bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soil microbial diversity drives the priming effect along climate gradients: a case study in Madagascar
Authors: Razanamalala Kanto , Razafimbelo Tantely , Maron Pierre-Alain , Ranjard Lionel , Chemidlin Nicolas , Lelièvre Mélanie , Dequiedt Samuel , Ramaroson Volaniaina H , Marsden Claire , Becquer Thierry , Trap Jean , Blanchart Eric , Bernard Laetitia 
Published: October 2017

Abstract
The priming effect in soil is proposed to be generated by two distinct mechanisms: ‘stoichiometric decomposition’ and/or ‘nutrient mining’ theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects. Abiotic and biotic soil descriptors were characterized including bacterial and fungal phylogenetic composition. Potential organic matter mineralization and PE were assessed 7 and 42 days after the beginning of incubation with 13C-enriched wheat straw. Both priming mechanisms were mainly driven by the mean annual temperature but in opposite directions. The priming effect generated by stoichiometric decomposition was fostered under colder climates, because of soil enrichment in less developed organic matter, as well as in fast-growing populations. Conversely, the priming effect generated by nutrient mining was enhanced under warmer climates, probably because of the lack of competition between slow-growing populations mining SOM and fast-growing populations for the energy-rich residue entering the soil. Our study leads to hypotheses about the consequences of climate change on both PE generation mechanisms and associated consequences on soil carbon sequestration.
Survival of pancreatic cancer cells lacking KRAS function
Authors: Muzumdar Mandar Deepak , Chen Pan-Yu , Dorans Kimberly Judith , Chung Katherine Minjee , Bhutkar Arjun , Hong Erin , Noll Elisa M. , Sprick Martin R. , Trumpp Andreas , Jacks Tyler 
Published: October 2017

AbstractActivating mutations in the proto-oncogene KRAS are a hallmark of pancreatic ductal adenocarcinoma (PDAC), an aggressive malignancy with few effective therapeutic options. Despite efforts to develop KRAS-targeted drugs, the absolute dependence of PDAC cells on KRAS remains incompletely understood. Here we model complete KRAS inhibition using CRISPR/Cas-mediated genome editing and demonstrate that KRAS is dispensable in a subset of human and mouse PDAC cells. Remarkably, nearly all KRAS deficient cells exhibit phosphoinositide 3-kinase (PI3K)-dependent mitogen-activated protein kinase (MAPK) signaling and induced sensitivity to PI3K inhibitors. Furthermore, comparison of gene expression profiles of PDAC cells retaining or lacking KRAS reveal a role of KRAS in the suppression of metastasis-related genes. Collectively, these data underscore the potential for PDAC resistance to even the very best KRAS inhibitors and provide insights into mechanisms of response and resistance to KRAS inhibition.
High grade serous ovarian carcinomas originate in the fallopian tube
Authors: Labidi-Galy S. Intidhar , Papp Eniko , Hallberg Dorothy , Niknafs Noushin , Adleff Vilmos , Noe Michael , Bhattacharya Rohit , Novak Marian , Jones Siân , Phallen Jillian , Hruban Carolyn A. , Hirsch Michelle S. , Lin Douglas I. , Schwartz Lauren , Maire Cecile L. , Tille Jean-Christophe , Bowden Michaela , Ayhan Ayse , Wood Laura D. , Scharpf Robert B. , Kurman Robert , Wang Tian-Li , Shih Ie-Ming , Karchin Rachel , Drapkin Ronny , Velculescu Victor E. 
Published: October 2017

AbstractHigh-grade serous ovarian carcinoma (HGSOC) is the most frequent type of ovarian cancer and has a poor outcome. It has been proposed that fallopian tube cancers may be precursors of HGSOC but evolutionary evidence for this hypothesis has been limited. Here, we perform whole-exome sequence and copy number analyses of laser capture microdissected fallopian tube lesions (p53 signatures, serous tubal intraepithelial carcinomas (STICs), and fallopian tube carcinomas), ovarian cancers, and metastases from nine patients. The majority of tumor-specific alterations in ovarian cancers were present in STICs, including those affecting TP53, BRCA1, BRCA2 or PTEN. Evolutionary analyses reveal that p53 signatures and STICs are precursors of ovarian carcinoma and identify a window of 7 years between development of a STIC and initiation of ovarian carcinoma, with metastases following rapidly thereafter. Our results provide insights into the etiology of ovarian cancer and have implications for prevention, early detection and therapeutic intervention of this disease.
A three-membered ring approach to carbonyl olefination
Authors: Niyomchon Supaporn , Oppedisano Alberto , Aillard Paul , Maulide Nuno 
Published: October 2017

AbstractThe carbon–carbon double bond, with its diverse and multifaceted reactivity, occupies a prominent position in organic synthesis. Although a variety of simple alkenes are readily available, the mild and chemoselective introduction of a unit of unsaturation into a functionalized organic molecule remains an ongoing area of research, and the olefination of carbonyl compounds is a cornerstone of such approaches. Here we show the direct olefination of hydrazones via the intermediacy of three-membered ring species generated by addition of sulfoxonium ylides, departing from the general dogma of alkenes synthesis from carbonyls. Moreover, the mild reaction conditions and operational simplicity of the transformation render the methodology appealing from a practical point of view.
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
Authors: Wong Emily S. , Schmitt Bianca M. , Kazachenka Anastasiya , Thybert David , Redmond Aisling , Connor Frances , Rayner Tim F. , Feig Christine , Ferguson-Smith Anne C. , Marioni John C. , Odom Duncan T. , Flicek Paul 
Published: October 2017

AbstractNoncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.
Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations
Authors: Paul Fabian , Wehmeyer Christoph , Abualrous Esam T. , Wu Hao , Crabtree Michael D. , Schöneberg Johannes , Clarke Jane , Freund Christian , Weikl Thomas R. , Noé Frank 
Published: October 2017

AbstractUnderstanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25–109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.
A framework to identify contributing genes in patients with Phelan-McDermid syndrome
Authors: Tabet Anne-Claude , Rolland Thomas , Ducloy Marie , Lévy Jonathan , Buratti Julien , Mathieu Alexandre , Haye Damien , Perrin Laurence , Dupont Céline , Passemard Sandrine , Capri Yline , Verloes Alain , Drunat Séverine , Keren Boris , Mignot Cyril , Marey Isabelle , Jacquette Aurélia , Whalen Sandra , Pipiras Eva , Benzacken Brigitte , Chantot-Bastaraud Sandra , Afenjar Alexandra , Héron Delphine , Le Caignec Cédric , Beneteau Claire , Pichon Olivier , Isidor Bertrand , David Albert , El Khattabi Laila , Kemeny Stephan , Gouas Laetitia , Vago Philippe , Mosca-Boidron Anne-Laure , Faivre Laurence , Missirian Chantal , Philip Nicole , Sanlaville Damien , Edery Patrick , Satre Véronique , Coutton Charles , Devillard Françoise , Dieterich Klaus , Vuillaume Marie-Laure , Rooryck Caroline , Lacombe Didier , Pinson Lucile , Gatinois Vincent , Puechberty Jacques , Chiesa Jean , Lespinasse James , Dubourg Christèle , Quelin Chloé , Fradin Mélanie , Journel Hubert , Toutain Annick , Martin Dominique , Benmansour Abdelamdjid , Leblond Claire S. , Toro Roberto , Amsellem Frédérique , Delorme Richard , Bourgeron Thomas 
Published: October 2017

AbstractPhelan-McDermid syndrome (PMS) is characterized by a variety of clinical symptoms with heterogeneous degrees of severity, including intellectual disability (ID), absent or delayed speech, and autism spectrum disorders (ASD). It results from a deletion of the distal part of chromosome 22q13 that in most cases includes the SHANK3 gene. SHANK3 is considered a major gene for PMS, but the factors that modulate the severity of the syndrome remain largely unknown. In this study, we investigated 85 patients with different 22q13 rearrangements (78 deletions and 7 duplications). We first explored the clinical features associated with PMS, and provide evidence for frequent corpus callosum abnormalities in 28% of 35 patients with brain imaging data. We then mapped several candidate genomic regions at the 22q13 region associated with high risk of clinical features, and suggest a second locus at 22q13 associated with absence of speech. Finally, in some cases, we identified additional clinically relevant copy-number variants (CNVs) at loci associated with ASD, such as 16p11.2 and 15q11q13, which could modulate the severity of the syndrome. We also report an inherited SHANK3 deletion transmitted to five affected daughters by a mother without ID nor ASD, suggesting that some individuals could compensate for such mutations. In summary, we shed light on the genotype-phenotype relationship of patients with PMS, a step towards the identification of compensatory mechanisms for a better prognosis and possibly treatments of patients with neurodevelopmental disorders.
Enhancing quantum control by bootstrapping a quantum processor of 12 qubits
Authors: Lu Dawei , Li Keren , Li Jun , Katiyar Hemant , Park Annie Jihyun , Feng Guanru , Xin Tao , Li Hang , Long Guilu , Brodutch Aharon , Baugh Jonathan , Zeng Bei , Laflamme Raymond 
Published: October 2017

AbstractAccurate and efficient control of quantum systems is one of the central challenges for quantum information processing. Current state-of-the-art experiments rarely go beyond 10 qubits and in most cases demonstrate only limited control. Here we demonstrate control of a 12-qubit system, and show that the system can be employed as a quantum processor to optimize its own control sequence by using measurement-based feedback control (MQFC). The final product is a control sequence for a complex 12-qubit task: preparation of a 12-coherent state. The control sequence is about 10% more accurate than the one generated by the standard (classical) technique, showing that MQFC can correct for unknown imperfections. Apart from demonstrating a high level of control over a relatively large system, our results show that even at the 12-qubit level, a quantum processor can be a useful lab instrument. As an extension of our work, we propose a method for combining the MQFC technique with a twirling protocol, to optimize the control sequence that produces a desired Clifford gate.
The implications of dust ice nuclei effect on cloud top temperature in a complex mesoscale convective system
Authors: Li Rui , Dong Xue , Guo Jingchao , Fu Yunfei , Zhao Chun , Wang Yu , Min Qilong 
Published: October 2017

AbstractMineral dust is the most important natural source of atmospheric ice nuclei (IN) which may significantly mediate the properties of ice cloud through heterogeneous nucleation and lead to crucial impacts on hydrological and energy cycle. The potential dust IN effect on cloud top temperature (CTT) in a well-developed mesoscale convective system (MCS) was studied using both satellite observations and cloud resolving model (CRM) simulations. We combined satellite observations from passive spectrometer, active cloud radar, lidar, and wind field simulations from CRM to identify the place where ice cloud mixed with dust particles. For given ice water path, the CTT of dust-mixed cloud is warmer than that in relatively pristine cloud. The probability distribution function (PDF) of CTT for dust-mixed clouds shifted to the warmer end and showed two peaks at about −45 °C and −25 °C. The PDF for relatively pristine cloud only show one peak at −55 °C. Cloud simulations with different microphysical schemes agreed well with each other and showed better agreement with satellite observations in pristine clouds, but they showed large discrepancies in dust-mixed clouds. Some microphysical schemes failed to predict the warm peak of CTT related to heterogeneous ice formation.
A comparative Raman study between PrMnO
3, NdMnO
3, TbMnO
3 and DyMnO
3
Authors: Mansouri Sabeur , Jandl Serge , Mukhin Alexander , Ivanov Vsevolod Yu , Balbashov Anatoly 
Published: October 2017

AbstractIn this paper, we present a detailed Raman study of the non-multiferroic compounds PrMnO3 and NdMnO3 and the multiferroic compounds TbMnO3 and DyMnO3 as a function of temperature and magnetic field. All studied systems show anomalous phonon shifts close to the Néel transition T
N
. In PrMnO3 and NdMnO3, the frequency softenings are partly attributed to an orbital-spin-phonon coupling whereas in TbMnO3 and DyMnO3, the relatively weak frequency shifts are rather attributed to an expansion of the Mn−O bond lengths. On the other hand, the frequencies of TbMnO3 phonons are shifted as a function of magnetic field, while those of PrMnO3 remain unaffected. These frequency shifts are interpreted in terms of local oxygen rearrangements under magnetic field that could play an important role in the multiferroicity of TbMnO3 and DyMnO3.
Elucidation of Plasma-induced Chemical Modifications on Glutathione and Glutathione Disulphide
Authors: Klinkhammer Christina , Verlackt Christof , śmiłowicz Dariusz , Kogelheide Friederike , Bogaerts Annemie , Metzler-Nolte Nils , Stapelmann Katharina , Havenith Martina , Lackmann Jan-Wilm 
Published: October 2017

AbstractCold atmospheric pressure plasmas are gaining increased interest in the medical sector and clinical trials to treat skin diseases are underway. Plasmas are capable of producing several reactive oxygen and nitrogen species (RONS). However, there are open questions how plasma-generated RONS interact on a molecular level in a biological environment, e.g. cells or cell components. The redox pair glutathione (GSH) and glutathione disulphide (GSSG) forms the most important redox buffer in organisms responsible for detoxification of intracellular reactive species. We apply Raman spectroscopy, mass spectrometry, and molecular dynamics simulations to identify the time-dependent chemical modifications on GSH and GSSG that are caused by dielectric barrier discharge under ambient conditions. We find GSSG, S-oxidised glutathione species, and S-nitrosoglutathione as oxidation products with the latter two being the final products, while glutathione sulphenic acid, glutathione sulphinic acid, and GSSG are rather reaction intermediates. Experiments using stabilized pH conditions revealed the same main oxidation products as were found in unbuffered solution, indicating that the dominant oxidative or nitrosative reactions are not influenced by acidic pH. For more complex systems these results indicate that too long treatment times can cause difficult-to-handle modifications to the cellular redox buffer which can impair proper cellular function.
High-frequency, low-coverage “false positives” mutations may be true in GS Junior sequencing studies
Authors: Yang Zhiliang , Sun Guilian 
Published: October 2017

AbstractThe GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
Abrupt stop of deep water turnover with lake warming: Drastic consequences for algal primary producers
Authors: Yankova Yana , Neuenschwander Stefan , Köster Oliver , Posch Thomas 
Published: October 2017

AbstractAfter strong fertilization in the 20thcentury, many deep lakes in Central Europe are again nutrient poor due to long-lasting restoration (re-oligotrophication). In line with reduced phosphorus and nitrogen loadings, total organismic productivity decreased and lakes have now historically low nutrient and biomass concentrations. This caused speculations that restoration was overdone and intended fertilizations are needed to ensure ecological functionality. Here we show that recent re-oligotrophication processes indeed accelerated, however caused by lake warming. Rising air temperatures strengthen thermal stabilization of water columns which prevents thorough turnover (holomixis). Reduced mixis impedes down-welling of oxygen rich epilimnetic (surface) and up-welling of phosphorus and nitrogen rich hypolimnetic (deep) water. However, nutrient inputs are essential for algal spring blooms acting as boost for annual food web successions. We show that repeated lack (since 1977) and complete stop (since 2013) of holomixis caused drastic epilimnetic phosphorus depletions and an absence of phytoplankton spring blooms in Lake Zurich (Switzerland). By simulating holomixis in experiments, we could induce significant vernal algal blooms, confirming that there would be sufficient hypolimnetic phosphorus which presently accumulates due to reduced export. Thus, intended fertilizations are highly questionable, as hypolimnetic nutrients will become available during future natural or artificial turnovers.
Association between pulse wave velocity and hot flashes/sweats in middle-aged women
Authors: Yang Ruwei , Zhou Yang , Li Changbin , Tao Minfang 
Published: October 2017

AbstractAs women age and go through menopause, they suffer a higher incidence of cardiovascular morbidity and mortality. Previous studies have shown that a relationship exists between hot flashes/sweats and an increased risk of cardiovascular disease. However, the association between hot flashes/sweats and arterial stiffness is unclear. We aim to explore the relationship between hot flashes/sweats and arterial stiffness using the modified Kupperman index (KMI) questionnaire and measure the brachial-ankle pulse wave velocity (baPWV). The prevalence of hot flashes in our research was reported to be 41.77%. There was a statistically significant difference between the mean baPWV among groups that experienced different severities of hot flashes/sweats according to one-way ANOVA test (p < 0.001). The baPWV values were positively associated with the severity of hot flashes/sweats based on linear regression after adjusting for established cardiovascular confounders (95% CI: (5.86, 43.23), p = 0.01). To the best of our knowledge, this study is the first investigation to propose that baPWV may serve both as an objective index for evaluating the severity of hot flashes/sweats and as a predictor of arterial stiffness beyond Cardiac Vascular Disease (CVD) risk factors in middle-aged women.
The role of EZH2 in overall survival of colorectal cancer: a meta-analysis
Authors: Vilorio-Marqués Laura , Martín Vicente , Diez-Tascón Cristina , González-Sevilla María Francisca , Fernández-Villa Tania , Honrado Emiliano , Davila-Batista Veronica , Molina Antonio J. 
Published: October 2017

AbstractEnhancer of zeste homolog 2 (EZH2) is the catalitic subunit of polycomb repressive complex 2 and mediates gene silencing. EZH2 is overexpressed in many cancers and correlates with poor prognosis. The role of the gene EZH2 in colorectal cancer survival is uncertainly, the aim of this study is clear this relationship. Relevant literaure was searched from electronic databases. A meta-analysis was performed with elegible studies which quantitatively evaluated the relationship between EZH2 overexpression and survival of patients with colorectal cancer. Survival data were aggregated and quantitatively analyzed. We performed a meta-analysis of 8 studies (n = 1059 patients) that evaluated the correlation between EZH2 overexpression and survival in patients with colorectal cancer. Combined hazard ratios suggested that EZH2 overexpression was associated with better prognosis of overall survival (OS) HR(hazard ratio) = 0.61 95% CI (0.38–0.84) We performed bias analysis according Egger and Begg,s test and we did not find publication bias. EZH2 overexpression indicates a better prognosis for colorectal cancer.