bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type studies in theRhizocarpon geographicumgroup (Rhizocarpaceae, lichenized Ascomycota)
Authors: ROCA-VALIENTE Beatriz , HAWKSWORTH David L. , PÉREZ-ORTEGA Sergio , SANCHO Leopoldo G. , CRESPO Ana 
Published: February 2016

AbstractAs part of a comprehensive revision of theRhizocarpon geographicumspecies group using molecular and morphological approaches, we examined the name-bearing types of 15 species. We report ambiguities and inconsistencies with the reported features of some type specimens, original descriptions, and circumscriptions employed in keys for the identification of taxa within the complex. The reporting of chemical reactions and some morphological characters was found to be inconsistent and likely to lead to errors of identification. This is unfortunate in view of the widespread use of the complex in glaciology for lichenometry. Issues surrounding the typification of the basionymLichen geographicusare clarified, and the epitype is illustrated. The complex nomenclatural situation regarding the nameRhizocarpon lecanorinumand its typification is also made clear. The examination of the anatomical and morphological characters presented here needs to be considered together with molecular phylogenetic information to provide a more informed new taxonomy of the group.
Three new species ofAtlafrom calcareous rocks (Verrucariaceae, lichenized Ascomycota)
Authors: PYKÄLÄ Juha , MYLLYS Leena 
Published: February 2016

AbstractThree new species ofAtlaare described from calcareous rocks in northern Finland based on morphology and ITS sequences. All new species have dark brown spores but have smaller perithecia and spores than previously known brown-spored species ofAtla.Atla tibelliorumsp. nov. resemblesSporodictyon arcticum, but has a dark brown exciple and larger spores.Atla oulankaensissp. nov. andA. vitikaineniisp. nov. differ fromA. alpinain the smaller perithecia and spores. Atla vitikaineniihas an involucrellum often slightly diverging from the exciple.Atla oulankaensisis similar toA. vitikainenii, differing in slightly narrower spores and in having some involucrella incurving under the exciple or even enveloping the exciple. An unidentified ITS sequence from Canada obtained from GenBank most probably belongs toA. oulankaensisand another unidentified sequence from the USA toA. tibelliorum. The new results strengthen the conclusion that the genera ofAtlaandSporodictyoncannot be separated by morphology alone. A key to all known species ofAtlaandSporodictyonis provided.
The genusBulbothrix(Parmeliaceae) in China
Authors: ZHANG Yan Yun , WANG Xin Yu , LIU Dong , SHI Hai Xia , YE Xin , YANG Mei Xia , WANG Li Song 
Published: February 2016

AbstractThe morphology, chemistry and phylogenetic relationships of Chinese populations ofBulbothrixare described. Nine species, including two new speciesB. mammillariaY. Y. Zhang & Li S. Wang sp. nov. andB. laciniaY. Y. Zhang & Li S. Wang sp. nov., and two newly recorded for the flora,B. scortellaandB. meizospora, are reported.Bulbothrix mammillariacan be recognized by the sparse cilia that are reduced to a bulbate structure and the broad lobes (3–11 mm).Bulbothrix laciniadiffers from other species of the genus by dark brown, spherical to short-cylindrical isidia and common lacinulae on the upper surface. Phylogenetic relationships of currently known ITS sequences fromBulbothrixwere inferred to assess the affinities of the new species. A key to all known species from China is presented.
Household food insecurity, nutritional status and morbidity in Brazilian children
Authors: Gubert Muriel Bauermann , Spaniol Ana Maria , Bortolini Gisele Ane , Pérez-Escamilla Rafael 
Published: February 2016

AbstractObjectiveTo identify the association of household food insecurity (HFI) with anthropometric status, the risk of vitamin A deficiency and anaemia, morbidities such as cough and fever, and hospitalizations for diarrhoea and pneumonia in children under 5 years old.DesignCross-sectional study using data from the 2006 Brazilian Demographic and Health Survey. HFI was measured with the Brazilian Food Insecurity Measurement Scale (EBIA). Vitamin A deficiency and anaemia were assessed in blood samples. Child morbidities were reported by the child’s mother and included cough, fever, and hospitalizations for diarrhoea and pneumonia. Regression results were expressed as unadjusted and adjusted OR and corresponding 95 % CI for severe food insecurity, with statistical significance set atP<0·05.SettingNationally representative survey.SubjectsChildren (n4064) under 5 years old.ResultsThere was no association between HFI and vitamin A deficiency, pneumonia, wasting or overweight. The prevalence of cough, fever, hospitalization for diarrhoea and stunting were associated with degree of HFI severity. There was a significant association of morbidities and stunting with severe food insecurity (v. food secure). After controlling for confounders, the association between severe food insecurity (v. food secure/rest of food insecurity categories) and the prevalence of common morbidities remained strong, showing that severely food-insecure children had a greater likelihood of experiencing cough (adjusted OR=1·79) and of being hospitalized for diarrhoea (adjusted OR=2·55).ConclusionsSevere HFI was associated with cough and severe diarrhoea among Brazilian children.
Pigment Degradation in Oil Paint Induced by Indoor Climate: Comparison of Visual and Computational Backscattered Electron Images
Authors: Keune Katrien , Kramer Rick P. , Huijbregts Zara , Schellen Henk L. , Stappers Marc H.L. , van Eikema Hommes Margriet H. 
Published: February 2016

AbstractFor the first time the degradation of lead white pigment in mature oil paint has been used as an internal marker for the degree of saponification and hence chemical degradation of oil paint. Computational image analysis of the backscattered electron images quantified the degree of the intact lead white pigment versus the nonpigmented and lead-rich areas (degraded lead white) in the paint layers. This new methodology was applied to a series of paint samples taken from four painted wall hangings (dated 1778), which makes it possible to study the influence of indoor climate on chemical degradation of aged oil paintings. The visual interpretation and computational image analysis of the backscattered electron images revealed clear trends. The highest degree of lead white degradation in the room was found in samples from the north wall close to the windows, whereas degradation diminished further away from the window. Lead white from the south wall was less degraded, but showed a similar trend as in the paintings on the north wall. These results imply a strong relationship between chemical degradation of paint and location of the paint in the room.
Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics
Authors: Flury Pascale , Aellen Nora , Ruffner Beat , Péchy-Tarr Maria , Fataar Shakira , Metla Zane , Dominguez-Ferreras Ana , Bloemberg Guido , Frey Joachim , Goesmann Alexander , Raaijmakers Jos M , Duffy Brion , Höfte Monica , Blom Jochen , Smits Theo H M , Keel Christoph , Maurhofer Monika 
Published: February 2016

Abstract
Bacteria of the genus Pseudomonas occupy diverse environments. The Pseudomonas fluorescens group is particularly well-known for its plant-beneficial properties including pathogen suppression. Recent observations that some strains of this group also cause lethal infections in insect larvae, however, point to a more versatile ecology of these bacteria. We show that 26 P. fluorescens group strains, isolated from three continents and covering three phylogenetically distinct sub-clades, exhibited different activities toward lepidopteran larvae, ranging from lethal to avirulent. All strains of sub-clade 1, which includes Pseudomonas chlororaphis and Pseudomonas protegens, were highly insecticidal regardless of their origin (animals, plants). Comparative genomics revealed that strains in this sub-clade possess specific traits allowing a switch between plant- and insect-associated lifestyles. We identified 90 genes unique to all highly insecticidal strains (sub-clade 1) and 117 genes common to all strains of sub-clade 1 and present in some moderately insecticidal strains of sub-clade 3. Mutational analysis of selected genes revealed the importance of chitinase C and phospholipase C in insect pathogenicity. The study provides insight into the genetic basis and phylogenetic distribution of traits defining insecticidal activity in plant-beneficial pseudomonads. Strains with potent dual activity against plant pathogens and herbivorous insects have great potential for use in integrated pest management for crops.
Whole-genome mutational burden analysis of three pluripotency induction methods
Authors: Bhutani Kunal , Nazor Kristopher L. , Williams Roy , Tran Ha , Dai Heng , Džakula Željko , Cho Edward H. , Pang Andy W. C. , Rao Mahendra , Cao Han , Schork Nicholas J. , Loring Jeanne F. 
Published: February 2016

AbstractThere is concern that the stresses of inducing pluripotency may lead to deleterious DNA mutations in induced pluripotent stem cell (iPSC) lines, which would compromise their use for cell therapies. Here we report comparative genomic analysis of nine isogenic iPSC lines generated using three reprogramming methods: integrating retroviral vectors, non-integrating Sendai virus and synthetic mRNAs. We used whole-genome sequencing and de novo genome mapping to identify single-nucleotide variants, insertions and deletions, and structural variants. Our results show a moderate number of variants in the iPSCs that were not evident in the parental fibroblasts, which may result from reprogramming. There were only small differences in the total numbers and types of variants among different reprogramming methods. Most importantly, a thorough genomic analysis showed that the variants were generally benign. We conclude that the process of reprogramming is unlikely to introduce variants that would make the cells inappropriate for therapy.
Nonmagnetic band gap at the Dirac point of the magnetic topological insulator (Bi1−xMnx)2Se3
Authors: Sánchez-Barriga J. , Varykhalov A. , Springholz G. , Steiner H. , Kirchschlager R. , Bauer G. , Caha O. , Schierle E. , Weschke E. , Ünal A. A. , Valencia S. , Dunst M. , Braun J. , Ebert H. , Minár J. , Golias E. , Yashina L. V. , Ney A. , Holý V. , Rader O. 
Published: February 2016

AbstractMagnetic doping is expected to open a band gap at the Dirac point of topological insulators by breaking time-reversal symmetry and to enable novel topological phases. Epitaxial (Bi1−xMnx)2Se3 is a prototypical magnetic topological insulator with a pronounced surface band gap of ∼100 meV. We show that this gap is neither due to ferromagnetic order in the bulk or at the surface nor to the local magnetic moment of the Mn, making the system unsuitable for realizing the novel phases. We further show that Mn doping does not affect the inverted bulk band gap and the system remains topologically nontrivial. We suggest that strong resonant scattering processes cause the gap at the Dirac point and support this by the observation of in-gap states using resonant photoemission. Our findings establish a mechanism for gap opening in topological surface states which challenges the currently known conditions for topological protection.
Influenza A virus targets a cGAS-independent STING pathway that controls enveloped RNA viruses
Authors: Holm Christian K. , Rahbek Stine H. , Gad Hans Henrik , Bak Rasmus O. , Jakobsen Martin R. , Jiang Zhaozaho , Hansen Anne Louise , Jensen Simon K. , Sun Chenglong , Thomsen Martin K. , Laustsen Anders , Nielsen Camilla G. , Severinsen Kasper , Xiong Yingluo , Burdette Dara L. , Hornung Veit , Lebbink Robert Jan , Duch Mogens , Fitzgerald Katherine A. , Bahrami Shervin , Mikkelsen Jakob Giehm , Hartmann Rune , Paludan Søren R. 
Published: February 2016

AbstractStimulator of interferon genes (STING) is known be involved in control of DNA viruses but has an unexplored role in control of RNA viruses. During infection with DNA viruses STING is activated downstream of cGAMP synthase (cGAS) to induce type I interferon. Here we identify a STING-dependent, cGAS-independent pathway important for full interferon production and antiviral control of enveloped RNA viruses, including influenza A virus (IAV). Further, IAV interacts with STING through its conserved hemagglutinin fusion peptide (FP). Interestingly, FP antagonizes interferon production induced by membrane fusion or IAV but not by cGAMP or DNA. Similar to the enveloped RNA viruses, membrane fusion stimulates interferon production in a STING-dependent but cGAS-independent manner. Abolishment of this pathway led to reduced interferon production and impaired control of enveloped RNA viruses. Thus, enveloped RNA viruses stimulate a cGAS-independent STING pathway, which is targeted by IAV.
Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells
Authors: Ramirez Michael , Rajaram Satwik , Steininger Robert J. , Osipchuk Daria , Roth Maike A. , Morinishi Leanna S. , Evans Louise , Ji Weiyue , Hsu Chien-Hsiang , Thurley Kevin , Wei Shuguang , Zhou Anwu , Koduru Prasad R. , Posner Bruce A. , Wu Lani F. , Altschuler Steven J. 
Published: February 2016

AbstractCancer therapy has traditionally focused on eliminating fast-growing populations of cells. Yet, an increasing body of evidence suggests that small subpopulations of cancer cells can evade strong selective drug pressure by entering a ‘persister’ state of negligible growth. This drug-tolerant state has been hypothesized to be part of an initial strategy towards eventual acquisition of bona fide drug-resistance mechanisms. However, the diversity of drug-resistance mechanisms that can expand from a persister bottleneck is unknown. Here we compare persister-derived, erlotinib-resistant colonies that arose from a single, EGFR-addicted lung cancer cell. We find, using a combination of large-scale drug screening and whole-exome sequencing, that our erlotinib-resistant colonies acquired diverse resistance mechanisms, including the most commonly observed clinical resistance mechanisms. Thus, the drug-tolerant persister state does not limit—and may even provide a latent reservoir of cells for—the emergence of heterogeneous drug-resistance mechanisms.
A competitive and reversible deactivation approach to catalysis-based quantitative assays
Authors: Koide Kazunori , Tracey Matthew P. , Bu Xiaodong , Jo Junyong , Williams Michael J. , Welch Christopher J. 
Published: February 2016

AbstractCatalysis-based signal amplification makes optical assays highly sensitive and widely useful in chemical and biochemical research. However, assays must be fine-tuned to avoid signal saturation, substrate depletion and nonlinear performance. Furthermore, once stopped, such assays cannot be restarted, limiting the dynamic range to two orders of magnitude with respect to analyte concentrations. In addition, abundant analytes are difficult to quantify under catalytic conditions due to rapid signal saturation. Herein, we report an approach in which a catalytic reaction competes with a concomitant inactivation of the catalyst or consumption of a reagent required for signal generation. As such, signal generation proceeds for a limited time, then autonomously and reversibly stalls. In two catalysis-based assays, we demonstrate restarting autonomously stalled reactions, enabling accurate measurement over five orders of magnitude, including analyte levels above substrate concentration. This indicates that the dynamic range of catalysis-based assays can be significantly broadened through competitive and reversible deactivation.
Unfolding the physics of URu2Si2 through silicon to phosphorus substitution
Authors: Gallagher A. , Chen K.-W. , Moir C. M. , Cary S. K. , Kametani F. , Kikugawa N. , Graf D. , Albrecht-Schmitt T. E. , Riggs S. C. , Shekhter A. , Baumbach R. E. 
Published: February 2016

AbstractThe heavy fermion intermetallic compound URu2Si2 exhibits a hidden-order phase below the temperature of 17.5 K, which supports both anomalous metallic behavior and unconventional superconductivity. While these individual phenomena have been investigated in detail, it remains unclear how they are related to each other and to what extent uranium f-electron valence fluctuations influence each one. Here we use ligand site substituted URu2Si2-xPx to establish their evolution under electronic tuning. We find that while hidden order is monotonically suppressed and destroyed for x≤0.035, the superconducting strength evolves non-monotonically with a maximum near x≈0.01 and that superconductivity is destroyed near x≈0.028. This behavior reveals that hidden order depends strongly on tuning outside of the U f-electron shells. It also suggests that while hidden order provides an environment for superconductivity and anomalous metallic behavior, it’s fluctuations may not be solely responsible for their progression.
Gene expression in human brain implicates sexually dimorphic pathways in autism spectrum disorders
Authors: Werling Donna M. , Parikshak Neelroop N. , Geschwind Daniel H. 
Published: February 2016

AbstractAutism spectrum disorder (ASD) is more prevalent in males, and the mechanisms behind this sex-differential risk are not fully understood. Two competing, but not mutually exclusive, hypotheses are that ASD risk genes are sex-differentially regulated, or alternatively, that they interact with characteristic sexually dimorphic pathways. Here we characterized sexually dimorphic gene expression in multiple data sets from neurotypical adult and prenatal human neocortical tissue, and evaluated ASD risk genes for evidence of sex-biased expression. We find no evidence for systematic sex-differential expression of ASD risk genes. Instead, we observe that genes expressed at higher levels in males are significantly enriched for genes upregulated in post-mortem autistic brain, including astrocyte and microglia markers. This suggests that it is not sex-differential regulation of ASD risk genes, but rather naturally occurring sexually dimorphic processes, potentially including neuron–glial interactions, that modulate the impact of risk variants and contribute to the sex-skewed prevalence of ASD.
Selective labelling and eradication of antibiotic-tolerant bacterial populations in Pseudomonas aeruginosa biofilms
Authors: Chua Song Lin , Yam Joey Kuok Hoong , Hao Piliang , Adav Sunil S. , Salido May Margarette , Liu Yang , Givskov Michael , Sze Siu Kwan , Tolker-Nielsen Tim , Yang Liang 
Published: February 2016

AbstractDrug resistance and tolerance greatly diminish the therapeutic potential of antibiotics against pathogens. Antibiotic tolerance by bacterial biofilms often leads to persistent infections, but its mechanisms are unclear. Here we use a proteomics approach, pulsed stable isotope labelling with amino acids (pulsed-SILAC), to quantify newly expressed proteins in colistin-tolerant subpopulations of Pseudomonas aeruginosa biofilms (colistin is a ‘last-resort’ antibiotic against multidrug-resistant Gram-negative pathogens). Migration is essential for the formation of colistin-tolerant biofilm subpopulations, with colistin-tolerant cells using type IV pili to migrate onto the top of the colistin-killed biofilm. The colistin-tolerant cells employ quorum sensing (QS) to initiate the formation of new colistin-tolerant subpopulations, highlighting multicellular behaviour in antibiotic tolerance development. The macrolide erythromycin, which has been previously shown to inhibit the motility and QS of P. aeruginosa, boosts biofilm eradication by colistin. Our work provides insights on the mechanisms underlying the formation of antibiotic-tolerant populations in bacterial biofilms and indicates research avenues for designing more efficient treatments against biofilm-associated infections.
Antibody-based PET imaging of amyloid beta in mouse models of Alzheimer’s disease
Authors: Sehlin Dag , Fang Xiaotian T. , Cato Linda , Antoni Gunnar , Lannfelt Lars , Syvänen Stina 
Published: February 2016

AbstractOwing to their specificity and high-affinity binding, monoclonal antibodies have potential as positron emission tomography (PET) radioligands and are currently used to image various targets in peripheral organs. However, in the central nervous system, antibody uptake is limited by the blood–brain barrier (BBB). Here we present a PET ligand to be used for diagnosis and evaluation of treatment effects in Alzheimer’s disease. The amyloid β (Aβ) antibody mAb158 is radiolabelled and conjugated to a transferrin receptor antibody to enable receptor-mediated transcytosis across the BBB. PET imaging of two different mouse models with Aβ pathology clearly visualize Aβ in the brain. The PET signal increases with age and correlates closely with brain Aβ levels. Thus, we demonstrate that antibody-based PET ligands can be successfully used for brain imaging.
YY1 inhibits differentiation and function of regulatory T cells by blocking Foxp3 expression and activity
Authors: Hwang Soo Seok , Jang Sung Woong , Kim Min Kyung , Kim Lark Kyun , Kim Bong-Sung , Kim Hyeong Su , Kim Kiwan , Lee Wonyong , Flavell Richard A. , Lee Gap Ryol 
Published: February 2016

AbstractRegulatory T (Treg) cells are essential for maintenance of immune homeostasis. Foxp3 is the key transcription factor for Treg-cell differentiation and function; however, molecular mechanisms for its negative regulation are poorly understood. Here we show that YY1 expression is lower in Treg cells than Tconv cells, and its overexpression causes a marked reduction of Foxp3 expression and abrogation of suppressive function of Treg cells. YY1 is increased in Treg cells under inflammatory conditions with concomitant decrease of suppressor activity in dextran sulfate-induced colitis model. YY1 inhibits Smad3/4 binding to and chromatin remodelling of the Foxp3 locus. In addition, YY1 interrupts Foxp3-dependent target gene expression by physically interacting with Foxp3 and by directly binding to the Foxp3 target genes. Thus, YY1 inhibits differentiation and function of Treg cells by blocking Foxp3.
Preventive obesity agent montmorillonite adsorbs dietary lipids and enhances lipid excretion from the digestive tract
Authors: Xu Pengfei , Dai Shu , Wang Jing , Zhang Jun , Liu Jin , Wang Fang , Zhai Yonggong 
Published: February 2016

AbstractWestern diets are typically high in fat and are associated with long-term complications such as obesity and hepatic steatosis. Because of the enjoyable taste of high-fat diets (HFDs), we are interested in determining how to decrease lipid absorption and enhance lipid excretion from the digestive tract after the consumption of eating fatty foods. Montmorillonite was initially characterized as a gastrointestinal mucosal barrier protective agent for the treatment of diarrhoea. Dietary lipid adsorbent- montmorillonite (DLA-M) was isolated and purified from Xinjiang montmorillonite clay via the water extraction method. Here, we show that DLA-M has an unexpected role in preventing obesity, hyperlipidaemia and hepatic steatosis in HFD-fed rats. Interestingly, combined application of polarized light microscopy and lipid staining analyses, showed that DLA-M crystals have dietary lipid-adsorbing ability in vitro and in vivo, which enhances lipid excretion via bowel movements. In summary, our results indicate that DLA-M prevent HFD-induced obesity. This novel dietary lipid-adsorbing agent can help prevent obesity and its comorbidities.