bluuebunny/crossref_metadata_2025 huggingface dataset:
The Stoichiometry of Carbon, Hydrogen, and Oxygen in Peat
Authors: Moore Tim R. , Large David , Talbot Julie , Wang Meng , Riley John L.
Published: September 2018

Carbon (C), hydrogen (H), and oxygen (O) form ~90% by mass of peat, a product of the input of plant tissues and litter and the output of decomposition under aerobic and anaerobic conditions. We examined patterns of these elements, as the O:C and H:C atomic ratios, in over 1,300 peat samples collected from over 400 profiles in Ontario, Canada, representing bogs, fens, and swamps. The overall O:C ratio decreased from the surface (0.6 to 0.7) to ~0.5 at a depth of 50 cm and showed little further change to a depth of 5 m. In contrast, the H:C ratio decreased only slightly (1.30 to 1.25) over the top 1 m and showed no further significant decline with depth. The C oxidative state (Cox) and oxidation ratio showed strong decreases and increases, respectively, with depth with most changes occurring in the top 0.5 m. The O:C ratio, and Cox and oxidation ratio values were significantly correlated with the von Post humification index, with most changes occurring in index values 1 through 4, the latter representing a slight degree of decomposition. Collation of the Ontario peats with other data sets revealed the very large range in O:C and H:C values, with a general decrease from temperate to tropical and subtropical peatlands. Estimation of the O:C and H:C ratios of input (litter) and output (mineralization to CO2, methanogenesis to CH4 and CO2, and loss as dissolved organic C) allowed an estimation of the degree of decomposition or C loss.
Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85–90 °N
Authors: Fernández-Gómez Beatriz , Díez Beatriz , Polz Martin F , Arroyo José Ignacio , Alfaro Fernando D , Marchandon Germán , Sanhueza Cynthia , Farías Laura , Trefault Nicole , Marquet Pablo A , Molina-Montenegro Marco A , Sylvander Peter , Snoeijs-Leijonmalm Pauline
Published: September 2018

Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4–9.6) and immediate sub-ice seawater (SW; salinity 33.3–34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.
Heritability of obsessive–compulsive trait dimensions in youth from the general population
Authors: Burton Christie L. , Park Laura S. , Corfield Elizabeth C. , Forget-Dubois Nadine , Dupuis Annie , Sinopoli Vanessa M. , Shan Janet , Goodale Tara , Shaheen S.-M. , Crosbie Jennifer , Schachar Russell J. , Arnold Paul D.
Published: September 2018

Obsessive–compulsive disorder (OCD) is a heritable childhood-onset psychiatric disorder that may represent the extreme of obsessive–compulsive (OC) traits that are widespread in the general population. We report the heritability of the Toronto Obsessive–Compulsive Scale (TOCS), a new measure designed to assess the complete range of OC traits in youth. We also examined the dimensional nature of the TOCS and the degree to which genetic effects are unique or shared between dimensions. OC traits were measured using the TOCS in 16,718 youth (6–18 years) at a science museum. We conducted a factor analysis to identify OC trait dimensions. We used univariate and multivariate twin models to estimate the heritability of OC trait dimensions in a subset of twins (220 pairs). Six OC dimensions were identified: Cleaning/Contamination, Symmetry/Ordering, Rumination, Superstition, Counting/Checking, and Hoarding. The TOCS total score (74%) and each OC dimension was heritable (30–77%). Hoarding was not highly correlated with other OC dimensions, but did share genetic effects. Shared genetics accounted for most of the shared variance among dimensions, whereas unique environment accounted for the majority of dimension-specific variance. One exception was Hoarding, which had considerable unique genetic factors. A latent trait did not account for the shared variance between dimensions. In conclusion, OC traits and individual OC dimensions were heritable, although the degree of shared and dimension-specific etiological factors varied by dimension. The TOCS may be informative for genetic research of OC traits in youth. Genetic research of OC traits should consider both OC dimension and total trait scores.
Functional characterization of TBR1 variants in neurodevelopmental disorder
Authors: den Hoed Joery , Sollis Elliot , Venselaar Hanka , Estruch Sara B. , Deriziotis Pelagia , Fisher Simon E.
Published: September 2018

Recurrent de novo variants in the TBR1 transcription factor are implicated in the etiology of sporadic autism spectrum disorders (ASD). Disruptions include missense variants located in the T-box DNA-binding domain and previous work has demonstrated that they disrupt TBR1 protein function. Recent screens of thousands of simplex families with sporadic ASD cases uncovered additional T-box variants in TBR1 but their etiological relevance is unclear. We performed detailed functional analyses of de novo missense TBR1 variants found in the T-box of ASD cases, assessing many aspects of protein function, including subcellular localization, transcriptional activity and protein-interactions. Only two of the three tested variants severely disrupted TBR1 protein function, despite in silico predictions that all would be deleterious. Furthermore, we characterized a putative interaction with BCL11A, a transcription factor that was recently implicated in a neurodevelopmental syndrome involving developmental delay and language deficits. Our findings enhance understanding of molecular functions of TBR1, as well as highlighting the importance of functional testing of variants that emerge from next-generation sequencing, to decipher their contributions to neurodevelopmental disorders like ASD.
A two-step DNA barcoding approach for delimiting moth species: moths of Dongling Mountain (Beijing, China) as a case study
Authors: Jin Qian , Hu Xi-Min , Han Hui-Lin , Chen Fen , Cai Wei-Jia , Ruan Qian-Qian , Liu Bo , Luo Gui-Jie , Wang Hao , Liu Xu , Ward Robert D. , Wu Chun-Sheng , Wilson John-James , Zhang Ai-Bing
Published: September 2018

DNA barcoding, based on a fragment of cytochrome c oxidase I (COI) mtDNA, is as an effective molecular tool for identification, discovery, and biodiversity assessment for most animals. However, multiple gene markers coupled with more sophisticated analytical approaches may be necessary to clarify species boundaries in cases of cryptic diversity or morphological plasticity. Using 339 moths collected from mountains surrounding Beijing, China, we tested a pipeline consisting of two steps: (1) rapid morphospecies sorting and screening of the investigated fauna with standard COI barcoding approaches; (2) additional analyses with multiple molecular markers for those specimens whose morphospecies and COI barcode grouping were incongruent. In step 1, 124 morphospecies were delimited into 116 barcode units, with 90% of the conflicts being associated with specimens identified to the genus Hypena. In step 2, 55 individuals representing all 12 Hypena morphospecies were analysed using COI, COII, 28S, EF-1a, Wgl sequences or their combinations with the BPP (Bayesian Phylogenetics and Phylogeography) multigene species delimitation method. The multigene analyses supported the delimitation of 5 species, consistent with the COI analysis. We conclude that a two-step barcoding analysis pipeline is able to rapidly characterize insect biodiversity and help to elucidate species boundaries for taxonomic complexes without jeopardizing overall project efficiency by substantially increasing analytical costs.
Pleomorphic xanthoastrocytomas of adults: MRI features, molecular markers, and clinical outcomes
Authors: Yan Jing , Cheng Jingliang , Liu Furong , Liu Xianzhi
Published: September 2018

Fifty adult patients with pathologically-confirmed pleomorphic xanthoastrocytomas (PXAs) were retrospectively analyzed. Adult PXAs appeared as a single lesion in 47 patients and multiple lesions in 3 patients. Temporal lobe was the most common location (17/50). Twenty-two cases were superficial with obvious meningeal contact and 9 were closely adjacent to lateral ventricles. Three imaging patterns were differentiated, including a predominantly solid mass with or without cystic changes (n = 33), a predominantly cystic mass with an obvious mural nodule (n = 14), and a predominantly cystic mass with an uneven wall thickness (n = 3). The mean tumoral apparent diffusion coefficient (ADC) was 0.83 ± 0.17 × 10−3 mm2/s, and the mean ADC ratio was 1.02 ± 0.22. The V-raf murine sarcoma viral oncogenes homolog B1 (BRAF)V600E mutation was found in 12 of 29 patients. In 36 patients with isocitrate dehydrogenases 1 and 2 (IDH1/2) data, only one had IDH1 mutation and no patient had IDH2 mutation. Anaplastic features were common (24/50) and significantly associated with high rates of recurrence or progression (P < 0.001). In conclusion, this study expands our knowledge on the MRI features, molecular markers, and clinical outcomes of adult PXAs, to some extent different from pediatric PXAs.
Circulating microRNAs -192 and -194 are associated with the presence and incidence of diabetes mellitus
Authors: Jaeger Andrea , Zollinger Lukas , Saely Christoph H. , Muendlein Axel , Evangelakos Ioannis , Nasias Dimitris , Charizopoulou Nikoleta , Schofield Jonathan D. , Othman Alaa , Soran Handrean , Kardassis Dimitris , Drexel Heinz , Eckardstein Arnold von
Published: September 2018

We sought to identify circulating microRNAs as biomarkers of prevalent or incident diabetes. In a pilot study of 18 sex- and age-matched patients with metabolic syndrome, nine of whom developed diabetes during 6 years of follow-up, an array of 372 microRNAs discovered significantly elevated serum levels of microRNAs -122, -192, -194, and -215 in patients who developed diabetes mellitus type 2 (T2DM). In two cross-sectional validation studies, one encompassing sex- and age-matched groups of patients with T2DM, impaired fasting glucose (IFG) and euglycemic controls (n = 43 each) and the other 53 patients with type 1 diabetes and 54 age- and BMI-matched euglycemic controls, serum levels of miR-192, miR-194, and mi215 were significantly higher in diabetic subjects than in probands with euglycemia or IFG. In a longitudinal study of 213 initially diabetes-free patients of whom 35 developed diabetes during 6 years of follow-up, elevated serum levels of microRNAs 192 and 194 were associated with incident T2DM, independently of fasting glucose, HbA1c and other risk factors. Serum levels of miR-192 and miR-194 were also elevated in diabetic Akt2 knockout mice compared to wild type mice. In conclusion, circulating microRNAs -192 and -194 are potential biomarkers for risk of diabetes.
Intranasal administration of resveratrol successfully prevents lung cancer in A/J mice
Authors: Monteillier Aymeric , Voisin Aymone , Furrer Pascal , Allémann Eric , Cuendet Muriel
Published: September 2018

Lung cancer is the most lethal cancer in the world. About 80% of lung cancer deaths are linked to tobacco use. As a complement to tobacco control, efficient chemoprevention strategies are needed to tackle lung cancer epidemic. Resveratrol is one of the most studied natural products, notably for its cancer chemoprevention properties. However, its low oral bioavailability has often limited the translation of in vitro activities to in vivo effects. While oral administration of resveratrol effectively inhibited colorectal carcinogenesis, it failed to protect mice from chemically-induced lung carcinogenesis. Therefore, non-invasive parenteral routes must be considered to bring resveratrol to the lungs. In the present study, intranasal administration of a concentrated formulation proved to be a valid method to expose the lungs to a sufficient amount of resveratrol. This formulation was administered three times a week for 25 weeks to A/J mice having 4-[methyl(nitroso)amino]-1-(3-pyridinyl)-1-butanone-induced lung carcinogenesis. Resveratrol-treated mice showed a 27% decrease in tumour multiplicity, with smaller tumours, resulting in 45% decrease in tumour volume/mouse. In vitro investigations highlighted apoptosis as a potential mechanism of action. This study presents an effective way to overcome resveratrol low oral bioavailability, encouraging a reevaluation of its use in future clinical trials.
Down-regulation of Skp2 expression inhibits invasion and lung metastasis in osteosarcoma
Authors: Zhang Yidan , Zvi Yoav S. , Batko Brian , Zaphiros Nikolas , O’Donnell Edmond F. , Wang Jichuan , Sato Kenji , Yang Rui , Geller David S. , Koirala Pratistha , Zhang Wendong , Du Xiuquan , Piperdi Sajida , Liu Yang , Zheng Deyou , Roth Michael , Gill Jonathan , Zhang Jinghang , Ren Tingting , Gorlick Richard , Zi Xiaolin , Hoang Bang H.
Published: September 2018

Osteosarcoma (OS), the most common primary cancer of bone, exhibits a high propensity for local invasion and distant metastasis. This study sought to elucidate the role of S phase kinase-associated protein (Skp2) in osteosarcoma invasion and metastasis and to explore flavokawain A (FKA), a natural chalcone from kava extract, as a potential Skp2 targeting agent for preventing osteosarcoma progression. Skp2 was found to be overexpressed in multiple osteosarcoma cell lines, including 5 standard and 8 primary patient-derived cell lines. Patients whose tumors expressed high levels of Skp2 sustained a significantly worse metastasis-free (p = 0.0095) and overall survival (p = 0.0013) than those with low Skp2. Skp2 knockdown markedly reduced in vitro cellular invasion and in vivo lung metastasis in an orthotopic mouse model of osteosarcoma. Similar to Skp2 knockdown, treatment with FKA also reduced Skp2 expression in osteosarcoma cell lines and blocked the invasion of osteosarcoma cells in vitro and lung metastasis in vivo. Together, our findings suggest that Skp2 is a promising therapeutic target in osteosarcoma, and that FKA may be an effective Skp2-targeted therapy to reduce osteosarcoma metastasis.
Analysis of the role of GSK3 in the mitotic checkpoint
Authors: Rashid M. S. , Mazur T. , Ji W. , Liu S. T. , Taylor W. R.
Published: September 2018

The mitotic checkpoint ensures proper chromosome segregation; defects in this checkpoint can lead to aneuploidy, a hallmark of cancer. The mitotic checkpoint blocks progression through mitosis as long as chromosomes remain unattached to spindle microtubules. Unattached kinetochores induce the formation of a mitotic checkpoint complex (MCC) composed of Mad2, BubR1, Bub1 and Bub3 which inhibits anaphase onset. Spindle toxins induce prolonged mitotic arrest by creating persistently unattached kinetochores which trigger MCC formation. We find that the multifunctional ser/thr kinase, glycogen synthase kinase 3 (GSK3) is required for a strong mitotic checkpoint. Spindle toxin-induced mitotic arrest is relieved by GSK3 inhibitors SB 415286 (SB), RO 318220 (RO) and lithium chloride. Similarly, targeting GSK3β with knockout or RNAi reduced mitotic arrest in the presence of Taxol. GSK3 was required for optimal localization of Mad2, BubR1, and Bub1 at kinetochores and for optimal assembly of the MCC in spindle toxin-arrested cells. The WNT- and PI3K/Akt signaling pathways negatively regulate GSK3β activity. Inhibition of WNT and PI3K/Akt signaling, in the presence of Taxol, induced a longer mitotic arrest compared to Taxol alone. Our observations provide novel insight into the regulation of the mitotic checkpoint and its connection to growth-signaling pathways.
Crystal structure of FlgL and its implications for flagellar assembly
Authors: Hong Ho Jeong , Kim Tae Hee , Song Wan Seok , Ko Hyun-Jeong , Lee Geun-Shik , Kang Seung Goo , Kim Pyeung-Hyeun , Yoon Sung-il
Published: September 2018

Bacteria move toward attractants and away from repellants by rotating their flagellum. The bacterial flagellum assembles through the ordered organization of more than 30 different proteins. Among the diverse flagellar proteins, FlgL forms the junction between the hook and the filament in the flagellum together with FlgK and provides a structural base where flagellin, a filament-forming protein, is inserted for the initiation of filament elongation. However, the functional and structural information available for FlgL is highly limited. To provide structural insights into the cross-linkage between the FlgL junction and the flagellin filament, we determined the crystal structures of FlgL from gram-positive Bacillus cereus (bcFlgL) and gram-negative Xanthomonas campestris (xcFlgL). bcFlgL contains one domain (D1), whereas xcFlgL adopts a two-domain structure that consists of the D1 and D2 domains. The constant D1 domain of FlgL adopts a rod structure that is generated by four longitudinal segments. This four-segment structure is recapitulated in filament and junction proteins but not in hook and rod proteins, allowing us to propose a junction-filament assembly mechanism based on a quasi-homotypic interaction. The D2 domain of xcFlgL resembles that of another junction protein, FlgK, suggesting the structural and functional relatedness of FlgL and FlgK.
Functional Studies of Anodic Oxidized β-Ti-28Nb-11Ta-8Zr Alloy for Mechanical, In-vitro and Antibacterial Capability
Authors: Lin Hsin-I , Kuo Yu-Ming , Hu Chun-Chih , Lee Mu-Huan , Chen Ling-Hsiang , Li Chung-Tien , Wong Tze-Hong , Yen Ta-Jen
Published: September 2018

We developed an osseocompatible β-type Ti-28Nb-11Ta-8Zr (TNTZ) alloy that displays the excellent elastic modulus, cellular response, corrosion resistance and antibacterial capability demanded for bone-mimetic materials. The TNTZ alloy exhibited an elastic modulus of 49 GPa, which approximates that of human bones and prevent stress shielding effects. A further anodic oxidation and subsequent post-annealing modification formed a crystalline nanoporous TNTZ oxide layer (NPTNTZO(c)) on the alloy surface, potentially promoting interlocking with the extracellular matrix of bone cells and cell proliferation. Osteoblast viability tests also verified that NPTNTZO(c) enhanced cell growth more significantly than that of flat TNTZ. In addition, potentiodynamic polarization tests in Hanks’ balanced salt solution (HBSS) revealed that both TNTZ and NPTNTZO(c) exhibited better corrosion resistance than commercial pure titanium. Finally, NPTNTZO(c) reinforced with silver nanoparticles (NPTNTZO(c)/AgNPs) intensified the antibacterial efficiency againstPseudomonas aeruginosa,Staphylococcus aureusandEscherichia colifor 8 h with antibacterial efficiencies of 87.82%, 97.68%, and 93.90%, respectively, facilitating infection prevention during surgery and recovery stages.
Transcriptional Regulatory Networks in Hepatitis C Virus-induced Hepatocellular Carcinoma
Authors: Zahra Marwa , Azzazy Hassan , Moustafa Ahmed
Published: September 2018

Understanding the transcriptional regulatory elements that influence the progression of liver disease in the presence of hepatitis C virus (HCV) infection is critical for the development of diagnostic and therapeutic approaches. Systems biology provides a roadmap by which these elements may be integrated. In this study, a previously published dataset of 124 microarray samples was analyzed in order to determine differentially expressed genes across four tissue types/conditions (normal, cirrhosis, cirrhosis HCC, and HCC). Differentially expressed genes were assessed for their functional clustering and those genes were annotated with their potential transcription factors and miRNAs. Transcriptional regulatory networks were constructed for each pairwise comparison between the 4 tissue types/conditions. Based on our analysis, it is predicted that the disruption in the regulation of transcription factors such as AP-1, PPARγ, and NF-κB could contribute to the liver progression from cirrhosis to steatosis and eventually to HCC. Whereas the condition of the liver digresses, the downregulation of miRNAs’ (such as miR-27, Let-7, and miR-106a) expression makes the transition of the liver through each pathological stage more apparent. This preliminary data can be used to guide future experimental work. An understanding of the transcriptional regulatory attributes acts as a road map to help design interference strategies in order to target the key regulators of progression of HCV induced HCC.
Identification of mesothelioma-specific sialylated epitope recognized with monoclonal antibody SKM9-2 in a mucin-like membrane protein HEG1
Authors: Matsuura Rieko , Kaji Hiroyuki , Tomioka Azusa , Sato Takashi , Narimatsu Hisashi , Moriwaki Yasuhiro , Misawa Hidemi , Imai Kohzoh , Tsuji Shoutaro
Published: September 2018

The anti-mesothelioma mAb SKM9-2 recognizes the sialylated protein HEG homolog 1 (HEG1). HEG1 is a 400 kDa mucin-like membrane protein found on mesothelioma. SKM9-2 can detect mesothelioma more specifically and sensitively than other antibodies against current mesothelioma markers; therefore, SKM9-2 would be likely useful for the precise detection and diagnosis of malignant mesothelioma. In the present study, we investigated the epitope of SKM9-2. We analyzed the binding of SKM9-2 to truncated HEG1 and candidate epitope-fused glycosylphosphatidylinositol-anchor proteins. The epitope of SKM9-2 was identified as an O-glycosylated region, 893-SKSPSLVSLPT-903, in HEG1. An alanine scanning assay of the epitope showed that SKM9-2 bound to a simple epitope in HEG1, and the SKxPSxVS sequence within the epitope was essential for SKM9-2 recognition. Mass spectrometry analysis and lectin binding analysis of soluble epitope peptides indicated that the SKM9-2 epitope, in which Ser897 was not glycosylated, contained two disialylated core 1 O-linked glycan-modified serine residues, Ser893 and Ser900. Neuraminidase treatment analysis also confirmed that the epitope in mesothelioma cells contained a similar glycan modification. The specific detection of mesothelioma with SKM9-2 can thus be performed by the recognition of sialylated glycan modification in the specific region of HEG1.
CcpA Coordinates Growth/Damage Balance for Streptococcus pyogenes Pathogenesis
Authors: Paluscio Elyse , Watson Michael E. , Caparon Michael G.
Published: September 2018

To achieve maximum fitness, pathogens must balance growth with tissue damage, coordinating metabolism and virulence factor expression. In the gram-positive bacterium Streptococcus pyogenes, the DNA-binding transcriptional regulator Carbon Catabolite Protein A (CcpA) is a master regulator of both carbon catabolite repression and virulence, suggesting it coordinates growth/damage balance. To examine this, two murine models were used to compare the virulence of a mutant lacking CcpA with a mutant expressing CcpA locked into its high-affinity DNA-binding conformation (CcpAT307Y). In models of acute soft tissue infection and of long-term asymptomatic mucosal colonization, both CcpA mutants displayed altered virulence, albeit with distinct growth/damage profiles. Loss of CcpA resulted in a diminished ability to grow in tissue, leading to less damage and early clearance. In contrast, constitutive DNA-binding activity uncoupled the growth/damage relationship, such that high tissue burdens and extended time of carriage were achieved, despite reduced tissue damage. These data demonstrate that growth/damage balance can be actively controlled by the pathogen and implicate CcpA as a master regulator of this relationship. This suggests a model where the topology of the S. pyogenes virulence network has evolved to couple carbon source selection with growth/damage balance, which may differentially influence pathogenesis at distinct tissues.
Effect of transition metal alloying elements on the deformation of Ti-44Al-8Nb-0.2B-0.2Y alloys
Authors: Zhang Laiqi , Ge Gengwu , Lin Junpin , Aindow Mark , Zhang Lichun
Published: September 2018

A series of β-γ Ti-44Al-8Nb-0.2B-0.2Y alloys have been modified with 0.5 to 2.0 at.% of the β-stabilizing elements Mn, Cr, Mo and V. Additions of Cr and Mo alone result in a decrease in the flow stress, whereas the opposite effect was observed for additions of V. For alloys with Mn additions, a minimum value of the flow stress was achieved in the alloy with 1.5% Mn. For alloys with combined additions, optimum hot deformation behavior was obtained for the alloy with 1.5% Mn and 1.0% Cr.
Nod2 Deficiency in mice is Associated with Microbiota Variation Favouring the Expansion of mucosal CD4+ LAP+ Regulatory Cells
Authors: Butera A. , Di Paola M. , Pavarini L. , Strati F. , Pindo M. , Sanchez M. , Cavalieri D. , Boirivant M. , De Filippo C.
Published: September 2018

Nucleotide-binding Oligomerization Domain-2 (NOD2) mutations are associated with an increased risk to develop Crohn’s Disease. In previous studies, we have shown that Nod2−/− mice manifest increased proportion of Lamina Propria (LP) CD4+ LAP+ Foxp3− regulatory cells, when compared with Nod2+/+ mice, while CD4+ Foxp3 + regulatory cells were not affected. Here, we investigated the Nod2 gut microbiota, by 16S rRNA pyrosequencing, at steady state and after TNBS-colitis induction in mice reared separately or in cohousing, correlating the microbial profiles with LP regulatory T cells proportion and tissue cytokines content. We found that enrichment of Rikenella and Alistipes (Rikenellaceae) in Nod2−/− mice at 8 weeks of age reared separately was associated with increased proportion of CD4+ LAP+ Foxp3− cells and less severe TNBS-colitis. In co-housed mice the acquisition of Rickenellaceae by Nod2+/+ mice was associated with increased CD4+ LAP+ Foxp3− proportion and less severe colitis. Severe colitis was associated with enrichment of gram-negative pathobionts (Escherichia and Enterococcus), while less severe colitis with protective bacteria (Barnesiella, Odoribacter and Clostridium IV). Environmental factors acting on genetic background with different outcomes according to their impact on microbiota, predispose in different ways to inflammation. These results open a new scenario for therapeutic attempt to re-establish eubiosis in Inflammatory Bowel Disease patients with NOD2 polymorphisms.
Enrichment of gut-derived Fusobacterium is associated with suboptimal immune recovery in HIV-infected individuals
Authors: Lee Soo Ching , Chua Ling Ling , Yap Siew Hwei , Khang Tsung Fei , Leng Chan Yoon , Raja Azwa Raja Iskandar , Lewin Sharon R. , Kamarulzaman Adeeba , Woo Yin Ling , Lim Yvonne Ai Lian , Loke P’ng , Rajasuriar Reena
Published: September 2018

We explored the gut microbiota profile among HIV-infected individuals with diverse immune recovery profiles following long-term suppressive ART and investigated the relationship between the altered bacteria with markers of immune dysfunction. The microbiota profile of rectal swabs from 26 HIV-infected individuals and 20 HIV-uninfected controls were examined. Patients were classified as suboptimal responders, sIR (n = 10, CD4 T-cell <350 cells/ul) and optimal responders, oIR (n = 16, CD4 T-cell >500 cells/ul) after a minimum of 2 years on suppressive ART. Canonical correlation analysis(CCA) and multiple regression modelling were used to explore the association between fecal bacterial taxa abundance and immunological profiles in optimal and suboptimal responders. We foundFusobacteriumwas significantly enriched among the HIV-infected and the sIR group. CCA results showed thatFusobacteriumabundance was negatively correlated with CD4 T-cell counts, but positively correlated with CD4 T-cell activation and CD4 Tregs. Multiple linear regression analysis adjusted for age, baseline CD4 T-cell count, antibiotic exposure and MSM status indicated that higherFusobacteriumrelative abundance was independently associated with poorer CD4 T-cell recovery following ART. Enrichment ofFusobacteriumwas associated with reduced immune recovery and persistent immune dysfunction following ART. Modulating the abundance of this bacterial taxa in the gut may be a viable intervention to improve immune reconstitution in our setting.
Sleep Disturbance and Related Factors in Patients with Nasopharyngeal Carcinoma and Their Family Caregivers Prior to the Initiation of Treatment
Authors: Lai Xiao-Ying , Tang Zhong-Min , Zhu Xiao-Dong , Li Ling , Qin Xue-Yan , Lan Jiang-Ling , Lu Chun-Ping , Lyu Zhi-Chan , Liang Li-Qiao , Chen Li-Jun
Published: September 2018

Sleep disturbance is a common complaint in cancer patients. However, less is known about the parameters of sleep in patients with nasopharyngeal cancer (NPC) and their family caregivers (FCs) when they are about to begin treatment. We investigated the sleep quality in patients with NPC and their FCs before treatment and determined the related factors that predict sleep disturbance in these patients before therapy. A total of 101 patient-FC dyads were recruited. They completed the Pittsburgh Sleep Quality Index (PSQI) prior to treatment. No differences were found in sleep disturbance between patients (38.6%) and their FCs (31.7%). Patients reported significantly higher rates of short sleep duration than their FCs (P = 0.011). Logistic regression analyses showed that older patients were more prone to suffer from poor sleep quality before treatment (OR = 1.06, 95% CI = 1.01–1.10, P = 0.008), while patients with a higher BMI were less likely to experience sleep disturbance (OR = 0.83, 95% CI = 0.71–0.96, P = 0.012). Sleep disturbance is a significant problem in patients with NPC and their FCs before therapy. Older patients and those with a lower BMI appear to be more inclined to suffer from poor sleep before treatment.
The evolution of fruit colour: phylogeny, abiotic factors and the role of mutualists
Authors: Valenta Kim , Kalbitzer Urs , Razafimandimby Diary , Omeja Patrick , Ayasse Manfred , Chapman Colin A. , Nevo Omer
Published: September 2018

The adaptive significance of fruit colour has been investigated for over a century. While colour can fulfil various functions, the most commonly tested hypothesis is that it has evolved to increase fruit visual conspicuousness and thus promote detection and consumption by seed dispersing animals. However, fruit colour is a complex trait which is subjected to various constraints and selection pressures. As a result, the effect of animal selection on fruit colour are often difficult to identify, and several studies have failed to detect it. Here, we employ an integrative approach to examine what drives variation in fruit colour. We quantified the colour of ripe fruit and mature leaves of 97 tropical plant species from three study sites in Madagascar and Uganda. We used phylogenetically controlled models to estimate the roles of phylogeny, abiotic factors, and dispersal mode on fruit colour variation. Our results show that, independent of phylogeny and leaf coloration, mammal dispersed fruits are greener than bird dispersed fruits, while the latter are redder than the former. In addition, fruit colour does not correlate with leaf colour in the visible spectrum, but fruit reflection in the ultraviolet area of the spectrum is strongly correlated with leaf reflectance, emphasizing the role of abiotic factors in determining fruit colour. These results demonstrate that fruit colour is affected by both animal sensory ecology and abiotic factors and highlight the importance of an integrative approach which controls for the relevant confounding factors.
Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes
Authors: Shahbazi Ali , Kinnison Jeffery , Vescovi Rafael , Du Ming , Hill Robert , Joesch Maximilian , Takeno Marc , Zeng Hongkui , da Costa Nuno Maçarico , Grutzendler Jaime , Kasthuri Narayanan , Scheirer Walter J.
Published: September 2018

Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively.
Protecting quantum resources via frequency modulation of qubits in leaky cavities
Authors: Mortezapour Ali , Lo Franco Rosario
Published: September 2018

Finding strategies to preserve quantum resources in open systems is nowadays a main requirement for reliable quantum-enhanced technologies. We address this issue by considering structured cavities embedding qubits driven by a control technique known as frequency modulation. We first study a single qubit in a lossy cavity to determine optimal modulation parameters and qubit-cavity coupling regime allowing a gain of four orders of magnitude concerning coherence lifetimes. We relate this behavior to the inhibition of the qubit effective decay rate rather than to stronger memory effects (non-Markovianity) of the system. We then exploit these findings in a system of noninteracting qubits embedded in separated cavities to gain basic information about scalability of the procedure. We show that the determined modulation parameters enable lifetimes of quantum resources, such as entanglement, discord and coherence, three orders of magnitude longer than their natural (uncontrolled) decay times. We discuss the feasibility of the system within the circuit-QED scenario, typically employed in the current quantum computer prototypes. These results provide new insights towards efficient experimental strategies against decoherence.
Visual salience of the stop signal affects the neuronal dynamics of controlled inhibition
Authors: Pani Pierpaolo , Giarrocco Franco , Giamundo Margherita , Montanari Roberto , Brunamonti Emiliano , Ferraina Stefano
Published: September 2018

The voluntary control of movement is often tested by using the countermanding, or stop-signal task that sporadically requires the suppression of a movement in response to an incoming stop-signal. Neurophysiological recordings in monkeys engaged in the countermanding task have shown that dorsal premotor cortex (PMd) is implicated in movement control. An open question is whether and how the perceptual demands inherent the stop-signal affects inhibitory performance and their underlying neuronal correlates. To this aim we recorded multi-unit activity (MUA) from the PMd of two male monkeys performing a countermanding task in which the salience of the stop-signals was modulated. Consistently to what has been observed in humans, we found that less salient stimuli worsened the inhibitory performance. At the neuronal level, these behavioral results were subtended by the following modulations: when the stop-signal was not noticeable compared to the salient condition the preparatory neuronal activity in PMd started to be affected later and with a less sharp dynamic. This neuronal pattern is probably the consequence of a less efficient inhibitory command useful to interrupt the neural dynamic that supports movement generation in PMd.
The Stochastic Transport Dynamics of a Conserved Quantity on a Complex Network
Authors: Medina Pablo , Clark Jaime , Kiwi Miguel , Torres Felipe , Rogan José , Valdivia Juan Alejandro
Published: September 2018

The stochastic dynamics of conserved quantities is an emergent phenomena observed in many complex systems, ranging from social and to biological networks. Using an extension of the Ehrenfest urn model on a complex network, over which a conserved quantity is transported in a random fashion, we study the dynamics of many elementary packets transported through the network by means of a master equation approach and compare with the mean field approximation and stochastic simulations. By use of the mean field theory, it is possible to compute an approximation to the ensemble average evolution of the number of packets in each node which, in the thermodynamic limit, agrees quite well with the results of the master equation. However, the master equation gives a more complete description of the stochastic system and provides a probabilistic view of the occupation number at each node. Of particular relevance is the standard deviation of the occupation number at each node, which is not uniform for a complex network. We analyze and compare different network topologies (small world, scale free, Erdos-Renyi, among others). Given the computational complexity of directly evaluating the asymptotic, or equilibrium, occupation number probability distribution, we propose a scaling relation with the number of packets in the network, that allows to construct the asymptotic probability distributions from the network with one packet. The approximation, which relies on the same matrix found in the mean field approach, becomes increasingly more accurate for a large number of packets.
Neural correlates of multi-day learning and savings in sensorimotor adaptation
Authors: Ruitenberg M. F. L. , Koppelmans V. , De Dios Y. E. , Gadd N. E. , Wood S. J. , Reuter-Lorenz P. A. , Kofman I. , Bloomberg J. J. , Mulavara A. P. , Seidler R. D.
Published: September 2018

In the present study we evaluated changes in neural activation that occur over the time course of multiple days of sensorimotor adaptation, and identified individual neural predictors of adaptation and savings magnitude. We collected functional MRI data while participants performed a manual adaptation task during four separate test sessions over a three-month period. This allowed us to examine changes in activation and associations with adaptation and savings at subsequent sessions. Participants exhibited reliable savings of adaptation across the four sessions. Brain activity associated with early adaptation increased across the sessions in a variety of frontal, parietal, cingulate, and temporal cortical areas, as well as various subcortical areas. We found that savings was positively associated with activation in several striatal, parietal, and cingulate cortical areas including the putamen, precuneus, angular gyrus, dorsal anterior cingulate cortex (dACC), and cingulate motor area. These findings suggest that participants may learn how to better engage cognitive processes across days, potentially reflecting improvements in action selection. We propose that such improvements may rely on action-value assignments, which previously have been linked to the dACC and striatum. As correct movements are assigned a higher value than incorrect movements, the former are more likely to be performed again.
MyD88 signaling causes autoimmune sialadenitis through formation of high endothelial venules and upregulation of LTβ receptor-mediated signaling
Authors: Into Takeshi , Niida Shumpei , Shibata Ken-ichiro
Published: September 2018

Autoimmune sialadenitis (AS), chronic inflammation of the salivary glands (SGs) with focal lymphocyte infiltration, appears in autoimmune diseases such as Sjӧgren’s syndrome. The pathological role of MyD88-dependent innate immune signaling in autoimmune diseases including AS has been studied using mouse models, such as NOD mice. Although AS development in NOD mice was reported to be suppressed byMyd88deficiency, its specific role remains unclear. Here, we determined the potent suppressive effects ofMyd88deficiency on AS development in lupus-prone B6/lprmice, which have lymphoproliferation abnormalities, and also in NOD mice, which have no lymphoproliferation abnormalities. This indicates that MyD88 signaling triggers AS through both lymphoproliferation-dependent and -independent mechanisms. To address the MyD88-dependent lymphoproliferation-independent AS manifestation, SGs from C57BL/6 mice were analyzed. Remarkable upregulation ofGlycam1and high endothelial venule (HEV)-associated changes were unexpectedly found inMyd88+/+mice, compared withMyd88−/−mice. MyD88-dependent HEV-associated changes were also observed in NOD mice. Additionally,Lta,Ltb, andLtbrin SGs of NOD mice were lowered byMyd88deficiency. Interestingly, LTβR-induced HEV-associated gene expression in cultured cells was impaired byMyd88deficiency. Our findings highlight novel roles for MyD88 in AS development, which imply the existence of MyD88-dependent HEV formation in ectopic lymphoid neogenesis.
Evaluation of absorbable hemostatic agents of polyelectrolyte complexes using carboxymethyl starch and chitosan oligosaccharide both in vitro and in vivo
Authors: Chen Xingtao , Yan Yonggang , Li Hong , Wang Xuehong , Tang Songchao , Li Quan , Wei Jie , Su Jiacan
Published: September 2018

CMS/COS PECs with a suitable COS content were promising absorbable hemostatic agents for internal use.
Electroreduction of carbon dioxide to formate over a thin-layered tin diselenide electrode
Authors: Yang Hui , Liu Haoxuan , Liu Xijun , Zhao Zhe , Luo Jun
Published: September 2018

We first report a thin-layered SnSe2 film as a robust catalyst for CO2 electroreduction, efficiently affording formate with a faradaic efficiency of 91% and a stable activity for more than 100 h at −0.8 V versus the reversible hydrogen electrode.
Correlation of instrumental texture properties from textural profile analysis (TPA) with eating behaviours and macronutrient composition for a wide range of solid foods
Authors: Wee May Sui Mei , Goh Ai Ting , Stieger Markus , Forde Ciarán G.
Published: September 2018

The correlation between instrumental texture properties and oral processing provides guidance on the parameters that produce ‘faster’ and ‘slower’ versions of foods, and suggests how texture modifications can be applied to moderate eating rate and energy intake within meals.
Bioactive properties and phytochemical assessment of Bacupari-anão (Garcinia brasiliensis Mart.) leaves native to Rondônia, Brazil
Authors: Zan Renato André , Fernandes Ângela , Jedoz Stephanie , Oludemi Taofiq , Calhelha Ricardo C. , Pires Tânia C. S. P. , Alves Maria José , Martins Roberto Carlos Campos , Barros Lillian , Ferreira Isabel C. F. R.
Published: September 2018

Extracts of Garcinia brasiliensis Mart. revealed health promoting biological properties.
Evaluation of diagnostic ratios of phenanthrenes and chrysenes for the identification of severely weathered spilled oils from the simulation weathering and the Sinopec pipeline explosion at Huangdao, 2013
Authors: Han Bin , Zheng Li , Yu Shun
Published: September 2018

The composition and physical properties of spilled oil undergo great changes during a serious weathering process.
Periodic DFT study of structural transformations of cocrystal NTO/TZTN under high pressure
Authors: Zhao Guo-zheng , Yang Dong-fang
Published: September 2018

Three structural transformations occurred at pressures of 4, 8, and 23 GPa. The cyclization plays an important role in stabilizing the systems.
Integrating plasmonic nanostructures with natural photonic architectures in Pd-modified Morpho butterfly wings for sensitive hydrogen gas sensing
Authors: He Jiaqing , Villa Nicolò Simone , Luo Zhen , An Shun , Shen Qingchen , Tao Peng , Song Chengyi , Wu Jianbo , Deng Tao , Shang Wen
Published: September 2018

Three-dimensional heterogeneous nanostructures that integrate plasmonic nanostructures of Pd with photonic architecture of Morpho butterfly wings can achieve sensitive hydrogen gas detection.
Decontamination of radionuclides by functionalized mesoporous silica under gamma irradiation
Authors: Iqbal Sajid , Yun Jong-Il
Published: September 2018

Schiff base functionalized mesoporous silica (SA-SBA-15) was synthesized by the co-condensation method to remove the radioactive corrosion products from contaminated water coming from nuclear installations.
Preparation of a Cu(BTC)-rGO catalyst loaded on a Pt deposited Cu foam cathode to reduce CO2 in a photoelectrochemical cell
Authors: Cheng Jun , Xuan Xiaoxu , Yang Xiao , Zhou Junhu , Cen Kefa
Published: September 2018

Schematic of a photoelectrochemical cell for CO2 reduction: the H+ generation process and the CO2 process run in two separated chambers respectively.
Role of C, S, Se and P donor ligands in copper(i) mediated C–N and C–Si bond formation reactions
Authors: Srinivas Katam , Prabusankar Ganesan
Published: September 2018

The first comparative study of C, S, Se and P donor ligands-supported copper(i) complexes for C–N and C–Si bond formation reactions.
Influencing characteristics of short-time aerobic digestion on spatial distribution and adsorption capacity of extracellular polymeric substances in waste activated sludge
Authors: Liu Ying , Lv Wenzhou , Zhang Zhiqiang , Xia Siqing
Published: September 2018

The spatial distribution and adsorption capacity of extracellular polymeric substances (EPS) were systematically investigated for waste activated sludge (WAS) treated by a short-time aerobic digestion (STAD) process.
The role of soil components in the sorption of tetracycline and heavy metals in soils
Authors: Zhao Zhendong , Nie Tiantian , Yang Zhenyu , Zhou Wenjun
Published: September 2018

A natural black soil (BS) was treated to obtain three individual soils to investigate the sorption behaviors of tetracycline (TC) and heavy metals (Cu2+ and Cd2+) and evaluate the role and contribution of different soil components.
Traceless mitigation of laser damage precursors on a fused silica surface by combining reactive ion beam etching with dynamic chemical etching
Authors: Sun Laixi , Shao Ting , Xu Jianfeng , Zhou Xiangdong , Ye Xin , Huang Jin , Bai Jian , Jiang Xiaodong , Zheng Wanguo , Yang Liming
Published: September 2018

RIBE and DCE techniques can be combined to tracelessly mitigate laser damage precursors on a fused silica surface.
Growth of form in thin elastic structures
Authors: Al Mosleh Salem , Gopinathan Ajay , Santangelo Christian
Published: September 2018

Stability of a growing cylinder under geometric and mechanical feedback mechanisms. Feedback mechanisms are constrained by symmetry and locality.
Stepped surface-rich copper fiber felt as an efficient electrocatalyst for the CO2RR to formate
Authors: Shen Sibo , He Jia , Peng Xianyun , Xi Wei , Zhang Lihan , Xi Desheng , Wang Lei , Liu Xijun , Luo Jun
Published: September 2018

We developed a novel biomass carbon-templated route to synthesize stepped surface-rich Cu fiber felt as an efficient and stable electrocatalyst for the CO2RR to formate, whose FE reaches 71.1 ± 3.1% in KHCO3 solution.