bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct protein-lipid interactions shape the conformational landscape of secondary transporters
Authors: Martens Chloe , Shekhar Mrinal , Borysik Antoni J. , Lau Andy M. , Reading Eamonn , Tajkhorshid Emad , Booth Paula J. , Politis Argyris 
Published: October 2018

AbstractSecondary transporters undergo structural rearrangements to catalyze substrate translocation across the cell membrane – yet how such conformational changes happen within a lipid environment remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS) with molecular dynamics (MD) simulations to understand how lipids regulate the conformational dynamics of secondary transporters at the molecular level. Using the homologous transporters XylE, LacY and GlpT from Escherichia coli as model systems, we discover that conserved networks of charged residues act as molecular switches that drive the conformational transition between different states. We reveal that these molecular switches are regulated by interactions with surrounding phospholipids and show that phosphatidylethanolamine interferes with the formation of the conserved networks and favors an inward-facing state. Overall, this work provides insights into the importance of lipids in shaping the conformational landscape of an important class of transporters.
Designed synthesis of stable light-emitting two-dimensional sp2 carbon-conjugated covalent organic frameworks
Authors: Jin Enquan , Li Juan , Geng Keyu , Jiang Qiuhong , Xu Hong , Xu Qing , Jiang Donglin 
Published: October 2018

AbstractCovalent organic frameworks enable the topological connection of organic chromophores into π lattices, making them attractive for creating light-emitting polymers that are predesignable for both the primary- and high-order structures. However, owing to linkages, covalent organic frameworks are either unstable or poor luminescent, leaving the practical synthesis of stable light-emitting frameworks challenging. Here, we report the designed synthesis of sp2 carbon-conjugated frameworks that combine stability with light-emitting activity. The C=C linkages topologically connect pyrene knots and arylyenevinylene linkers into two-dimensional all sp2 carbon lattices that are designed to be π conjugated along both the x and y directions and develop layer structures, creating exceptionally stable frameworks. The resulting frameworks are capable of tuning band gap and emission by the linkers, are highly luminescent under various conditions and can be exfoliated to produce brilliant nanosheets. These results suggest a platform based on sp2 carbon frameworks for designing robust photofunctional materials.
Personalized Integrated Network Modeling of the Cancer Proteome Atlas
Authors: Ha Min Jin , Banerjee Sayantan , Akbani Rehan , Liang Han , Mills Gordon B. , Do Kim-Anh , Baladandayuthapani Veerabhadran 
Published: October 2018

AbstractPersonalized (patient-specific) approaches have recently emerged with a precision medicine paradigm that acknowledges the fact that molecular pathway structures and activity might be considerably different within and across tumors. The functional cancer genome and proteome provide rich sources of information to identify patient-specific variations in signaling pathways and activities within and across tumors; however, current analytic methods lack the ability to exploit the diverse and multi-layered architecture of these complex biological networks. We assessed pan-cancer pathway activities for >7700 patients across 32 tumor types from The Cancer Proteome Atlas by developing a personalized cancer-specific integrated network estimation (PRECISE) model. PRECISE is a general Bayesian framework for integrating existing interaction databases, data-driven de novo causal structures, and upstream molecular profiling data to estimate cancer-specific integrated networks, infer patient-specific networks and elicit interpretable pathway-level signatures. PRECISE-based pathway signatures, can delineate pan-cancer commonalities and differences in proteomic network biology within and across tumors, demonstrates robust tumor stratification that is both biologically and clinically informative and superior prognostic power compared to existing approaches. Towards establishing the translational relevance of the functional proteome in research and clinical settings, we provide an online, publicly available, comprehensive database and visualization repository of our findings (https://mjha.shinyapps.io/PRECISE/).
Illustrating the effect of viscoelastic additives on cavitation and turbulence with X-ray imaging
Authors: Karathanassis I. K. , Trickett K. , Koukouvinis P. , Wang J. , Barbour R. , Gavaises M. 
Published: October 2018

AbstractThe effect of viscoelastic additives on the topology and dynamics of the two-phase flow arising within an axisymmetric orifice with a flow path constriction along its main axis has been investigated employing high-flux synchrotron radiation. X-ray Phase Contrast Imaging (XPCI) has been conducted to visualise the cavitating flow of different types of diesel fuel within the orifice. An additised blend containing Quaternary Ammonium Salt (QAS) additives with a concentration of 500 ppm has been comparatively examined against a pure (base) diesel compound. A high-flux, 12 keV X-ray beam has been utilised to obtain time resolved radiographs depicting the vapour extent within the orifice from two views (side and top) with reference to its main axis. Different test cases have been examined for both fuel types and for a range of flow conditions characterised by Reynolds number of 35500 and cavitation numbers (CN) lying in the range 3.0–7.7. It has been established that the behaviour of viscoelastic micelles in the regions of shear flow is not consistent depending on the cavitation regimes encountered. Namely, viscoelastic effects enhance vortical (string) cavitation, whereas hinder cloud cavitation. Furthermore, the use of additised fuel has been demonstrated to suppress the level of turbulence within the orifice.
Stable and discriminating features are predictive of cancer presence and Gleason grade in radical prostatectomy specimens: a multi-site study
Authors: Leo Patrick , Elliott Robin , Shih Natalie N. C. , Gupta Sanjay , Feldman Michael , Madabhushi Anant 
Published: October 2018

AbstractSite variation in fixation, staining, and scanning can confound automated tissue based image classifiers for disease characterization. In this study we incorporated stability into four feature selection methods for identifying the most robust and discriminating features for two prostate histopathology classification tasks. We evaluated 242 morphology features from N = 212 prostatectomy specimens from four sites for automated cancer detection and grading. We quantified instability as the rate of significant cross-site feature differences. We mapped feature stability and discriminability using 188 non-cancerous and 210 cancerous regions via 3-fold cross validation, then held one site out, creating independent training and testing sets. In training, one feature set was selected only for discriminability, another for discriminability and stability. We trained a classifier with each feature set, testing on the hold out site. Experiments were repeated with 117 Gleason grade 3 and 112 grade 4 regions. Stability was calculated across non-cancerous regions. Gland shape features yielded the best stability and area under the receiver operating curve (AUC) trade-off while co-occurrence texture features were generally unstable. Our stability-informed method produced a cancer detection AUC of 0.98 ± 0.05 and increased average Gleason grading AUC by 4.38%. Color normalization of the images tended to exacerbate feature instability.
Transplantation of a bone marrow mesenchymal stem cell line increases neuronal progenitor cell migration in a cerebral ischemia animal model
Authors: Shiota Yuri , Nagai Atsushi , Sheikh Abdullah Md. , Mitaki Shingo , Mishima Seiji , Yano Shozo , Haque Md. Ahsanul , Kobayashi Shotai , Yamaguchi Shuhei 
Published: October 2018

AbstractMesenchymal stem cell (MSC) transplantation is demonstrated to improve functional and pathological recovery in cerebral ischemia. To understand the underlying mechanism, we transplanted a MSC line (B10) in a rat middle cerebral artery occlusion (MCAO) model and checked the proliferation and migration of neuronal progenitor cells (NPCs). B10 transplantation increased NPCs in the subventricular zone and their migration towards the lesion area at an earlier time. Fourteen days after MCAO, some NPCs were differentiated to neurons and astrocytes. Although B10 transplantation increased total number of both astrocytes and neurons, it only increased the differentiation of NPC to astrocyte. The mRNA of polysialylation enzyme ST8SiaIV and a chemokine SDF-1 were persistently increased in B10-transplanted groups. SDF-1-positive cell number was increased in the core and penumbra area, which was expressed in macrophage/microglia and transplanted B10 cells at 3 days after MCAO. Furthermore, SDF-1 mRNA expression in cell culture was high in B10 compared to a microglia (HMO) or a neuronal (A1) cell line. B10 culture supernatant increased in vitro A1 cell migration, which was significantly inhibited by siRNA-mediated SDF-1 silencing in B10. Thus, our results suggested that MSC transplantation increased endogenous NPC migration in cerebral ischemic condition by increasing chemokine and polysialylation enzyme expression, which could be helpful for the restorative management of cerebral ischemia.
Probing the origin of matching functional jaws: roles of Dlx5/6 in cranial neural crest cells
Authors: Shimizu Miki , Narboux-Nême Nicolas , Gitton Yorick , de Lombares Camille , Fontaine Anastasia , Alfama Gladys , Kitazawa Taro , Kawamura Yumiko , Heude Eglantine , Marshall Lindsey , Higashiyama Hiroki , Wada Youichiro , Kurihara Yukiko , Kurihara Hiroki , Levi Giovanni 
Published: October 2018

AbstractGnathostome jaws derive from the first pharyngeal arch (PA1), a complex structure constituted by Neural Crest Cells (NCCs), mesodermal, ectodermal and endodermal cells. Here, to determine the regionalized morphogenetic impact of Dlx5/6 expression, we specifically target their inactivation or overexpression to NCCs. NCC-specific Dlx5/6 inactivation (NCC∆Dlx5/6) generates severely hypomorphic lower jaws that present typical maxillary traits. Therefore, differently from Dlx5/6 null-embryos, the upper and the lower jaws of NCC∆Dlx5/6 mice present a different size. Reciprocally, forced Dlx5 expression in maxillary NCCs provokes the appearance of distinct mandibular characters in the upper jaw. We conclude that: (1) Dlx5/6 activation in NCCs invariably determines lower jaw identity; (2) the morphogenetic processes that generate functional matching jaws depend on the harmonization of Dlx5/6 expression in NCCs and in distinct ectodermal territories. The co-evolution of synergistic opposing jaws requires the coordination of distinct regulatory pathways involving the same transcription factors in distant embryonic territories.
Evolutionary changes in growth, regrowth and carbohydrate storage in an invasive plant
Authors: Lin Tiantian , Klinkhamer Peter G. L. , Vrieling Klaas 
Published: October 2018

AbstractWe hypothesized that due to the absence of specialist herbivores in introduced ranges, invasive plants have evolved decreased allocation to carbohydrate storage for regrowth ability and as a consequence allocate more to growth. In this study, we compared plant growth, carbohydrate storage and regrowth ability of invasive and native Jacobaea vulgaris in response to complete shoot defoliation. We used invasive J. vulgaris genotypes from three geographically and climactically distinct regions and compared these with native genotypes from Europe. We found that invasive genotypes initially grew larger while native genotypes regrew larger after defoliation. Before defoliation, the carbohydrate storage in roots of invasive genotypes was 38% lower than native genotypes. Biomass after regrowth increased with root carbohydrate storage while it decreased with structural root mass, showing that it is crucial to study root storage and structural components separately in order to investigate plant regrowth. All studied traits of invasive populations from the three geographically and climatologically distinct regions changed in the same expected direction suggesting that the shifts in herbivore guild were causal to the observed change in growth and regrowth ability rather than environmental factors.
A reference document on Permissible Limits for solvents and buffers during in vitro antimalarial screening
Authors: Naidu Renugah , Subramanian Gowtham , Lim Ying Bena , Lim Chwee Teck , Chandramohanadas Rajesh 
Published: October 2018

AbstractAntimalarial drug discovery expands on targeted and phenotype-based screening of potential inhibitory molecules to ascertain overall efficacy, phenotypic characteristics and toxicity, prior to exploring pharmacological optimizations. Candidate inhibitors may have varying chemical properties, thereby requiring specific reconstitution conditions to ensure solubility, stability or bioavailability. Hence, a variety of solvents, buffers, detergents and stabilizers become part of antimalarial efficacy assays, all of which, above certain threshold could interfere with parasite viability, invasion or red blood cell properties leading to misinterpretation of the results. Despite their routine use across malaria research laboratories, there is no documentation on non-toxic range for common constituents including DMSO, glycerol, ethanol and methanol. We herein constructed a compatibility reference guide for 14 such chemicals and estimated their Permissible Limit against P. falciparum asexual stages at which viability and replication of parasites are not compromised. We also demonstrate that at the estimated Permissible Limit, red blood cells remain healthy and viable for infection by merozoites. Taken together, this dataset provides a valuable reference tool for the acceptable concentration range for common chemicals during in vitro antimalarial tests.
An Evolutionarily Conserved Mesodermal Enhancer in Vertebrate Zic3
Authors: Odaka Yuri S. , Tohmonda Takahide , Toyoda Atsushi , Aruga Jun 
Published: October 2018

AbstractZic3 encodes a zinc finger protein essential for the development of meso-ectodermal tissues. In mammals, Zic3 has important roles in the development of neural tube, axial skeletons, left-right body axis, and in maintaining pluripotency of ES cells. Here we characterized cis-regulatory elements required for Zic3 expression. Enhancer activities of human-chicken-conserved noncoding sequences around Zic1 and Zic3 were screened using chick whole-embryo electroporation. We identified enhancers for meso-ectodermal tissues. Among them, a mesodermal enhancer (Zic3-ME) in distant 3′ flanking showed robust enhancement of reporter gene expression in the mesodermal tissue of chicken and mouse embryos, and was required for mesodermal Zic3 expression in mice. Zic3-ME minimal core region is included in the DNase hypersensitive region of ES cells, mesoderm, and neural progenitors, and was bound by T (Brachyury), Eomes, Lef1, Nanog, Oct4, and Zic2. Zic3-ME is derived from an ancestral sequence shared with a sequence encoding a mitochondrial enzyme. These results indicate that Zic3-ME is an integrated cis-regulatory element essential for the proper expression of Zic3 in vertebrates, serving as a hub for a gene regulatory network including Zic3.
Comparative transcriptomic profile of tolerogenic dendritic cells differentiated with vitamin D3, dexamethasone and rapamycin
Authors: Navarro-Barriuso Juan , Mansilla María José , Naranjo-Gómez Mar , Sánchez-Pla Alex , Quirant-Sánchez Bibiana , Teniente-Serra Aina , Ramo-Tello Cristina , Martínez-Cáceres Eva M. 
Published: October 2018

AbstractTolerogenic dendritic cell (tolDC)-based therapies have become a promising approach for the treatment of autoimmune diseases by their potential ability to restore immune tolerance in an antigen-specific manner. However, the broad variety of protocols used to generate tolDCin vitroand their functional and phenotypical heterogeneity are evidencing the need to find robust biomarkers as a key point towards their translation into the clinic, as well as better understanding the mechanisms involved in the induction of immune tolerance. With that aim, in this study we have compared the transcriptomic profile of tolDC induced with either vitamin D3 (vitD3-tolDC), dexamethasone (dexa-tolDC) or rapamycin (rapa-tolDC) through a microarray analysis in 5 healthy donors. The results evidenced that common differentially expressed genes could not be found for the three different tolDC protocols. However, individually,CYP24A1,MUCL1andMAP7for vitD3-tolDC;CD163,CCL18,C1QBandC1QCfor dexa-tolDC; andCNGA1andCYP7B1for rapa-tolDC, constituted good candidate biomarkers for each respective cellular product. In addition, a further gene set enrichment analysis of the data revealed that dexa-tolDC and vitD3-tolDC share several immune regulatory and anti-inflammatory pathways, while rapa-tolDC seem to be playing a totally different role towards tolerance induction through a strong immunosuppression of their cellular processes.
Berry phase theory of planar Hall effect in topological insulators
Authors: Nandy S. , Taraphder A. , Tewari Sumanta 
Published: October 2018

AbstractThe appearance of negative longitudinal magnetoresistance (LMR) in topological semimetals such as Weyl and Dirac semimetals is understood as an effect of chiral anomaly, whereas such an anomaly is not well-defined in topological insulators. Nevertheless, it has been shown recently in both theory and experiments that nontrivial Berry phase effects can give rise to negative LMR in topological insulators even in the absence of chiral anomaly. In this paper, we present a quasi-classical theory of another intriguing phenomenon in topological insulators – also ascribed to chiral anomaly in Weyl and Dirac semimetals– the so-called planar Hall effect (PHE). PHE implies the appearance of a transverse voltage in the plane of applied non-parallel electric and magnetic fields, in a configuration in which the conventional Hall effect vanishes. Starting from Boltzmann transport equations we derive the expressions for PHE and LMR in topological insulators in the bulk conduction limit, and show the important role played by orbital magnetic moment. Our theoretical results for magnetoconductance with non-parallel electric and magnetic fields predict detailed experimental signatures in topological insulators – specifically of planar Hall effect – that can be observed in experiments.
Human blastocysts of normal and abnormal karyotypes display distinct transcriptome profiles
Authors: Licciardi Frederick , Lhakhang Tenzin , Kramer Yael G. , Zhang Yutong , Heguy Adriana , Tsirigos Aristotelis 
Published: October 2018

AbstractUnveiling the transcriptome of human blastocysts can provide a wealth of important information regarding early embryonic ontology. Comparing the mRNA production of embryos with normal and abnormal karyotypes allows for a deeper understanding of the protein pathways leading to viability and aberrant fetal development. In addition, identifying transcripts specific for normal or abnormal chromosome copy number could aid in the search for secreted substances that could be used to non-invasively identify embryos best suited for IVF embryo transfer. Using RNA-seq, we characterized the transcriptome of 71 normally developing human blastocysts that were karyotypically normal vs. trisomic or monosomic. Every monosomy and trisomy of the autosomal and sex chromosomes were evaluated, mostly in duplicate. We first mapped the transcriptome of three normal embryos and found that a common core of more than 3,000 genes is expressed in all embryos. These genes represent pathways related to actively dividing cells, such as ribosome biogenesis and function, spliceosome, oxidative phosphorylation, cell cycle and metabolic pathways. We then compared transcriptome profiles of aneuploid embryos to those of normal embryos. We observed that non-viable embryos had a large number of dysregulated genes, some showing a hundred-fold difference in expression. On the contrary, sex chromosome abnormalities, XO and XXX displayed transcriptomes more closely mimicking those embryos with 23 normal chromosome pairs. Intriguingly, we identified a set of commonly deregulated genes in the majority of both trisomies and monosomies. This is the first paper demonstrating a comprehensive transcriptome delineation of karyotypic abnormalities found in the human pre-implantation embryo. We believe that this information will contribute to the development of new pre-implantation genetic screening methods as well as a better understanding of the underlying developmental abnormalities of abnormal embryos, fetuses and children.
Separating sexual dimorphism from other morphological variation in a specimen complex of fossil marine reptiles (Reptilia, Ichthyosauriformes, Chaohusaurus)
Authors: Motani Ryosuke , Huang Jiandong , Jiang Da-yong , Tintori Andrea , Rieppel Olivier , You Hailu , Hu Yuan-chao , Zhang Rong 
Published: October 2018

AbstractThe Early Triassic Chaohu Fauna from Anhui Province, China, contains the oldest record of Mesozoic marine reptiles, such as Cartorhynchus and Sclerocormus. Most specimens from the fauna belong to the ichthyosauriform Chaohusaurus, more specifically resembling C. chaoxianensis. However, a wide range of morphological variation exists within about 40 skeletons that have been prepared, likely reflecting mixed signals from both sexual and taxonomic differences. We test whether the sexual and taxonomic signals are separable based on quantification, aided by the knowledge of sexual dimorphism in extant marine tetrapods. There are two different suites of dimorphism that divide the specimens differently from each other yet consistently within each suite, resulting in four morphotypes in combination, likely representing two sexes of two taxa. Presumed males have larger ‘organ of prehension’ sensu Darwin, specifically limbs in the present case, for a given body length. This sexing criterion is supported by the only specimen of a gravid female, which belongs to the morphotype with short limbs. Males also have larger skulls for the trunk length compared to females. This study demonstrates that sexual and taxonomic signals are separable in fossil reptiles, with a sufficient sample size and careful analyses.
Generation of two-cell cloned embryos from mouse faecal cell
Authors: Kamimura Satoshi , Wakayama Sayaka , Kuwayama Hiroki , Tanabe Yoshiaki , Kishigami Satoshi , Wakayama Teruhiko 
Published: October 2018

AbstractCloning animals using nuclear transfer (NT) provides the opportunity to preserve endangered species. However, there are risks associated with the collection of donor cells from a body, which may cause accidental death of the animal. Here, we tried to collect faeces-derived cells and examined the usability of those nuclei as a donor for NT. A relatively large number of cells could be collected from GFP-Tg mouse faeces by this method. After NT, only 4.2% of the reconstructed oocytes formed pseudo-pronucleus. This rate increased up to 25% when GFP and Hoechst were used as a marker to select better cells. However, the reconstructed oocytes/embryos showed several abnormalities, such as shrunken nuclear membranes and abnormal distribution of tubulin, and none of them developed beyond one-cell stage embryos. These developmental failures were caused by not only toxic substances derived from faeces but also intrinsic DNA damage of donor cell nuclei. However, when the serial NT was performed, some of the cloned embryos could develop to the two-cell stage. This method may remove toxic substances and enhance DNA repair in the oocyte cytoplasm. Thus, these results indicate that faeces cells might be useful for the conservation of endangered species when technical improvements are achieved.