bluuebunny/crossref_metadata_2025_split huggingface dataset:
Latent classes in diagnoses among psychiatric inpatients predicting mortality and imprisonment – a nationwide cohort study
Authors: Carlsen H.K. , Steingrimsson S. , Sigurdsson M.I. , Sigfússon S. , Magnússon A. 
Published: December 2016

AbstractPurposeIdentify risk factors of death or imprisonment within classes defined by demographic factors and diagnoses within one year of first psychiatric admission.MethodsNationwide data was obtained from hospital registers from psychiatric hospitals in Iceland 1983–2007. Mortality and cause of death as well as information about imprisonments during the study period, and discharge diagnoses for the first year after initial admission were obtained for each individual. Individuals aged 18 during the study period with at least one year of follow-up were included. Latent Class Analysis was used to identify groups with distinguishable risk of either being alive, dead or having been imprisoned at the end of follow-up.ResultsAmong psychiatric patients, 4677 were included, average age was 27 years (range 18–43). Four latent classes were identified with different risks of adverse outcomes. Class B (16%), predominantly males with substance use disorder (SUD) diagnoses, had highly increased risk of imprisonment and death accounting for 85 and 34% of these outcomes, respectively. Class A (12%), all with alcohol use disorder, had similar mortality rate as the general population and no imprisonments. Class C (23%) were younger at first admission with some SUD and increased risk of mortality. Class D (46%) had increased mortality rate, SUDs were rare but depression common.ConclusionsRisk of mortality and criminal trends among psychiatric inpatients can be described as distinct clusters of risk factors present at first admission to a psychiatric hospital. Treatment and interventions to reduce mortality and criminality should take these risk differences into account.
Which DSM validated tools for diagnosing depression are usable in primary care research? A systematic literature review
Authors: Nabbe P. , Le Reste J.Y. , Guillou-Landreat M. , Munoz Perez M.A. , Argyriadou S. , Claveria A. , Fernández San Martín M.I. , Czachowski S. , Lingner H. , Lygidakis C. , Sowinska A. , Chiron B. , Derriennic J. , Le Prielec A. , Le Floch B. , Montier T. , Van Marwijk H. , Van Royen P. 
Published: December 2016

AbstractIntroductionDepression occurs frequently in primary care. Its broad clinical variability makes it difficult to diagnose. This makes it essential that family practitioner (FP) researchers have validated tools to minimize bias in studies of everyday practice. Which tools validated against psychiatric examination, according to the major depression criteria of DSM-IV or 5, can be used for research purposes?MethodAn international FP team conducted a systematic review using the following databases: Pubmed, Cochrane and Embase, from 2000/01/01 to 2015/10/01.ResultsThe three databases search identified 770 abstracts: 546 abstracts were analyzed after duplicates had been removed (224 duplicates); 50 of the validity studies were eligible and 4 studies were included. In 4 studies, the following tools were found: GDS-5, GDS-15, GDS-30, CESD-R, HADS, PSC-51 and HSCL-25. Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value were collected. The Youden index was calculated.DiscussionUsing efficiency data alone to compare these studies could be misleading. Additional reliability, reproducibility and ergonomic data will be essential for making comparisons.ConclusionThis study selected seven tools, usable in primary care research, for the diagnosis of depression. In order to define the best tools in terms of efficiency, reproducibility, reliability and ergonomics for research in primary care, and for care itself, further research will be essential.
The complexity of interpreting genomic data in patients with acute myeloid leukemia
Authors: Nazha A , Zarzour A , Al-Issa K , Radivoyevitch T , Carraway H E , Hirsch C M , Przychodzen B , Patel B J , Clemente M , Sanikommu S R , Kalaycio M , Maciejewski J P , Sekeres M A 
Published: December 2016

AbstractAcute myeloid leukemia (AML) is a heterogeneous neoplasm characterized by the accumulation of complex genetic alterations responsible for the initiation and progression of the disease. Translating genomic information into clinical practice remained challenging with conflicting results regarding the impact of certain mutations on disease phenotype and overall survival (OS) especially when clinical variables are controlled for when interpreting the result. We sequenced the coding region for 62 genes in 468 patients with secondary AML (sAML) and primary AML (pAML). Overall, mutations in FLT3, DNMT3A, NPM1 and IDH2 were more specific for pAML whereas UTAF1, STAG2, BCORL1, BCOR, EZH2, JAK2, CBL, PRPF8, SF3B1, ASXL1 and DHX29 were more specific for sAML. However, in multivariate analysis that included clinical variables, only FLT3 and DNMT3A remained specific for pAML and EZH2, BCOR, SF3B1 and ASXL1 for sAML. When the impact of mutations on OS was evaluated in the entire cohort, mutations in DNMT3A, PRPF8, ASXL1, CBL EZH2 and TP53 had a negative impact on OS; no mutation impacted OS favorably; however, in a cox multivariate analysis that included clinical data, mutations in DNMT3A, ASXL1, CBL, EZH2 and TP53 became significant. Thus, controlling for clinical variables is important when interpreting genomic data in AML.
Risk stratification in myeloma by detection of circulating plasma cells prior to autologous stem cell transplantation in the novel agent era
Authors: Chakraborty R , Muchtar E , Kumar S K , Jevremovic D , Buadi F K , Dingli D , Dispenzieri A , Hayman S R , Hogan W J , Kapoor P , Lacy M Q , Leung N , Gertz M A 
Published: December 2016

AbstractThe impact of circulating plasma cells (CPCs) prior to autologous stem cell transplantation (ASCT) for multiple myeloma has not been defined in the novel agent era. We evaluated the impact of pre-transplant CPCs, detected by six-color flow cytometry in patients undergoing early ASCT on post-transplant response, progression-free survival (PFS) and overall survival (OS). CPCs were detected in 162 out of 840 (19.3%) patients, with the median number of CPCs being 58 per 150 000 events. Ninety-nine percent of patients had received proteasome inhibitor and/or immunomodulator-based induction. The incidence of post-transplant stringent complete response (sCR) in the subgroups with and without CPCs was 15% and 38%, respectively, (P<0.001). The median PFS in the subgroups with and without CPCs was 15.1 (95% confidence interval (CI), 12.5–17.8) and 29.6 months (95% CI, 26.2–32.8), respectively, and the median OS was 41.0 months (95% CI, 32.6–58.2) and not reached (NR) (95% CI, 99.1-NR), respectively, (P<0.001 for both). On multivariate analysis for OS, factors independently predictive of mortality were the presence of CPCs (hazard ratio (HR) 2.5; 95% CI, 1.8–3.6;P<0.001) and sCR post transplant (HR 0.4; 95% CI, 0.2–0.6;P<0.001). Presence of CPCs prior to transplant has a high prognostic impact and should be prospectively validated in clinical trials.
Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality
Authors: Fabian Jenny , Zlatanovic Sanja , Mutz Michael , Premke Katrin 
Published: December 2016

Abstract
Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial–aquatic C cycling in relation to environmental conditions.
Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts
Authors: Szabó Gitta , Schulz Frederik , Toenshoff Elena R , Volland Jean-Marie , Finkel Omri M , Belkin Shimshon , Horn Matthias 
Published: December 2016

Abstract
Mealybugs (Insecta: Hemiptera: Pseudococcidae) maintain obligatory relationships with bacterial symbionts, which provide essential nutrients to their insect hosts. Most pseudococcinae mealybugs harbor a unique symbiosis setup with enlarged betaproteobacterial symbionts (‘Candidatus Tremblaya princeps’), which themselves contain gammaproteobacterial symbionts. Here we investigated the symbiosis of the manna mealybug, Trabutina mannipara, using a metagenomic approach. Phylogenetic analyses revealed that the intrabacterial symbiont of T. mannipara represents a novel lineage within the Gammaproteobacteria, for which we propose the tentative name ‘Candidatus Trabutinella endobia’. Combining our results with previous data available for the nested symbiosis of the citrus mealybug Planococcus citri, we show that synthesis of essential amino acids and vitamins and translation-related functions partition between the symbiotic partners in a highly similar manner in the two systems, despite the distinct evolutionary origin of the intrabacterial symbionts. Bacterial genes found in both mealybug genomes and complementing missing functions in both symbioses were likely integrated in ancestral mealybugs before T. mannipara and P. citri diversified. The high level of correspondence between the two mealybug systems and their highly intertwined metabolic pathways are unprecedented. Our work contributes to a better understanding of the only known intracellular symbiosis between two bacteria and suggests that the evolution of this unique symbiosis included the replacement of intrabacterial symbionts in ancestral mealybugs.
Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota
Authors: Newbold Lindsay K , Burthe Sarah J , Oliver Anna E , Gweon Hyun S , Barnes Christopher J , Daunt Francis , van der Gast Christopher J 
Published: December 2016

Abstract
Infection by gastrointestinal helminths of humans, livestock and wild animals is common, but the impact of such endoparasites on wild hosts and their gut microbiota represents an important overlooked component of population dynamics. Wild host gut microbiota and endoparasites occupy the same physical niche spaces with both affecting host nutrition and health. However, associations between the two are poorly understood. Here we used the commonly parasitized European shag (Phalacrocorax aristotelis) as a model wild host. Forty live adults from the same colony were sampled. Endoscopy was employed to quantify helminth infection in situ. Microbiota from the significantly distinct proventriculus (site of infection), cloacal and faecal gastrointestinal tract microbiomes were characterised using 16S rRNA gene-targeted high-throughput sequencing. We found increasingly strong associations between helminth infection and microbiota composition progressing away from the site of infection, observing a pronounced dysbiosis in microbiota when samples were partitioned into high- and low-burden groups. We posit this dysbiosis is predominately explained by helminths inducing an anti-inflammatory environment in the proventriculus, diverting host immune responses away from themselves. This study, within live wild animals, provides a vital foundation to better understand the mechanisms that underpin the three-way relationship between helminths, microbiota and hosts.
Photosynthetic temperature adaptation during niche diversification of the thermophilic cyanobacterium Synechococcus A/B clade
Authors: Pedersen Deana , Miller Scott R 
Published: December 2016

Abstract
We take an in vivo fluorescence approach to investigate photosynthetic adaptation by ecologically divergent members of the A/B clade of the hot spring cyanobacterium Synechococcus, the most thermotolerant of which defines the upper thermal limit for photosynthesis. During Synechococcus diversification, both photosystem II and the light-harvesting phycobilisome have evolved greater thermostability as the group has invaded higher temperature habitats, particularly for the most thermotolerant lineage. This enhanced function at higher temperatures has come at the cost of reduced performance at lower temperatures, and these trade-offs contribute to niche specialization in the clade. Molecular evolutionary analyses revealed specific adaptive protein changes in the most thermotolerant lineage. Our study advances our understanding of the origins of Synechococcus diversity.
Viruses and the origin of microbiome selection and immunity
Authors: Quistad Steven D , Grasis Juris A , Barr Jeremy J , Rohwer Forest L 
Published: December 2016

Abstract
The last common metazoan ancestor (LCMA) emerged over half a billion years ago. These complex metazoans provided newly available niche space for viruses and microbes. Modern day contemporaries, such as cnidarians, suggest that the LCMA consisted of two cell layers: a basal endoderm and a mucus-secreting ectoderm, which formed a surface mucus layer (SML). Here we propose a model for the origin of metazoan immunity based on external and internal microbial selection mechanisms. In this model, the SML concentrated bacteria and their associated viruses (phage) through physical dynamics (that is, the slower flow fields near a diffusive boundary layer), which selected for mucin-binding capabilities. The concentration of phage within the SML provided the LCMA with an external microbial selective described by the bacteriophage adherence to mucus (BAM) model. In the BAM model, phage adhere to mucus protecting the metazoan host against invading, potentially pathogenic bacteria. The same fluid dynamics that concentrated phage and bacteria in the SML also concentrated eukaryotic viruses. As eukaryotic viruses competed for host intracellular niche space, those viruses that provided the LCMA with immune protection were maintained. If a resident virus became pathogenic or if a non-beneficial infection occurred, we propose that tumor necrosis factor (TNF)-mediated programmed cell death, as well as other apoptosis mechanisms, were utilized to remove virally infected cells. The ubiquity of the mucosal environment across metazoan phyla suggest that both BAM and TNF-induced apoptosis emerged during the Precambrian era and continue to drive the evolution of metazoan immunity.
Concepts of ferrovalley material and anomalous valley Hall effect
Authors: Tong Wen-Yi , Gong Shi-Jing , Wan Xiangang , Duan Chun-Gang 
Published: December 2016

AbstractValleytronics rooted in the valley degree of freedom is of both theoretical and technological importance as it offers additional opportunities for information storage, as well as electronic, magnetic and optical switches. In analogy to ferroelectric materials with spontaneous charge polarization, or ferromagnetic materials with spontaneous spin polarization, here we introduce a new member of ferroic family, that is, a ferrovalley material with spontaneous valley polarization. Combining a two-band k·p model with first-principles calculations, we show that 2H-VSe2 monolayer, where the spin–orbit coupling coexists with the intrinsic exchange interaction of transition-metal d electrons, is such a room-temperature ferrovalley material. We further predict that such system could demonstrate many distinctive properties, for example, chirality-dependent optical band gap and, more interestingly, anomalous valley Hall effect. On account of the latter, functional devices based on ferrovalley materials, such as valley-based nonvolatile random access memory and valley filter, are contemplated for valleytronic applications.
A TNFRSF14-FcɛRI-mast cell pathway contributes to development of multiple features of asthma pathology in mice
Authors: Sibilano Riccardo , Gaudenzio Nicolas , DeGorter Marianne K. , Reber Laurent L. , Hernandez Joseph D. , Starkl Philipp M. , Zurek Oliwia W. , Tsai Mindy , Zahner Sonja , Montgomery Stephen B. , Roers Axel , Kronenberg Mitchell , Yu Mang , Galli Stephen J. 
Published: December 2016

AbstractAsthma has multiple features, including airway hyperreactivity, inflammation and remodelling. The TNF superfamily member TNFSF14 (LIGHT), via interactions with the receptor TNFRSF14 (HVEM), can support TH2 cell generation and longevity and promote airway remodelling in mouse models of asthma, but the mechanisms by which TNFSF14 functions in this setting are incompletely understood. Here we find that mouse and human mast cells (MCs) express TNFRSF14 and that TNFSF14:TNFRSF14 interactions can enhance IgE-mediated MC signalling and mediator production. In mouse models of asthma, TNFRSF14 blockade with a neutralizing antibody administered after antigen sensitization, or genetic deletion of Tnfrsf14, diminishes plasma levels of antigen-specific IgG1 and IgE antibodies, airway hyperreactivity, airway inflammation and airway remodelling. Finally, by analysing two types of genetically MC-deficient mice after engrafting MCs that either do or do not express TNFRSF14, we show that TNFRSF14 expression on MCs significantly contributes to the development of multiple features of asthma pathology.
Interleukin-12 bypasses common gamma-chain signalling in emergency natural killer cell lymphopoiesis
Authors: Ohs Isabel , van den Broek Maries , Nussbaum Kathrin , Münz Christian , Arnold Sebastian J. , Quezada Sergio A. , Tugues Sonia , Becher Burkhard 
Published: December 2016

AbstractDifferentiation and homeostasis of natural killer (NK) cells relies on common gamma-chain (γc)-dependent cytokines, in particular IL-15. Consequently, NK cells do not develop in mice with targeted γc deletion. Herein we identify an alternative pathway of NK-cell development driven by the proinflammatory cytokine IL-12, which can occur independently of γc-signalling. In response to viral infection or upon exogenous administration, IL-12 is sufficient to elicit the emergence of a population of CD122+CD49b+ cells by targeting NK-cell precursors (NKPs) in the bone marrow (BM). We confirm the NK-cell identity of these cells by transcriptome-wide analyses and their ability to eliminate tumour cells. Rather than using the conventional pathway of NK-cell development, IL-12-driven CD122+CD49b+ cells remain confined to a NK1.1lowNKp46low stage, but differentiate into NK1.1+NKp46+ cells in the presence of γc-cytokines. Our data reveal an IL-12-driven hard-wired pathway of emergency NK-cell lymphopoiesis bypassing steady-state γc-signalling.
Evolution of multiple cell clones over a 29-year period of a CLL patient
Authors: Zhao Zhikun , Goldin Lynn , Liu Shiping , Wu Liang , Zhou Weiyin , Lou Hong , Yu Qichao , Tsang Shirley X. , Jiang Miaomiao , Li Fuqiang , McMaster MaryLou , Li Yang , Lin Xinxin , Wang Zhifeng , Xu Liqin , Marti Gerald , Li Guibo , Wu Kui , Yeager Meredith , Yang Huanming , Xu Xun , Chanock Stephen J. , Li Bo , Hou Yong , Caporaso Neil , Dean Michael 
Published: December 2016

AbstractChronic lymphocytic leukaemia (CLL) is a frequent B-cell malignancy, characterized by recurrent somatic chromosome alterations and a low level of point mutations. Here we present single-nucleotide polymorphism microarray analyses of a single CLL patient over 29 years of observation and treatment, and transcriptome and whole-genome sequencing at selected time points. We identify chromosome alterations 13q14−, 6q− and 12q+ in early cell clones, elimination of clonal populations following therapy, and subsequent appearance of a clone containing trisomy 12 and chromosome 10 copy-neutral loss of heterogeneity that marks a major population dominant at death. Serial single-cell RNA sequencing reveals an expression pattern with high FOS, JUN and KLF4 at disease acceleration, which resolves following therapy, but reoccurs following relapse and death. Transcriptome evolution indicates complex changes in expression occur over time. In conclusion, CLL can evolve gradually during indolent phases, and undergo rapid changes following therapy.
Cooperative redox activation for carbon dioxide conversion
Authors: Lian Zhong , Nielsen Dennis U. , Lindhardt Anders T. , Daasbjerg Kim , Skrydstrup Troels 
Published: December 2016

AbstractA longstanding challenge in production chemistry is the development of catalytic methods for the transformation of carbon dioxide into useful chemicals. Silane and borane promoted reductions can be fined-tuned to provide a number of C1-building blocks under mild conditions, but these approaches are limited because of the production of stoichiometric waste compounds. Here we report on the conversion of CO2with diaryldisilanes, which through cooperative redox activation generate carbon monoxide and a diaryldisiloxane that actively participate in a palladium-catalysed carbonylative Hiyama-Denmark coupling for the synthesis of an array of pharmaceutically relevant diarylketones. Thus the disilane reagent not only serves as the oxygen abstracting agent from CO2, but the silicon-containing ‘waste’, produced through oxygen insertion into the Si–Si bond, participates as a reagent for the transmetalation step in the carbonylative coupling. Hence this concept of cooperative redox activation opens up for new avenues in the conversion of CO2.
Global repositioning of transcription start sites in a plant-fermenting bacterium
Authors: Boutard Magali , Ettwiller Laurence , Cerisy Tristan , Alberti Adriana , Labadie Karine , Salanoubat Marcel , Schildkraut Ira , Tolonen Andrew C. 
Published: December 2016

AbstractBacteria respond to their environment by regulating mRNA synthesis, often by altering the genomic sites at which RNA polymerase initiates transcription. Here, we investigate genome-wide changes in transcription start site (TSS) usage by Clostridium phytofermentans, a model bacterium for fermentation of lignocellulosic biomass. We quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which combines capture of synthetically capped 5′ mRNA fragments with template-switching reverse transcription. We find the locations and expression levels of TSS for hundreds of genes change during metabolism of different plant substrates. We show that TSS reveals riboswitches, non-coding RNA and novel transcription units. We identify sequence motifs associated with carbon source-specific TSS and use them for regulon discovery, implicating a LacI/GalR protein in control of pectin metabolism. We discuss how the high resolution and specificity of Capp-Switch enables study of condition-specific changes in transcription initiation in bacteria.