bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coherent superpositions of three states for phosphorous donors in silicon prepared using THz radiation
Authors: Chick S. , Stavrias N. , Saeedi K. , Redlich B. , Greenland P. T. , Matmon G. , Naftaly M. , Pidgeon C. R. , Aeppli G. , Murdin B. N. 
Published: July 2017

AbstractSuperposition of orbital eigenstates is crucial to quantum technology utilizing atoms, such as atomic clocks and quantum computers, and control over the interaction between atoms and their neighbours is an essential ingredient for both gating and readout. The simplest coherent wavefunction control uses a two-eigenstate admixture, but more control over the spatial distribution of the wavefunction can be obtained by increasing the number of states in the wavepacket. Here we demonstrate THz laser pulse control of Si:P orbitals using multiple orbital state admixtures, observing beat patterns produced by Zeeman splitting. The beats are an observable signature of the ability to control the path of the electron, which implies we can now control the strength and duration of the interaction of the atom with different neighbours. This could simplify surface code networks which require spatially controlled interaction between atoms, and we propose an architecture that might take advantage of this.
Non-canonical WNT/PCP signalling in cancer: Fzd6 takes centre stage
Authors: Corda G , Sala A 
Published: July 2017

AbstractFrizzled receptors are the mediators of the wnt canonical and non-canonical pathways, which play fundamental roles in cell differentiation and organism development. A large body of work indicates that dysregulation of wnt signalling is a feature of oncogenic transformation, but most of the studies published so far focus on the assessment of the consequences of aberrations of the canonical pathway in human cancer. In this review, we discuss the emerging role of the wnt non-canonical pathway regulated by frizzled receptor 6 (Fzd6) in the pathogenesis of different types of human malignancies. The function played by Fzd6 in the physiology of normal and cancer cells has been highlighted in the view that an increased knowledge of the signalling pathways upstream and downstream of this receptor could ultimately result in the identification of new targets for cancer therapy.
Initial pulse of Siberian Traps sills as the trigger of the end-Permian mass extinction
Authors: Burgess S. D. , Muirhead J. D. , Bowring S. A. 
Published: July 2017

AbstractMass extinction events are short-lived and characterized by catastrophic biosphere collapse and subsequent reorganization. Their abrupt nature necessitates a similarly short-lived trigger, and large igneous province magmatism is often implicated. However, large igneous provinces are long-lived compared to mass extinctions. Therefore, if large igneous provinces are an effective trigger, a subinterval of magmatism must be responsible for driving deleterious environmental effects. The onset of Earth’s most severe extinction, the end-Permian, coincided with an abrupt change in the emplacement style of the contemporaneous Siberian Traps large igneous province, from dominantly flood lavas to sill intrusions. Here we identify the initial emplacement pulse of laterally extensive sills as the critical deadly interval. Heat from these sills exposed untapped volatile-fertile sediments to contact metamorphism, likely liberating the massive greenhouse gas volumes needed to drive extinction. These observations suggest that large igneous provinces characterized by sill complexes are more likely to trigger catastrophic global environmental change than their flood basalt- and/or dike-dominated counterparts.
Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer
Authors: Maderbocus Riyaz , Fields Blanche L. , Hamilton Keith , Luo Shukun , Tran Timothy H. , Dietrich Lars E. P. , Tong Liang 
Published: July 2017

AbstractPseudomonas species and other aerobic bacteria have a biotin-independent malonate decarboxylase that is crucial for their utilization of malonate as the sole carbon and energy source. The malonate decarboxylase holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD–MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Here we report the crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer, as well as biochemical and functional studies based on the structural information. We observe a malonate molecule in the active site of MdcA and we also determine the structure of malonate decarboxylase with CoA in the active site of MdcD–MdcE. Both structures provide molecular insights into malonate decarboxylase catalysis. Mutations in the hetero-tetramer interface can abolish holoenzyme formation. Mutations in the hetero-tetramer interface and the active sites can abolish Pseudomonas aeruginosa growth in a defined medium with malonate as the sole carbon source.
The low-temperature highly correlated quantum phase in the charge-density-wave 1T-TaS2 compound
Authors: Kratochvilova Marie , Hillier Adrian D. , Wildes Andrew R. , Wang Lihai , Cheong Sang-Wook , Park Je-Geun 
Published: July 2017

AbstractA prototypical quasi-2D metallic compound, 1T-TaS2 has been extensively studied due to an intricate interplay between a Mott-insulating ground state and a charge-density-wave order. In the low-temperature phase, 12 out of 13 Ta4+ 5d-electrons form molecular orbitals in hexagonal star-of-David patterns, leaving one 5d-electron with S  = ½ spin free. This orphan quantum spin with a large spin-orbit interaction is expected to form a highly correlated phase of its own. And it is most likely that they will form some kind of a short-range order out of a strongly spin-orbit coupled Hilbert space. In order to investigate the low-temperature magnetic properties, we performed a series of measurements including neutron scattering and muon experiments. The obtained data clearly indicate the presence of the short-ranged phase and put the upper bound on ~0.4 µB for the size of the magnetic moment, consistent with the orphan-spin scenario.
Integrated regulatory network reveals the early salt tolerance mechanism of Populus euphratica
Authors: Chen Jiafei , Zhang Jin , Hu Jianjun , Xiong Wenwei , Du Chunguang , Lu Mengzhu 
Published: July 2017

AbstractSalinization is one of the major factors that threaten the existence of plants worldwide. Populus euphratica has been deemed to be a promising candidate for stress response research because of its high capacity to tolerate extreme salt stress. We carried out a genome-wide transcriptome analysis to identify the differentially expressed genes (DEGs) response to salt shock and elucidate the early salt tolerance mechanisms in P. euphratica. Both hierarchical clustering and DEG analysis demonstrated a predominant variation from time-course rather than NaCl intensity within 24 hours salt shock. Among the identified 1,678 salt-responsive DEGs, 74.1% (1,244) have not been reported before. We further created an integrated regulatory gene network of the salt response in P. euphratica by combining DEGs, transcription factors (TFs), Helitrons, miRNAs and their targets. The prominent pathways in this network are plant hormone transduction, starch and sucrose metabolism, RNA transport, protein processing in endoplasmic reticulum, etc. In addition, the network indicates calcium-related genes play key roles in P. euphratica response to salt shock. These results illustrated an overview of the systematic molecular response in P. euphratica under different intensities of salt shock and revealed the complex regulatory mechanism.
Biodegradation of 2-hydroxyl-1,4 naphthoquinone (lawsone) by Pseudomonas taiwanensis LH-3 isolated from activated sludge
Authors: Yang Li , Cai Tianming , Ding Dahu , Cai Tianjin , Jiang Canlan , Li Hua , Yang Qian , Chen Liwei 
Published: July 2017

Abstract2-hydroxy-1,4 naphthoquinone (lawsone) is widely used and induces environmental pollutions during its production and application. In the present study, a lawsone-degrading bacterium strain, LH-3 was successfully isolated from the activated sludge. Based on the 16S rRNA gene analysis, the strain LH-3 phylogenetically belonged to the Pseudomonas taiwanensis. It could degrade 200 mg L−1 lawsone completely in 9 h with an inoculum quantity of 1% (v/v). The effects of environmental conditions on the degradation process and the degradation pathway were systematically investigated. LH-3 could maintain its high degradation efficiency under high salt condition. The identified intermediates of salicylic acid, 2-hydroxy-4-oxo-chroman-2-carboxylic acid, and catechol elucidated the potential degradation pathway. Furthermore, the immobilized LH-3 strain cells prepared with alginate gel and biochar performed excellent stability in nine successive degradation runs. It could sucessfully survive in laboratory scale sequencing batch reactor and become to be the dominant species. This study clearly revealed that LH-3 could serve as an attractive candidate for the microbial remediation of lawsone-containing wastewater.
Transcriptome profiling of monocytes from XLA patients revealed the innate immune function dysregulation due to the BTK gene expression deficiency
Authors: Mirsafian Hoda , Ripen Adiratna Mat , Leong Wai-Mun , Chear Chai Teng , Bin Mohamad Saharuddin , Merican Amir Feisal 
Published: July 2017

AbstractX-linked agammaglobulinemia (XLA) is a rare genetic disorder, caused by mutations in BTK (Bruton’s Tyrosine Kinase) gene. Deep high-throughput RNA sequencing (RNA-Seq) approach was utilized to explore the possible differences in transcriptome profiles of primary monocytes in XLA patients compared with healthy subjects. Our analysis revealed the differences in expression of 1,827 protein-coding genes, 95 annotated long non-coding RNAs (lncRNAs) and 20 novel lincRNAs between XLA patients and healthy subjects. GO and KEGG pathway analysis of differentially expressed (DE) protein-coding genes showed downregulation of several innate immune-related genes and upregulation of oxidative phosphorylation and apoptosis-related genes in XLA patients compared to the healthy subjects. Moreover, the functional prediction analysis of DE lncRNAs revealed their potential role in regulating the monocytes cell cycle and apoptosis in XLA patients. Our results suggested that BTK mutations may contribute to the dysregulation of innate immune system and increase susceptibility to apoptosis in monocytes of XLA patients. This study provides significant finding on the regulation of BTK gene in monocytes and the potential for development of innovative biomarkers and therapeutic monitoring strategies to increase the quality of life in XLA patients.
Identification of clusters of rapid and slow decliners among subjects at risk for Alzheimer’s disease
Authors: Gamberger Dragan , Lavrač Nada , Srivatsa Shantanu , Tanzi Rudolph E. , Doraiswamy P. Murali 
Published: July 2017

AbstractThe heterogeneity of Alzheimer’s disease contributes to the high failure rate of prior clinical trials. We analyzed 5-year longitudinal outcomes and biomarker data from 562 subjects with mild cognitive impairment (MCI) from two national studies (ADNI) using a novel multilayer clustering algorithm. The algorithm identified homogenous clusters of MCI subjects with markedly different prognostic cognitive trajectories. A cluster of 240 rapid decliners had 2-fold greater atrophy and progressed to dementia at almost 5 times the rate of a cluster of 184 slow decliners. A classifier for identifying rapid decliners in one study showed high sensitivity and specificity in the second study. Characterizing subgroups of at risk subjects, with diverse prognostic outcomes, may provide novel mechanistic insights and facilitate clinical trials of drugs to delay the onset of AD.
DMF-MALDI: droplet based microfluidic combined to MALDI-TOF for focused peptide detection
Authors: Mesbah Kiarach , Thai Robert , Bregant Sarah , Malloggi Florent 
Published: July 2017

AbstractWe present an automated droplet microfluidic system (DMF) to generate monitored nanoliter aqueous droplets in oil and their deposition on a commercial stainless steel plate for MALDI-TOF analysis of peptides or protein digests. We demonstrate that DMF-MALDI combination focuses the analyte on the MALDI plate, increasing considerably the homogeneity of the dried material. This results in a 30times enhanced MALDI-TOF MS signal for a model peptide, allowing a significant improvement of the detection sensitivity limit (down to few tens of attomoles). Moreover, positive detection can be achieved from sub-nanomolar peptides solutions and better overall protein sequence coverages are obtained from few tens attomoles of protein digest. These results make DMF-MALDI a promising approach for the treatment of peptides samples as well as a key component for an integrated approach in the proteomic field.
Activation of TGF-β signaling induces cell death via the unfolded protein response in Fuchs endothelial corneal dystrophy
Authors: Okumura Naoki , Hashimoto Keisuke , Kitahara Miu , Okuda Hirokazu , Ueda Emi , Watanabe Kyoko , Nakahara Makiko , Sato Takahiko , Kinoshita Shigeru , Tourtas Theofilos , Schlötzer-Schrehardt Ursula , Kruse Friedrich , Koizumi Noriko 
Published: July 2017

AbstractFuchs endothelial corneal dystrophy (FECD) is a slowly progressive bilateral disease of corneal endothelium in which accumulation of extracellular matrix (ECM) and loss of corneal endothelial cells (CECs) are phenotypic features. The corneal endothelium maintains corneal transparency by regulating water hydration; consequently, corneal endothelial dysfunction causes serious vision loss. The only therapy for corneal haziness due to corneal endothelial diseases, including FECD, is corneal transplantation using donor corneas, and no pharmaceutical treatment is available. We provide evidence that the expression levels of transforming growth factor-β (TGF-β) isoforms and TGF-β receptors are high in the corneal endothelium of patients with FECD. A cell model based on patients with FECD shows that TGF-β signaling induced a chronic overload of ECM proteins to the endoplasmic reticulum (ER), thereby enhancing the formation of unfolded protein and triggering the intrinsic apoptotic pathway through the unfolded protein response (UPR). We propose that inhibition of TGF-β signaling may represent a novel therapeutic target that suppresses cell loss as well as the accumulation of ECM in FECD.
Monitoring diffuse volcanic degassing during volcanic unrests: the case of Campi Flegrei (Italy)
Authors: Cardellini C. , Chiodini G. , Frondini F. , Avino R. , Bagnato E. , Caliro S. , Lelli M. , Rosiello A. 
Published: July 2017

AbstractIn volcanoes with active hydrothermal systems, diffuse CO2 degassing may constitute the primary mode of volcanic degassing. The monitoring of CO2 emissions can provide important clues in understanding the evolution of volcanic activity especially at calderas where the interpretation of unrest signals is often complex. Here, we report eighteen years of CO2 fluxes from the soil at Solfatara of Pozzuoli, located in the restless Campi Flegrei caldera. The entire dataset, one of the largest of diffuse CO2 degassing ever produced, is made available for the scientific community. We show that, from 2003 to 2016, the area releasing deep-sourced CO2 tripled its extent. This expansion was accompanied by an increase of the background CO2 flux, over most of the surveyed area (1.4 km2), with increased contributions from non-biogenic source. Concurrently, the amount of diffusively released CO2 increased up to values typical of persistently degassing active volcanoes (up to 3000 t d−1). These variations are consistent with the increase in the flux of magmatic fluids injected into the hydrothermal system, which cause pressure increase and, in turn, condensation within the vapor plume feeding the Solfatara emission.
Metabolic syndrome is associated with an increased incidence of subclinical hypothyroidism – A Cohort Study
Authors: Chang Chia-Hsuin , Yeh Yi-Chun , Caffrey James L. , Shih Shyang-Rong , Chuang Lee-Ming , Tu Yu-Kang 
Published: July 2017

AbstractPrior cross-sectional analyses have demonstrated an association between subclinical hypothyroidism and metabolic syndrome and selected components. However, the temporal relation between metabolic syndrome and declining thyroid function remains unclear. In a prospective study, an unselected cohort of 66,822 participants with and without metabolic syndrome were followed. A proportional hazards regression model was used to estimate hazard ratios (HRs) and 95% CIs for hypothyroidism. Exploratory analyses for the relation between components of metabolic syndrome and declining thyroid function were also undertaken. During an average follow-up of 4.2 years, the incident rates for subclinical hypothyroidism were substantially higher in participants who began the study with metabolic syndrome compared with metabolically normal controls. After controlling for risk factors, patients with metabolic syndrome were at a 21% excess risk of developing subclinical hypothyroidism (adjusted HR 1.21; 95% CI 1.03–1.42). When individual components were analyzed, an increased risk of subclinical hypothyroidism was associated with high blood pressure (1.24; 1.04–1.48) and high serum triglycerides (1.18; 1.00–1.39), with a trend of increasing risk as participants had additional more components. Individuals with metabolic syndrome are at a greater risk for developing subclinical hypothyroidism, while its mechanisms and temporal consequences of this observation remain to be determined.
High-throughput mutagenesis using a two-fragment PCR approach
Authors: Heydenreich Franziska M. , Miljuš Tamara , Jaussi Rolf , Benoit Roger , Milić Dalibor , Veprintsev Dmitry B. 
Published: July 2017

AbstractSite-directed scanning mutagenesis is a powerful protein engineering technique which allows studies of protein functionality at single amino acid resolution and design of stabilized proteins for structural and biophysical work. However, creating libraries of hundreds of mutants remains a challenging, expensive and time-consuming process. The efficiency of the mutagenesis step is the key for fast and economical generation of such libraries. PCR artefacts such as misannealing and tandem primer repeats are often observed in mutagenesis cloning and reduce the efficiency of mutagenesis. Here we present a high-throughput mutagenesis pipeline based on established methods that significantly reduces PCR artefacts. We combined a two-fragment PCR approach, in which mutagenesis primers are used in two separate PCR reactions, with an in vitro assembly of resulting fragments. We show that this approach, despite being more laborious, is a very efficient pipeline for the creation of large libraries of mutants.
Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence
Authors: Sugimura Satoshi , Kobayashi Norio , Okae Hiroaki , Yamanouchi Tadayuki , Matsuda Hideo , Kojima Takumi , Yajima Akira , Hashiyada Yutaka , Kaneda Masahiro , Sato Kan , Imai Kei , Tanemura Kentaro , Arima Takahiro , Gilchrist Robert B. 
Published: July 2017

AbstractDuring antral folliculogenesis, developmental competence of prospective oocytes is regulated in large part by the follicular somatic component to prepare the oocyte for the final stage of maturation and subsequent embryo development. The underlying molecular mechanisms are poorly understood. Oocytes reaching the advanced stage of follicular growth by administration of exogenous follicle-stimulating hormone (FSH) possess higher developmental competence than oocytes in FSH-untreated smaller follicles. In this study, the transcriptomic profile of the cumulus cells from cows receiving FSH administration (FSH-priming) was compared, as a model of high oocyte competence, with that from untreated donor cows (control). Ingenuity Pathway Analysis showed that cumulus cells receiving FSH-priming were rich in down-regulated transcripts associated with cell movement and migration, including the extracellular matrix-related transcripts, probably preventing the disruption of cell-to-cell contacts. Interestingly, the transcriptomic profile of up-regulated genes in the control group was similar to that of granulosa cells from atretic follicles. Interferon regulatory factor 7 was activated as the key upstream regulator of FSH-priming. Thus, acquisition of developmental competence by oocytes can be ensured by the integrity of cumulus cells involved in cell-to-cell communication and cell survival, which may help achieve enhanced oocyte-somatic cell coupling.
Epigenetic changes in myelofibrosis: Distinct methylation changes in the myeloid compartments and in cases with ASXL1 mutations
Authors: Nielsen Helene Myrtue , Andersen Christen Lykkegaard , Westman Maj , Kristensen Lasse Sommer , Asmar Fazila , Kruse Torben Arvid , Thomassen Mads , Larsen Thomas Stauffer , Skov Vibe , Hansen Lise Lotte , Bjerrum Ole Weis , Hasselbalch Hans Carl , Punj Vasu , Grønbæk Kirsten 
Published: July 2017

AbstractThis is the first study to compare genome-wide DNA methylation profiles of sorted blood cells from myelofibrosis (MF) patients and healthy controls. We found that differentially methylated CpG sites located to genes involved in ‘cancer’ and ‘embryonic development’ in MF CD34+ cells, in ‘inflammatory disease’ in MF mononuclear cells, and in ‘immunological diseases’ in MF granulocytes. Only few differentially methylated CpG sites were common among the three cell populations. Mutations in the epigenetic regulators ASXL1 (47%) and TET2 (20%) were not associated with a specific DNA methylation pattern using an unsupervised approach. However, in a supervised analysis of ASXL1 mutated versus wild-type cases, differentially methylated CpG sites were enriched in regions marked by histone H3K4me1, histone H3K27me3, and the bivalent histone mark H3K27me3 + H3K4me3 in human CD34+ cells. Hypermethylation of selected CpG sites was confirmed in a separate validation cohort of 30 MF patients by pyrosequencing. Altogether, we show that individual MF cell populations have distinct differentially methylated genes relative to their normal counterparts, which likely contribute to the phenotypic characteristics of MF. Furthermore, differentially methylated CpG sites in ASXL1 mutated MF cases are found in regulatory regions that could be associated with aberrant gene expression of ASXL1 target genes.
Blockade of high-mobility group box 1 attenuates intestinal mucosal barrier dysfunction in experimental acute pancreatitis
Authors: Chen Xia , Zhao Hong-Xian , Bai Chao , Zhou Xiang-Yu 
Published: July 2017

AbstractThe release of inflammatory cytokines, that plays a dominant role in local pancreatic inflammation and systemic complications in severe acute pancreatitis (SAP). High-mobility group box 1 (HMGB1) is implicated in the mechanism of organ dysfunction and bacterial translocation in SAP. This current study aims to investigate possible role of HMGB1 in the intestinal mucosal barrier dysfunction of SAP, and the effect of anti-HMGB1 antibody treatment in intestinal mucosal injury in SAP. Our data revealed that the HMGB1 expression was significantly increased in AP mice induced by caerulein and LPS, and the inhibition of HMGB1 played a protective role in intestinal mucosal barrier dysfunction, reduced the serum level of other proinflammatory cytokines include IL-1β, IL-6, TNF-α. Next we investigated the downstream receptors involving in HMGB1 signaling. We found that the expressions of toll-like receptor (TLR) 4 and TLR9 were elevated in ileum of AP mice, the administration of HMGB1 neutralizing antibody significantly reduced the TLR4 and TLR9 expression. It was concluded that HMGB1 contributed the mechanism to the intestinal mucosal barrier dysfunction during AP. Blockade of HMGB1 by administration of HMGB1 neutralizing antibody may be a beneficial therapeutic strategy in improving intestinal mucosal barrier dysfunction in SAP.