and away from threat. Here, we tested 28 combat Veterans with PTSD and 28 control Veterans on a dot probe task with negative-neutral word pairs. Combat-related words and generically negative words were presented in separate blocks. Replicating previous results, neither group showed a bias to attend towards or away from threat, but PTSD patients showed greater attentional bias variability (ABV), which correlated with symptom severity. However, the cognitive processes indexed by ABV are unclear. The present results indicated that ABV was strongly correlated with standard deviation at the reaction time (RT) level and with excessively long RTs (ex-Gaussian tau) related to cognitive failures. These findings suggest an overall increase in response variability unrelated to threat-related biases in spatial attention, and support a disruption in more general cognitive control processes in PTSD.
NMR relaxation properties of the synthetic malaria pigment β-hematin
Authors: Gossuin Yves , Okusa Ndjolo Philippe , Vuong Quoc Lam , Duez Pierre 
Published: October 2017

Abstract200 million patients suffer from malaria, a parasitic disease caused by protozoans of the genus Plasmodium. Reliable diagnosis is crucial since it allows the early detection of the disease. The development of rapid, sensitive and low-cost diagnosis tools is an important research area. Different studies focused on the detection of hemozoin, a major by-product of hemoglobin detoxification by the parasite. Hemozoin and its synthetic analog, β-hematin, form paramagnetic crystals. A new detection method of malaria takes advantage of the paramagnetism of hemozoin through the effect that such magnetic crystals have on Nuclear Magnetic Resonance (NMR) relaxation of water protons. Indeed, magnetic microparticles cause a shortening of the relaxation times. In this work, the magnetic properties of two types of β-hematin are assessed at different temperatures and magnetic fields. The pure paramagnetism of β-hematin is confirmed. The NMR relaxation of β–hematin suspensions is also studied at different magnetic fields and for different echo-times. Our results help to identify the best conditions for β–hematin detection by NMR: T2 must be selected, at large magnetic fields and for long echo-times. However, the effect of β-hematin on relaxation does not seem large enough to achieve accurate detection of malaria without any preliminary sample preparation, as microcentrifugation.
Landscape-scale conservation design across biotic realms: sequential integration of aquatic and terrestrial landscapes
Authors: Leonard Paul B. , Baldwin Robert F. , Hanks R. Daniel 
Published: October 2017

AbstractSystematic conservation planning has been used extensively throughout the world to identify important areas for maintaining biodiversity and functional ecosystems, and is well suited to address large-scale biodiversity conservation challenges of the twenty-first century. Systematic planning is necessary to bridge implementation, scale, and data gaps in a collaborative effort that recognizes competing land uses. Here, we developed a conservation planning process to identify and unify conservation priorities around the central and southern Appalachian Mountains as part of the Appalachian Landscape Conservation Cooperative (App LCC). Through a participatory framework and sequential, cross-realm integration in spatial optimization modeling we highlight lands and waters that together achieve joint conservation goals from LCC partners for the least cost. This process was driven by a synthesis of 26 multi-scaled conservation targets and optimized for simultaneous representation inside the program Marxan to account for roughly 25% of the LCC geography. We identify five conservation design elements covering critical ecological processes and patterns including interconnected regions as well as the broad landscapes between them. Elements were then subjected to a cumulative threats index for possible prioritization. The evaluation of these elements supports multi-scaled decision making within the LCC planning community through a participatory, dynamic, and iterative process.