bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond the tip of the iceberg; a new view of the diversity of sulfite- and sulfate-reducing microorganisms
Authors: Vigneron Adrien , Cruaud Perrine , Alsop Eric , de Rezende Julia R , Head Ian M , Tsesmetzis Nicolas 
Published: May 2018

Abstract
Sulfite-reducing and sulfate-reducing microorganisms (SRM) play important roles in anoxic environments, linking the sulfur and carbon cycles. With climate warming, the distribution of anoxic habitats conductive to dissimilatory SRM is expanding. Consequently, we hypothesize that novel SRM are likely to emerge from the rare biosphere triggered by environmental changes. Using the dsrB gene as a molecular marker of sulfite-reducers and sulfate-reducers, we analyzed the diversity, community composition, and abundance of SRM in 200 samples representing 14 different ecosystems, including marine and freshwater environments, oil reservoirs, and engineered infrastructure. Up to 167,397 species-level OTUs affiliated with 47 different families were identified. Up to 96% of these can be considered as “rare biosphere SRM”. One third of the dsrB genes identified belonged to uncharacterized lineages. The dsrB sequences exhibited a strong pattern of selection in different ecosystems. These results expand our knowledge of the biodiversity and distribution of SRM, with implications for carbon and sulfur cycling in anoxic ecosystems.
Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network
Authors: Jia Peilin , Chen Xiangning , Fanous Ayman H. , Zhao Zhongming 
Published: May 2018

AbstractGenetic components susceptible to complex disease such as schizophrenia include a wide spectrum of variants, including common variants (CVs) and de novo mutations (DNMs). Although CVs and DNMs differ by origin, it remains elusive whether and how they interact at the gene, pathway, and network levels that leads to the disease. In this work, we characterized the genes harboring schizophrenia-associated CVs (CVgenes) and the genes harboring DNMs (DNMgenes) using measures from network, tissue-specific expression profile, and spatiotemporal brain expression profile. We developed an algorithm to link the DNMgenes and CVgenes in spatiotemporal brain co-expression networks. DNMgenes tended to have central roles in the human protein–protein interaction (PPI) network, evidenced in their high degree and high betweenness values. DNMgenes and CVgenes connected with each other significantly more often than with other genes in the networks. However, only CVgenes remained significantly connected after adjusting for their degree. In our gene co-expression PPI network, we found DNMgenes and CVgenes connected in a tissue-specific fashion, and such a pattern was similar to that in GTEx brain but not in other GTEx tissues. Importantly, DNMgene–CVgene subnetworks were enriched with pathways of chromatin remodeling, MHC protein complex binding, and neurotransmitter activities. In summary, our results unveiled that both DNMgenes and CVgenes contributed to a core set of biologically important pathways and networks, and their interactions may attribute to the risk for schizophrenia. Our results also suggested a stronger biological effect of DNMgenes than CVgenes in schizophrenia.
HMGB1 released from intestinal epithelia damaged by cholera toxin adjuvant contributes to activation of mucosal dendritic cells and induction of intestinal cytotoxic T lymphocytes and IgA
Authors: Wakabayashi Ayako , Shimizu Masumi , Shinya Eiji , Takahashi Hidemi 
Published: May 2018

AbstractCholera toxin (CT) is a potent mucosal adjuvant and oral administration of ovalbumin (OVA) antigens plus CT induces OVA-specific CD8+cytotoxic T lymphocytes (CTLs) and IgA production in intestinal mucosa. However, the mechanisms of induction of these immune responses remain unknown. Intestinal OVA-specific CD8+CTLs were not induced by oral administration of the CT active (CTA) or CT binding (CTB) subunit as an adjuvant and CD11c+DCs were involved in cross-priming of intestinal CTLs. CD8+CD103+CD11c+CD11b−DCs and DCIR2+CD103+CD11c+CD11b+DCs were distributed in the intestinal lamina propria and mesenteric lymph nodes, both DC subsets expressed DEC-205, and the expression of co-stimulatory molecules such as CD80 and CD86 was enhanced in both DC subsets after oral administration of intact CT but not the CTA or CTB subunit. Intestinal DCs activated by the oral administration of OVA plus CT cross-presented OVA antigens and DCs that captured OVA antigen through DEC-205, but not DCIR2, could cross-present antigen. We found that oral administration of intact CT, but not the CTA or CTB subunit, enhanced cell death, cytoplasmic expression of high-mobility group box 1 protein (HMGB1) in epithelial cell adhesion molecule (EpCAM)+CD45−intestinal epithelial cells (IECs), and HMGB1 levels in fecal extracts. HMGB1 dose-dependently enhanced the expression of CD80 and CD86 on DCs in vitro, and intravenous or oral administration of glycyrrhizin, an HMGB1 inhibitor, significantly suppressed activation of mucosal DCs and induction of intestinal OVA-specific CTLs and IgA by oral CT administration. These results showed that oral administration of intact CT triggers epithelial cell death in the gut and the release of HMGB1 from damaged IECs, and that the released HMGB1 may mediate activation of mucosal DCs and induction of CTLs and IgA in the intestine.
MicroRNA regulation of the MRN complex impacts DNA damage, cellular senescence, and angiogenic signaling
Authors: Espinosa-Diez Cristina , Wilson RaeAnna , Chatterjee Namita , Hudson Clayton , Ruhl Rebecca , Hipfinger Christina , Helms Erin , Khan Omar F. , Anderson Daniel G. , Anand Sudarshan 
Published: May 2018

AbstractMicroRNAs (miRs) contribute to biological robustness by buffering cellular processes from external perturbations. Here we report an unexpected link between DNA damage response and angiogenic signaling that is buffered by a miR. We demonstrate that genotoxic stress-induced miR-494 inhibits the DNA repair machinery by targeting the MRE11a-RAD50-NBN (MRN) complex. Gain- and loss-of-function experiments show that miR-494 exacerbates DNA damage and drives endothelial senescence. Increase of miR-494 affects telomerase activity, activates p21, decreases pRb pathways, and diminishes angiogenic sprouting. Genetic and pharmacological disruption of the MRN pathway decreases VEGF signaling, phenocopies miR-494-induced senescence, and disrupts angiogenic sprouting. Vascular-targeted delivery of miR-494 decreases both growth factor-induced and tumor angiogenesis in mouse models. Our work identifies a putative miR-facilitated mechanism by which endothelial cells can be insulated against VEGF signaling to facilitate the onset of senescence and highlight the potential of targeting DNA repair to disrupt pathological angiogenesis.
Design principles for electronic charge transport in solution-processed vertically stacked 2D perovskite quantum wells
Authors: Tsai Hsinhan , Asadpour Reza , Blancon Jean-Christophe , Stoumpos Constantinos C. , Even Jacky , Ajayan Pulickel M. , Kanatzidis Mercouri G. , Alam Muhammad Ashraful , Mohite Aditya D. , Nie Wanyi 
Published: May 2018

AbstractState-of-the-art quantum-well-based devices such as photovoltaics, photodetectors, and light-emission devices are enabled by understanding the nature and the exact mechanism of electronic charge transport. Ruddlesden–Popper phase halide perovskites are two-dimensional solution-processed quantum wells and have recently emerged as highly efficient semiconductors for solar cell approaching 14% in power conversion efficiency. However, further improvements will require an understanding of the charge transport mechanisms, which are currently unknown and further complicated by the presence of strongly bound excitons. Here, we unambiguously determine that dominant photocurrent collection is through electric field-assisted electron–hole pair separation and transport across the potential barriers. This is revealed by in-depth device characterization, coupled with comprehensive device modeling, which can self-consistently reproduce our experimental findings. These findings establish the fundamental guidelines for the molecular and device design for layered 2D perovskite-based photovoltaics and optoelectronic devices, and are relevant for other similar quantum-confined systems.
Crystal step edges can trap electrons on the surfaces of n-type organic semiconductors
Authors: He Tao , Wu Yanfei , D’Avino Gabriele , Schmidt Elliot , Stolte Matthias , Cornil Jérôme , Beljonne David , Ruden P. Paul , Würthner Frank , Frisbie C. Daniel 
Published: May 2018

AbstractUnderstanding relationships between microstructure and electrical transport is an important goal for the materials science of organic semiconductors. Combining high-resolution surface potential mapping by scanning Kelvin probe microscopy (SKPM) with systematic field effect transport measurements, we show that step edges can trap electrons on the surfaces of single crystal organic semiconductors. n-type organic semiconductor crystals exhibiting positive step edge surface potentials display threshold voltages that increase and carrier mobilities that decrease with increasing step density, characteristic of trapping, whereas crystals that do not have positive step edge surface potentials do not have strongly step density dependent transport. A device model and microelectrostatics calculations suggest that trapping can be intrinsic to step edges for crystals of molecules with polar substituents. The results provide a unique example of a specific microstructure–charge trapping relationship and highlight the utility of surface potential imaging in combination with transport measurements as a productive strategy for uncovering microscopic structure–property relationships in organic semiconductors.
Adjuvant composition and delivery route shape immune response quality and protective efficacy of a recombinant vaccine for Entamoeba histolytica
Authors: Abhyankar Mayuresh M. , Orr Mark T. , Lin Susan , Suraju Mohammed O. , Simpson Adrian , Blust Molly , Pham Tiep , Guderian Jeffrey A. , Tomai Mark A. , Elvecrog James , Pedersen Karl , Petri William A. , Fox Christopher B. 
Published: May 2018

AbstractAmebiasis caused by Entamoeba histolytica is the third leading cause of parasitic mortality globally, with some 100,000 deaths annually, primarily among young children. Protective immunity to amebiasis is associated with fecal IgA and IFN-γ in humans; however, no vaccine exists. We have previously identified recombinant LecA as a potential protective vaccine antigen. Here we describe the development of a stable, manufacturable PEGylated liposomal adjuvant formulation containing two synthetic Toll-like receptor (TLR) ligands: GLA (TLR4) and 3M-052 (TLR7/8). The liposomes stimulated production of monocyte/macrophage chemoattractants MCP-1 and Mip-1β, and Th1-associated cytokines IL-12p70 and IFN-γ from human whole blood dependent on TLR ligand composition and dose. The liposomes also demonstrated acceptable physicochemical compatibility with the recombinant LecA antigen. Whereas mice immunized with LecA and GLA-liposomes demonstrated enhanced antigen-specific fecal IgA titers, mice immunized with LecA and 3M-052-liposomes showed a stronger Th1 immune profile. Liposomes containing GLA and 3M-052 together elicited both LecA-specific fecal IgA and Th1 immune responses. Furthermore, the quality of the immune response could be modulated with modifications to the liposomal formulation based on PEG length. Compared to subcutaneous administration, the optimized liposome adjuvant composition with LecA antigen administered intranasally resulted in significantly enhanced fecal IgA, serum IgG2a, as well as systemic IFN-γ and IL-17A levels in mice. The optimized intranasal regimen provided greater than 80% protection from disease as measured by parasite antigen in the colon. This work demonstrates the physicochemical and immunological characterization of an optimized mucosal adjuvant system containing a combination of TLR ligands with complementary activities and illustrates the importance of adjuvant composition and route of delivery to enhance a multifaceted and protective immune response to amebiasis.
Sensitivity of Transmission Raman Spectroscopy Signals to Temperature of Biological Tissues
Authors: Ghita Adrian , Matousek Pavel , Stone Nick 
Published: May 2018

AbstractOptical properties of biological tissues can be influenced by their temperature, thus affecting light transport inside the sample. This could potentially be exploited to deliver more photons inside large biological samples, when compared with experiments at room temperature, overcoming some of difficulties due to highly scattering nature of the tissue. Here we report a change in light transmitted inside biological tissue with temperature elevation from 20 to 40 °C, indicating a considerable enhancement of photons collected by the detector in transmission geometry. The measurement of Raman signals in porcine tissue samples, as large as 40 mm in thickness, indicates a considerable increase in signal ranging from 1.3 to 2 fold, subject to biological variability. The enhancements observed are ascribed to phase transitions of lipids in biological samples. This indicates that: 1) experiments performed on tissue at room temperature can lead to an underestimation of signals that would be obtained at depth in the body in vivo and 2) that experiments at room temperature could be modified to increase detection limits by elevating the temperature of the material of interest.
Ocean acidification promotes otolith growth and calcite deposition in gilthead sea bream (Sparus aurata) larvae
Authors: Coll-Lladó Clara , Giebichenstein Jan , Webb Paul B. , Bridges Christopher R. , de la serrana Daniel Garcia 
Published: May 2018

AbstractThe effects of ocean acidification on otolith crystallization and growth rates were investigated in gilthead sea bream (Sparus aurata) larvae. Larvae were exposed to three different pH levels: pH8.2, pH7.7 and pH7.3 for a period of 18 days post-fertilization. For the first time, we demonstrate that pH has a significant impact on the carbonate polymorph composition, showing calcite in a significant percentage of individuals at low pH. Around 21% of the larvae exposed to pH7.3 showed irregular calcitic otoliths rather than commonly found round aragonitic otoliths. Calcitic otoliths showed a moderate level of heritability suggesting an important role of genetic factors. We also observed significantly larger otoliths in larvae reared at pH7.7 and pH7.3 compared to pH8.2 in both sagittae and lapilli. Our results demonstrate that otolith growth rates in gilthead sea bream larvae increase at low pH while a significant proportion of larvae are prone to the formation of calcitic otoliths at pH7.3.
Oncological outcomes, quality of life outcomes and complications of partial cystectomy for selected cases of muscle-invasive bladder cancer
Authors: Ebbing Jan , Heckmann Robin Colja , Collins Justin William , Miller Kurt , Erber Barbara , Friedersdorff Frank , Fuller Tom Florian , Busch Jonas , Seifert Hans Helge , Ardelt Peter , Wetterauer Christian , Hosseini Abolfazl , Jentzmik Florian , Kempkensteffen Carsten 
Published: May 2018

AbstractTo evaluate the oncological results, associated complications, and postoperative health-related quality of life (HR-QoL) in patients treated with partial cystectomy (PC) for muscle-invasive bladder cancer (MIBC). 27 patients who underwent open PC for cT2 MIBC were included. A simple Cox’s proportional hazards regression model was used to assess the association of several potential prognostic factors with survival. Postoperative HR-QoL was assessed with the EORTC (European Organisation for the Research and Treatment of Cancer) QLQ-C30 questionnaire version 3.0. Final pathological tumour stages in PC specimen were: pT0: 18.5%, non-MIBC: 3.7%, MIBC: 74.1%, pCIS: 14.8%. Estimated 5-year overall- and progression-free survival rates were 53.7% and 62.1%. Five (18.5%) patients experienced local recurrence with MIBC. Overall, the salvage cystectomy rate was 18.5%. The 90-day mortality rate was 0%. Significant risk factors for progression-free survival were vascular invasion (HR 5.33) and tumour multilocularity (HR 4.5) in the PC specimen, and a ureteric reimplantation during PC (HR 4.53). The rates of intraoperative complications, 30- and 90-day major complications were 7.4%, respectively and 14.8% for overall long-term complications. Postoperatively, median (IQR) global health status and QoL in our PC cohort was 79.2 (52.1–97.9). Open PC can provide adequate cancer control of MIBC with good HR-QoL in highly selected cases. Open PC can lead to long-term bladder preservation and shows an acceptable rate of severe perioperative complications, even in highly comorbid patients.
A Rapid, Accurate, Single Molecule Counting Method Detects Clostridium difficile Toxin B in Stool Samples
Authors: Gite Sadanand , Archambault Destiny , Cappillino Michael P. , Cunha David , Dorich Victoria , Shatova Tatyana , Tempesta Andrew , Walsh Bruce , Walsh Jessica A. , Williams Adam , Kirby James E. , Bowers Jayson , Straus Don 
Published: May 2018

AbstractWe describe a new rapid and accurate immunoassay-based technology capable of counting single target molecules using digital imaging without magnification. Using the technology, we developed a rapid test for Clostridium difficile toxin B, which is responsible for the pathology underlying potentially fatal C. difficile infections (CDI). There are currently no tests for CDI that are rapid, sensitive, and specific. The MultiPath C. difficile toxin B test images and counts complexes of target-specific magnetic and fluorescent particles that have been tethered together by toxin B molecules in minimally processed stool samples. The performance characteristics of the 30 minute test include a limit of detection of 45 pg/mL, dynamic range covering 4–5 orders of magnitude, and coefficient of variation of less than 10%. The MultiPath test detected all toxinotypes and ribotypes tested, including the one most commonly occurring in the US and EU; shows no cross reactivity with relevant bacterial species; and is robust to potential interferants commonly present in stool samples. On a training set of 320 clinical stool samples, the MultiPath C. difficile toxin B test showed 97.0% sensitivity (95% CI, 91.4–99.4%); 98.3% specificity (95% CI, 96.8–99.2%); and 98.2% accuracy (95% CI, 96.7–99.0%) compared to the cellular cytotoxicity neutralization assay (CCNA) reference method. Based on these compelling performance characteristics, we believe the MultiPath technology can address the lack of rapid, sensitive, specific, and easy-to-use diagnostic tests for C. difficile.
Normal pre-attentive and impaired attentive processing of lexical tones in Cantonese-speaking congenital amusics
Authors: Zhang Caicai , Shao Jing 
Published: May 2018

AbstractThe neural underpinnings of congenital amusia, an innate neurogenetic disorder of musical pitch processing, are not well understood. Previous studies suggest that amusia primarily impairs attentive processing (P300) of small pitch deviations in music, leaving pre-attentive pitch processing (mismatch negativity or MMN) more or less intact. However, it remains unknown whether the same neuro-dynamic mechanism of deficiency underlies pitch processing in speech, where amusics also often show impairment behaviorally. The current study examined how lexical tones are processed in pre-attentive (MMN) and attentive (P300) conditions in 24 Cantonese-speaking amusics and 24 matched controls. At the pre-attentive level, Cantonese-speaking amusics exhibited normal MMN responses to lexical tone changes, even for tone pairs with small pitch differences (mid level vs. low level tone; high rising vs. low rising tone). However, at the attentive level, amusics exhibited reduced P3a amplitude for all tone pairs, and further reduced P3b amplitude for tone pairs with small pitch differences. These results suggest that the amusic brain detects tone changes normally pre-attentively, but shows impairment in consciously detecting the same tone differences. Consistent with previous findings in nonspeech pitch processing, this finding provides support for a domain-general neuro-dynamic mechanism of deficient attentive pitch processing in amusia.
Decellularised skeletal muscles allow functional muscle regeneration by promoting host cell migration
Authors: Urciuolo Anna , Urbani Luca , Perin Silvia , Maghsoudlou Panagiotis , Scottoni Federico , Gjinovci Asllan , Collins-Hooper Henry , Loukogeorgakis Stavros , Tyraskis Athanasios , Torelli Silvia , Germinario Elena , Fallas Mario Enrique Alvarez , Julia-Vilella Carla , Eaton Simon , Blaauw Bert , Patel Ketan , De Coppi Paolo 
Published: May 2018

AbstractPathological conditions affecting skeletal muscle function may lead to irreversible volumetric muscle loss (VML). Therapeutic approaches involving acellular matrices represent an emerging and promising strategy to promote regeneration of skeletal muscle following injury. Here we investigated the ability of three different decellularised skeletal muscle scaffolds to support muscle regeneration in a xenogeneic immune-competent model of VML, in which the EDL muscle was surgically resected. All implanted acellular matrices, used to replace the resected muscles, were able to generate functional artificial muscles by promoting host myogenic cell migration and differentiation, as well as nervous fibres, vascular networks, and satellite cell (SC) homing. However, acellular tissue mainly composed of extracellular matrix (ECM) allowed better myofibre three-dimensional (3D) organization and the restoration of SC pool, when compared to scaffolds which also preserved muscular cytoskeletal structures. Finally, we showed that fibroblasts are indispensable to promote efficient migration and myogenesis by muscle stem cells across the scaffolds in vitro. This data strongly support the use of xenogeneic acellular muscles as device to treat VML conditions in absence of donor cell implementation, as well as in vitro model for studying cell interplay during myogenesis.
Predators and nutrient availability favor protozoa-resisting bacteria in aquatic systems
Authors: Andersson A. , Ahlinder J. , Mathisen P. , Hägglund M. , Bäckman S. , Nilsson E. , Sjödin A. , Thelaus J. 
Published: May 2018

AbstractThe long co-existence of bacteria and protozoa has led to the development of bacterial protozoa resistance strategies, which are suggested to serve as drivers for the evolution of pathogenic bacteria. However, the ecological mechanisms underpinning selection for protozoa-resistance in aquatic bacteria are poorly known. To assess the role of nutrient availability and predation-pressure on selection for protozoa-resisting bacteria (PRB), an enrichment-dilution experiment was designed using laboratory microcosms containing natural lake water. PRB was monitored by screening 16S rRNA amplicon sequence data for reads assigned to bacteria that previously has been shown to resist degradation by amoebae. To estimate the effects of the microbial food web dynamics (microscopy of; heterotrophic bacteria, phytoplankton, protozoa and rotifers) and physicochemical variables on the PRB abundance in the study system, a joint species distribution modelling approach was used. The predation-pressure (ratio between predator and bacterial biomass) had a positive effect on the abundance of the PRB genusMycobacterium, while perturbation (enrichment and dilution) favored the PRB genusPseudomonasthat dominated the bacterial community in the disturbed systems. Our results show that PRB with different ecological strategies can be expected in water of high and intermediate nutrient levels and after major disturbances of an aquatic system.