bluuebunny/crossref_metadata_2025_split huggingface dataset:
Blast transformation and fibrotic progression in polycythemia vera and essential thrombocythemia: a literature review of incidence and risk factors
Authors: Cerquozzi S , Tefferi A 
Published: November 2015

AbstractPolycythemia vera (PV) and essential thrombocythemia (ET) constitute two of the three BCR-ABL1-negative myeloproliferative neoplasms and are characterized by relatively long median survivals (approximately 14 and 20 years, respectively). Potentially fatal disease complications in PV and ET include disease transformation into myelofibrosis (MF) or acute myeloid leukemia (AML). The range of reported frequencies for post-PV MF were 4.9–6% at 10 years and 6–14% at 15 years and for post-ET MF were 0.8–4.9% at 10 years and 4–11% at 15 years. The corresponding figures for post-PV AML were 2.3–14.4% at 10 years and 5.5–18.7% at 15 years and for post-ET AML were 0.7–3% at 10 years and 2.1–5.3% at 15 years. Risk factors cited for post-PV MF include advanced age, leukocytosis, reticulin fibrosis, splenomegaly and JAK2V617F allele burden and for post-ET MF include advanced age, leukocytosis, anemia, reticulin fibrosis, absence of JAK2V617F, use of anagrelide and presence of ASXL1 mutation. Risk factors for post-PV AML include advanced age, leukocytosis, reticulin fibrosis, splenomegaly, abnormal karyotype, TP53 or RUNX1 mutations as well as use of pipobroman, radiophosphorus (P32) and busulfan and for post-ET AML include advanced age, leukocytosis, anemia, extreme thrombocytosis, thrombosis, reticulin fibrosis, TP53 or RUNX1 mutations. It is important to note that some of the aforementioned incidence figures and risk factor determinations are probably inaccurate and at times conflicting because of the retrospective nature of studies and the inadvertent labeling, in some studies, of patients with prefibrotic primary MF or ‘masked’ PV, as ET. Ultimately, transformation of MPN leads to poor outcomes and management remains challenging. Further understanding of the molecular events leading to disease transformation is being investigated.
Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)
Authors: Kueneman Jordan G , Woodhams Douglas C , Van Treuren Will , Archer Holly M , Knight Rob , McKenzie Valerie J 
Published: November 2015

AbstractIncreasingly, host-associated microbiota are recognized to mediate pathogen establishment, providing new ecological perspectives on health and disease. Amphibian skin-associated microbiota interact with the fungal pathogen, Batrachochytrium dendrobatidis (Bd), but little is known about microbial turnover during host development and associations with host immune function. We surveyed skin microbiota of Colorado’s endangered boreal toads (Anaxyrus boreas), sampling 181 toads across four life stages (tadpoles, metamorphs, subadults and adults). Our goals were to (1) understand variation in microbial community structure among individuals and sites, (2) characterize shifts in communities during development and (3) examine the prevalence and abundance of known Bd-inhibitory bacteria. We used high-throughput 16S and 18S rRNA gene sequencing (Illumina MiSeq) to characterize bacteria and microeukaryotes, respectively. Life stage had the largest effect on the toad skin microbial community, and site and Bd presence also contributed. Proteobacteria dominated tadpole microbial communities, but were later replaced by Actinobacteria. Microeukaryotes on tadpoles were dominated by the classes Alveolata and Stramenopiles, while fungal groups replaced these groups after metamorphosis. Using a novel database of Bd-inhibitory bacteria, we found fewer Bd-inhibitory bacteria in post-metamorphic stages correlated with increased skin fungi, suggesting that bacteria have a strong role in early developmental stages and reduce skin-associated fungi.
Decreases in average bacterial community rRNA operon copy number during succession
Authors: Nemergut Diana R , Knelman Joseph E , Ferrenberg Scott , Bilinski Teresa , Melbourne Brett , Jiang Lin , Violle Cyrille , Darcy John L , Prest Tiffany , Schmidt Steven K , Townsend Alan R 
Published: November 2015

Abstract
Trait-based studies can help clarify the mechanisms driving patterns of microbial community assembly and coexistence. Here, we use a trait-based approach to explore the importance of rRNA operon copy number in microbial succession, building on prior evidence that organisms with higher copy numbers respond more rapidly to nutrient inputs. We set flasks of heterotrophic media into the environment and examined bacterial community assembly at seven time points. Communities were arrayed along a geographic gradient to introduce stochasticity via dispersal processes and were analyzed using 16 S rRNA gene pyrosequencing, and rRNA operon copy number was modeled using ancestral trait reconstruction. We found that taxonomic composition was similar between communities at the beginning of the experiment and then diverged through time; as well, phylogenetic clustering within communities decreased over time. The average rRNA operon copy number decreased over the experiment, and variance in rRNA operon copy number was lowest both early and late in succession. We then analyzed bacterial community data from other soil and sediment primary and secondary successional sequences from three markedly different ecosystem types. Our results demonstrate that decreases in average copy number are a consistent feature of communities across various drivers of ecological succession. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, ranging from cells to populations and communities, with implications for both microbial ecology and evolution.
The dual oxidase gene BdDuox regulates the intestinal bacterial community homeostasis of Bactrocera dorsalis
Authors: Yao Zhichao , Wang Ailin , Li Yushan , Cai Zhaohui , Lemaitre Bruno , Zhang Hongyu 
Published: November 2015

Abstract
The guts of metazoans are in permanent contact with the microbial realm that includes beneficial symbionts, nonsymbionts, food-borne microbes and life-threatening pathogens. However, little is known concerning how host immunity affects gut bacterial community. Here, we analyze the role of a dual oxidase gene (BdDuox) in regulating the intestinal bacterial community homeostasis of the oriental fruit fly Bactrocera dorsalis. The results showed that knockdown of BdDuox led to an increased bacterial load, and to a decrease in the relative abundance of Enterobacteriaceae and Leuconostocaceae bacterial symbionts in the gut. The resulting dysbiosis, in turn, stimulates an immune response by activating BdDuox and promoting reactive oxygen species (ROS) production that regulates the composition and structure of the gut bacterial community to normal status by repressing the overgrowth of minor pathobionts. Our results suggest that BdDuox plays a pivotal role in regulating the homeostasis of the gut bacterial community in B. dorsalis.
Single-molecule visualization of a formin-capping protein ‘decision complex’ at the actin filament barbed end
Authors: Bombardier Jeffrey P. , Eskin Julian A. , Jaiswal Richa , Corrêa Ivan R. , Xu Ming-Qun , Goode Bruce L. , Gelles Jeff 
Published: November 2015

AbstractPrecise control of actin filament length is essential to many cellular processes. Formins processively elongate filaments, whereas capping protein (CP) binds to barbed ends and arrests polymerization. While genetic and biochemical evidence has indicated that these two proteins function antagonistically, the mechanism underlying the antagonism has remained unresolved. Here we use multi-wavelength single-molecule fluorescence microscopy to observe the fully reversible formation of a long-lived ‘decision complex’ in which a CP dimer and a dimer of the formin mDia1 simultaneously bind the barbed end. Further, mDia1 displaced from the barbed end by CP can randomly slide along the filament and later return to the barbed end to re-form the complex. Quantitative kinetic analysis reveals that the CP-mDia1 antagonism that we observe in vitro occurs through the decision complex. Our observations suggest new molecular mechanisms for the control of actin filament length and for the capture of filament barbed ends in cells.
Propagation of oestrogen receptor-positive and oestrogen-responsive normal human breast cells in culture
Authors: Fridriksdottir Agla J. , Kim Jiyoung , Villadsen René , Klitgaard Marie Christine , Hopkinson Branden M. , Petersen Ole William , Rønnov-Jessen Lone 
Published: November 2015

AbstractInvestigating the susceptibility of oestrogen receptor-positive (ERpos) normal human breast epithelial cells (HBECs) for clinical purposes or basic research awaits a proficient cell-based assay. Here we set out to identify markers for isolating ERpos cells and to expand what appear to be post-mitotic primary cells into exponentially growing cultures. We report a robust technique for isolating ERpos HBECs from reduction mammoplasties by FACS using two cell surface markers, CD166 and CD117, and an intracellular cytokeratin marker, Ks20.8, for further tracking single cells in culture. We show that ERpos HBECs are released from growth restraint by small molecule inhibitors of TGFβ signalling, and that growth is augmented further in response to oestrogen. Importantly, ER signalling is functionally active in ERpos cells in extended culture. These findings open a new avenue of experimentation with normal ERpos HBECs and provide a basis for understanding the evolution of human breast cancer.
Compensating for population sampling in simulations of epidemic spread on temporal contact networks
Authors: Génois Mathieu , Vestergaard Christian L. , Cattuto Ciro , Barrat Alain 
Published: November 2015

AbstractData describing human interactions often suffer from incomplete sampling of the underlying population. As a consequence, the study of contagion processes using data-driven models can lead to a severe underestimation of the epidemic risk. Here we present a systematic method to alleviate this issue and obtain a better estimation of the risk in the context of epidemic models informed by high-resolution time-resolved contact data. We consider several such data sets collected in various contexts and perform controlled resampling experiments. We show how the statistical information contained in the resampled data can be used to build a series of surrogate versions of the unknown contacts. We simulate epidemic processes on the resulting reconstructed data sets and show that it is possible to obtain good estimates of the outcome of simulations performed using the complete data set. We discuss limitations and potential improvements of our method.
Fluid shear triggers microvilli formation via mechanosensitive activation of TRPV6
Authors: Miura Shigenori , Sato Koji , Kato-Negishi Midori , Teshima Tetsuhiko , Takeuchi Shoji 
Published: November 2015

AbstractMicrovilli are cellular membrane protrusions present on differentiated epithelial cells, which can sense and interact with the surrounding fluid environment. Biochemical and genetic approaches have identified a set of factors involved in microvilli formation; however, the underlying extrinsic regulatory mechanism of microvilli formation remains largely unknown. Here we demonstrate that fluid shear stress (FSS), an external mechanical cue, serves as a trigger for microvilli formation in human placental trophoblastic cells. We further reveal that the transient receptor potential, vanilloid family type-6 (TRPV6) calcium ion channel plays a critical role in flow-induced Ca2+ influx and microvilli formation. TRPV6 regulates phosphorylation of Ezrin via a Ca2+-dependent phosphorylation of Akt; this molecular event is necessary for microvillar localization of Ezrin in response to FSS. Our findings provide molecular insight into the microvilli-mediated mechanoresponsive cellular functions, such as epithelial absorption, signal perception and mechanotransduction.
Analysing black phosphorus transistors using an analytic Schottky barrier MOSFET model
Authors: Penumatcha Ashish V. , Salazar Ramon B. , Appenzeller Joerg 
Published: November 2015

AbstractOwing to the difficulties associated with substitutional doping of low-dimensional nanomaterials, most field-effect transistors built from carbon nanotubes, two-dimensional crystals and other low-dimensional channels are Schottky barrier MOSFETs (metal-oxide-semiconductor field-effect transistors). The transmission through a Schottky barrier-MOSFET is dominated by the gate-dependent transmission through the Schottky barriers at the metal-to-channel interfaces. This makes the use of conventional transistor models highly inappropriate and has lead researchers in the past frequently to extract incorrect intrinsic properties, for example, mobility, for many novel nanomaterials. Here we propose a simple modelling approach to quantitatively describe the transfer characteristics of Schottky barrier-MOSFETs from ultra-thin body materials accurately in the device off-state. In particular, after validating the model through the analysis of a set of ultra-thin silicon field-effect transistor data, we have successfully applied our approach to extract Schottky barrier heights for electrons and holes in black phosphorus devices for a large range of body thicknesses.
Combinatorial interventions inhibit TGFβ-driven epithelial-to-mesenchymal transition and support hybrid cellular phenotypes
Authors: Steinway Steven Nathaniel , Zañudo Jorge Gomez Tejeda , Michel Paul J , Feith David J , Loughran Thomas P , Albert Reka 
Published: November 2015

AbstractEpithelial-to-mesenchymal transition (EMT) is a developmental process hijacked by cancer cells to leave the primary tumor site, invade surrounding tissue and establish distant metastases. A hallmark of EMT is the loss of E-cadherin expression, and one major signal for the induction of EMT is transforming growth factor beta (TGFβ), which is dysregulated in up to 40% of hepatocellular carcinoma (HCC). We aim to identify network perturbations that suppress TGFβ-driven EMT, with the goal of suppressing invasive properties of cancer cells. We use a systems-level Boolean dynamic model of EMT to systematically screen individual and combination perturbations (inhibition or constitutive activation of up to four nodes). We use a recently developed network control approach to understand the mechanism through which the combinatorial interventions suppress EMT. We test the results of our in silico analysis using siRNA. Our model predicts that targeting key elements of feedback loops in combination with the SMAD complex is more effective than suppressing the SMAD complex alone. We demonstrate experimentally that expression of a majority of these elements is enriched in mesenchymal relative to epithelial phenotype HCC cell lines. An siRNA screen of the predicted combinations confirms that many targeting strategies suppress TGFβ-driven EMT measured by E-cadherin expression and cell migration. Our analysis reveals that some perturbations give rise to hybrid states intermediate to the epithelial and mesenchymal states. Our results indicate that EMT is driven by an interconnected signaling network and many apparently successful single interventions may lead to steady states that are in-between epithelial and mesenchymal states. As these putative hybrid or partial EMT states may retain invasive properties, our results suggest that combinatorial therapies are necessary to fully suppress invasive properties of tumor cells.
Plant-mediated interspecific horizontal transmission of an intracellular symbiont in insects
Authors: Gonella Elena , Pajoro Massimo , Marzorati Massimo , Crotti Elena , Mandrioli Mauro , Pontini Marianna , Bulgari Daniela , Negri Ilaria , Sacchi Luciano , Chouaia Bessem , Daffonchio Daniele , Alma Alberto 
Published: November 2015

AbstractIntracellular reproductive manipulators, such as Candidatus Cardinium and Wolbachia are vertically transmitted to progeny but rarely show co-speciation with the host. In sap-feeding insects, plant tissues have been proposed as alternative horizontal routes of interspecific transmission, but experimental evidence is limited. Here we report results from experiments that show that Cardinium is horizontally transmitted between different phloem sap-feeding insect species through plants. Quantitative PCR and in situ hybridization experiments indicated that the leafhopper Scaphoideus titanus releases Cardinium from its salivary glands during feeding on both artificial media and grapevine leaves. Successional time-course feeding experiments with S. titanus initially fed sugar solutions or small areas of grapevine leaves followed by feeding by the phytoplasma vector Macrosteles quadripunctulatus or the grapevine feeder Empoasca vitis revealed that the symbionts were transmitted to both species. Explaining interspecific horizontal transmission through plants improves our understanding of how symbionts spread, their lifestyle and the symbiont-host intermixed evolutionary pattern.
Magnetic field-dependent shape anisotropy in small patterned films studied using rotating magnetoresistance
Authors: Fan Xiaolong , Zhou Hengan , Rao Jinwei , Zhao Xiaobing , Zhao Jing , Zhang Fengzhen , Xue Desheng 
Published: November 2015

AbstractBased on the electric rotating magnetoresistance method, the shape anisotropy of a Co microstrip has been systematically investigated. We find that the shape anisotropy is dependent not only on the shape itself, but also on the magnetization distribution controlled by an applied magnetic field. Together with micro-magnetic simulations, we present a visualized picture of how non-uniform magnetization affects the values and polarities of the anisotropy constants "Equation missing" and "Equation missing". From the perspective of potential appliantions, our results are useful in designing and understanding the performance of micro- and nano-scale patterned ferromagnetic units and the related device properties.
Activin A/BMP2 chimera AB235 drives efficient redifferentiation of long term cultured autologous chondrocytes
Authors: Jiménez G. , López-Ruiz E. , Kwiatkowski W. , Montañez E. , Arrebola F. , Carrillo E. , Gray P. C. , Belmonte J. C. Izpisua , Choe S. , Perán M. , Marchal J. A. 
Published: November 2015

AbstractAutologous chondrocyte implantation (ACI) depends on the quality and quantity of implanted cells and is hindered by the fact that chondrocytes cultured for long periods of time undergo dedifferentiation. Here we have developed a reproducible and efficient chondrogenic protocol to redifferentiate chondrocytes isolated from osteoarthritis (OA) patients. We used morphological, histological and immunological analysis together with a RT-PCR detection of collagen I and collagen II gene expression to show that chondrocytes isolated from articular cartilage biopsies of patients and subjected to long-term culture undergo dedifferentiation and that these cells can be redifferentiated following treatment with the chimeric Activin A/BMP2 ligand AB235. Examination of AB235-treated cell pellets in both in vitro and in vivo experiments revealed that redifferentiated chondrocytes synthesized a cartilage-specific extracellular matrix (ECM), primarily consisting of vertically-orientated collagen fibres and cartilage-specific proteoglycans. AB235-treated cell pellets also integrated into the surrounding subcutaneous tissue following transplantation in mice as demonstrated by their dramatic increase in size while non-treated control pellets disintegrated upon transplantation. Thus, our findings describe an effective protocol for the promotion of redifferentiation of autologous chondrocytes obtained from OA patients and the formation of a cartilage-like ECM that can integrate into the surrounding tissue in vivo.
Broadband All-Polymer Phototransistors with Nanostructured Bulk Heterojunction Layers of NIR-Sensing n-Type and Visible Light-Sensing p-Type Polymers
Authors: Han Hyemi , Nam Sungho , Seo Jooyeok , Lee Chulyeon , Kim Hwajeong , Bradley Donal D. C. , Ha Chang-Sik , Kim Youngkyoo 
Published: November 2015

AbstractWe report ‘broadband light-sensing’ all-polymer phototransistors with the nanostructured bulk heterojunction (BHJ) layers of visible (VIS) light-sensing electron-donating (p-type) polymer and near infrared (NIR) light-sensing electron-accepting (n-type) polymer. Poly[{2,5-bis-(2-ethylhexyl)-3,6-bis-(thien-2-yl)-pyrrolo[3,4-c]pyrrole-1,4-diyl}-co-{2,2′-(2,1,3-benzothiadiazole)]-5,5′-diyl}] (PEHTPPD-BT), which is synthesized via Suzuki coupling and employed as the n-type polymer, shows strong optical absorption in the NIR region (up to 1100 nm) in the presence of weak absorption in the VIS range (400 ~ 600 nm). To strengthen the VIS absorption, poly(3-hexylthiophene) (P3HT) is introduced as the p-type polymer. All-polymer phototransistors with the BHJ (P3HT:PEHTPPD-BT) layers, featuring a peculiar nano-domain morphology, exhibit typical p-type transistor characteristics and efficiently detect broadband (VIS ~ NIR) lights. The maximum corrected responsivity (without contribution of dark current) reaches up to 85 ~ 88% (VIS) and 26 ~ 40% (NIR) of theoretical responsivity. The charge separation process between P3HT and PEHTPPD-BT components in the highest occupied molecular orbital is proposed as a major working mechanism for the effective NIR sensing.
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
Authors: Ziesemer Kirsten A. , Mann Allison E. , Sankaranarayanan Krithivasan , Schroeder Hannes , Ozga Andrew T. , Brandt Bernd W. , Zaura Egija , Waters-Rist Andrea , Hoogland Menno , Salazar-García Domingo C. , Aldenderfer Mark , Speller Camilla , Hendy Jessica , Weston Darlene A. , MacDonald Sandy J. , Thomas Gavin H. , Collins Matthew J. , Lewis Cecil M. , Hofman Corinne , Warinner Christina 
Published: November 2015

AbstractTo date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.