bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice
Authors: Le Bastard Quentin , Ward Tonya , Sidiropoulos Dimitri , Hillmann Benjamin M. , Chun Chan Lan , Sadowsky Michael J. , Knights Dan , Montassier Emmanuel 
Published: April 2018

AbstractFecal microbiota transplantation (FMT) is now widely used to treat recurrent Clostridium difficile infection, but has been less studied as a means to restore microbiome diversity and composition following antibiotic or chemotherapy treatments. The purpose of our study was to assess the efficacy of FMT to reverse antibiotic- and chemotherapy-induced gut dysbiosis in a mouse model. C57BL/6J mice were treated with ampicillin for 1 week and/or received a single intraperitoneal injection of 5-Fluorouracil. Fresh stool was collected and analyzed using shotgun metagenomics and the Illumina sequencing platform. Ampicillin caused a significant and immediate decrease in bacterial species richness and diversity that persisted for one week. In mice that received FMT, disruption of the intestinal microbiota was reversed immediately. Antibiotic and chemotherapy administration caused significant alteration in species distribution, including a decrease in the relative proportions of Clostridium scindens and Faecalibacterium prausnitzii, and an increase in known pathogenic species. In mice receiving FMT, we observed a significant increase in species known to exhibit anti-inflammatory properties. Moreover, chemotherapy led to a critical decrease in key ‘health-promoting’ species and to an altered functional profile, especially when chemotherapy was administered in tandem with antibiotics, and that FMT can ameliorate these effects.
Phase Diagram of Water Confined by Graphene
Authors: Gao Zhenghan , Giovambattista Nicolas , Sahin Ozgur 
Published: April 2018

AbstractThe behavior of water confined at the nanoscale plays a fundamental role in biological processes and technological applications, including protein folding, translocation of water across membranes, and filtration and desalination. Remarkably, nanoscale confinement drastically alters the properties of water. Using molecular dynamics simulations, we determine the phase diagram of water confined by graphene sheets in slab geometry, at T = 300 K and for a wide range of pressures. We find that, depending on the confining dimension D and density σ, water can exist in liquid and vapor phases, or crystallize into monolayer and bilayer square ices, as observed in experiments. Interestingly, depending on D and σ, the crystal-liquid transformation can be a first-order phase transition, or smooth, reminiscent of a supercritical liquid-gas transformation. We also focus on the limit of stability of the liquid relative to the vapor and obtain the cavitation pressure perpendicular to the graphene sheets. Perpendicular cavitation pressure varies non-monotonically with increasing D and exhibits a maximum at D ≈ 0.90 nm (equivalent to three water layers). The effect of nanoconfinement on the cavitation pressure can have an impact on water transport in technological and biological systems. Our study emphasizes the rich and apparently unpredictable behavior of nanoconfined water, which is complex even for graphene.
Comparison of strain and shear wave elastography for qualitative and quantitative assessment of breast masses in the same population
Authors: Kim Hyo Jin , Kim Sun Mi , Kim Bohyoung , La Yun Bo , Jang Mijung , Ko Yousun , Lee Soo Hyun , Jeong Heeyeong , Chang Jung Min , Cho Nariya 
Published: April 2018

AbstractWe investigated addition of strain and shear wave elastography to conventional ultrasonography for the qualitative and quantitative assessment of breast masses; cut-off points were determined for strain ratio, elasticity ratio, and visual score for differentiating between benign and malignant masses. In all, 108 masses from 94 patients were evaluated with strain and shear wave elastography and scored for suspicion of malignancy, visual score, strain ratio, and elasticity ratio. The diagnostic performance between ultrasonography alone and ultrasonography combined with either type of elastography was compared; cut-off points were determined for strain ratio, elasticity ratio, and visual score. Of the 108 masses, 44 were malignant and 64 were benign. The areas under the curves were significantly higher for strain and shear wave elastography-supplemented ultrasonography (0.839 and 0.826, respectively; P = 0.656) than for ultrasonography alone (0.764; P = 0.018 and 0.035, respectively). The diagnostic performances of strain and elasticity ratios were similar when differentiating benign from malignant masses. Cut-off values for strain ratio, elasticity ratio, and visual scores for strain and shear wave elastography were 2.93, 4, 3, and 2, respectively. Both forms of elastography similarly improved the diagnostic performance of conventional ultrasonography in the qualitative and quantitative assessment of breast masses.
Pineal-dependent increase of hypothalamic neurogenesis contributes to the timing of seasonal reproduction in sheep
Authors: Batailler Martine , Chesneau Didier , Derouet Laura , Butruille Lucile , Segura Stéphanie , Cognié Juliette , Dupont Joëlle , Pillon Delphine , Migaud Martine 
Published: April 2018

AbstractTo survive in temperate latitudes, species rely on the photoperiod to synchronize their physiological functions, including reproduction, with the predictable changes in the environment. In sheep, exposure to decreasing day length reactivates the hypothalamo-pituitary-gonadal axis, while during increasing day length, animals enter a period of sexual rest. Neural stem cells have been detected in the sheep hypothalamus and hypothalamic neurogenesis was found to respond to the photoperiod. However, the physiological relevance of this seasonal adult neurogenesis is still unexplored. This longitudinal study, therefore aimed to thoroughly characterize photoperiod-stimulated neurogenesis and to investigate whether the hypothalamic adult born-cells were involved in the seasonal timing of reproduction. Results showed that time course of cell proliferation reached a peak in the middle of the period of sexual activity, corresponding to decreasing day length period. This enhancement was suppressed when animals were deprived of seasonal time cues by pinealectomy, suggesting a role of melatonin in the seasonal regulation of cell proliferation. Furthermore, when the mitotic blocker cytosine-b-D-arabinofuranoside was administered centrally, the timing of seasonal reproduction was affected. Overall, our findings link the cyclic increase in hypothalamic neurogenesis to seasonal reproduction and suggest that photoperiod-regulated hypothalamic neurogenesis plays a substantial role in seasonal reproductive physiology.
Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO-1 barcoding
Authors: Crainey James Lee , Marín Michel Abanto , Silva Túllio Romão Ribeiro da , de Medeiros Jansen Fernandes , Pessoa Felipe Arley Costa , Santos Yago Vinícius , Vicente Ana Carolina Paulo , Luz Sérgio Luiz Bessa 
Published: April 2018

AbstractDespite the broad distribution ofM. ozzardiin Latin America and the Caribbean, there is still very little DNA sequence data available to study this neglected parasite’s epidemiology. Mitochondrial DNA (mtDNA) sequences, especially the cytochrome oxidase (CO1) gene’s barcoding region, have been targeted successfully for filarial diagnostics and for epidemiological, ecological and evolutionary studies. MtDNA-based studies can, however, be compromised by unrecognised mitochondrial pseudogenes, such as Numts. Here, we have used shot-gun Illumina-HiSeq sequencing to recover the first completeMansonellagenus mitogenome and to identify several mitochondrial-origin pseudogenes. Mitogenome phylogenetic analysis placedM. ozzardiin the Onchocercidae “ONC5” clade and suggested thatMansonellaparasites are more closely related toWuchereriaandBrugiagenera parasites than they are toLoagenus parasites. DNA sequence alignments, BLAST searches and conceptual translations have been used to compliment phylogenetic analysis showing thatM. ozzardifrom the Amazon and Caribbean regions are near-identical and that previously reported PeruvianM. ozzardiCO1 reference sequences are probably of pseudogene origin. In addition to adding a much-needed resource to theMansonellagenus’s molecular tool-kit and providing evidence that someM. ozzardiCO1 sequence deposits are pseudogenes, our results suggest that all NeotropicalM. ozzardiparasites are closely related.
Detection of functional protein domains by unbiased genome-wide forward genetic screening
Authors: Herzog Mareike , Puddu Fabio , Coates Julia , Geisler Nicola , Forment Josep V. , Jackson Stephen P. 
Published: April 2018

AbstractEstablishing genetic and chemo-genetic interactions has played key roles in elucidating mechanisms by which certain chemicals perturb cellular functions. In contrast to gene disruption/depletion strategies to identify mechanisms of drug resistance, searching for point-mutational genetic suppressors that can identify separation- or gain-of-function mutations has been limited. Here, by demonstrating its utility in identifying chemical-genetic suppressors of sensitivity to the DNA topoisomerase I poison camptothecin or the poly(ADP-ribose) polymerase inhibitor olaparib, we detail an approach allowing systematic, large-scale detection of spontaneous or chemically-induced suppressor mutations in yeast or haploid mammalian cells in a short timeframe, and with potential applications in other haploid systems. In addition to applications in molecular biology research, this protocol can be used to identify drug targets and predict drug-resistance mechanisms. Mapping suppressor mutations on the primary or tertiary structures of protein suppressor hits provides insights into functionally relevant protein domains. Importantly, we show that olaparib resistance is linked to missense mutations in the DNA binding regions of PARP1, but not in its catalytic domain. This provides experimental support to the concept of PARP1 trapping on DNA as the prime source of toxicity to PARP inhibitors, and points to a novel olaparib resistance mechanism with potential therapeutic implications.
A Novel S100A8/A9 Induced Fingerprint of Mesenchymal Stem Cells associated with Enhanced Wound Healing
Authors: Basu Abhijit , Munir Saira , Mulaw Medanie A. , Singh Karmveer , Crisan Diana , Sindrilaru Anca , Treiber Nicolai , Wlaschek Meinhard , Huber-Lang Markus , Gebhard Florian , Scharffetter-Kochanek Karin 
Published: April 2018

AbstractWe here investigated whether the unique capacity of mesenchymal stem cells (MSCs) to re-establish tissue homeostasis depends on their potential to sense danger associated molecular pattern (DAMP) and to mount an adaptive response in the interest of tissue repair. Unexpectedly, after injection of MSCs which had been pretreated with the calcium-binding DAMP protein S100A8/A9 into murine full-thickness wounds, we observed a significant acceleration of healing even exceeding that of non-treated MSCs. This correlates with a fundamental reprogramming of the transcriptome in S100A8/A9 treated MSCs as deduced from RNA-seq analysis and its validation. A network of genes involved in proteolysis, macrophage phagocytosis, and inflammation control profoundly contribute to the clean-up of the wound site. In parallel, miR582-5p and genes boosting energy and encoding specific extracellular matrix proteins are reminiscent of scar-reduced tissue repair. This unprecedented finding holds substantial promise to refine current MSC-based therapies for difficult-to-treat wounds and fibrotic conditions.
Temporary sequestration of cholesterol and phosphatidylcholine within extracellular domains of ABCA1 during nascent HDL generation
Authors: Ishigami Masato , Ogasawara Fumihiko , Nagao Kohjiro , Hashimoto Hidehiko , Kimura Yasuhisa , Kioka Noriyuki , Ueda Kazumitsu 
Published: April 2018

AbstractThe quality and quantity of high-density lipoprotein (HDL) in blood plasma are important for preventing coronary artery disease. ATP-binding cassette protein A1 (ABCA1) and apolipoprotein A-I (apoA-I) play essential roles in nascent HDL formation, but controversy persists regarding the mechanism by which nascent HDL is generated. In the “direct loading model”, apoA-I acquires lipids directly from ABCA1 while it is bound to the transporter. By contrast, in the “indirect model”, apoA-I acquires lipids from the specific membrane domains created by ABCA1. In this study, we found that trypsin treatment causes rapid release of phosphatidylcholine (PC) and cholesterol from BHK/ABCA1 cells, and that the time course of lipid release coincides with those of trypsin digestion of extracellular domains (ECDs) of surface ABCA1 and of release of ECD fragments into the medium. This trypsin-dependent lipid release was dependent on ABCA1 ATPase activity, and did not occur in cells that express ABCG1, which exports lipids like ABCA1 but does not have large ECDs. These results suggest that the trypsin-sensitive sites on the cell surface are the large ECDs of ABCA1, and that lipids transported by ABCA1 are temporarily sequestered within the ECDs during nascent HDL formation.
Direct-write of free-form building blocks for artificial magnetic 3D lattices
Authors: Keller Lukas , Al Mamoori Mohanad K. I. , Pieper Jonathan , Gspan Christian , Stockem Irina , Schröder Christian , Barth Sven , Winkler Robert , Plank Harald , Pohlit Merlin , Müller Jens , Huth Michael 
Published: April 2018

AbstractBy the fabrication of periodically arranged nanomagnetic systems it is possible to engineer novel physical properties by realizing artificial lattice geometries that are not accessible via natural crystallization or chemical synthesis. This has been accomplished with great success in two dimensions in the fields of artificial spin ice and magnetic logic devices, to name just two. Although first proposals have been made to advance into three dimensions (3D), established nanofabrication pathways based on electron beam lithography have not been adapted to obtain free-form 3D nanostructures. Here we demonstrate the direct-write fabrication of freestanding ferromagnetic 3D nano-architectures. By employing micro-Hall sensing, we have determined the magnetic stray field generated by our free-form structures in an externally applied magnetic field and we have performed micromagnetic and macro-spin simulations to deduce the spatial magnetization profiles in the structures and analyze their switching behavior. Furthermore we show that the magnetic 3D elements can be combined with other 3D elements of different chemical composition and intrinsic material properties.
Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system
Authors: Kakimoto Yuriko , Tashiro Shinya , Kojima Rieko , Morozumi Yuki , Endo Toshiya , Tamura Yasushi 
Published: April 2018

AbstractFunctional integrity of eukaryotic organelles relies on direct physical contacts between distinct organelles. However, the entity of organelle-tethering factors is not well understood due to lack of means to analyze inter-organelle interactions in living cells. Here we evaluate the split-GFP system for visualizing organelle contact sites in vivo and show its advantages and disadvantages. We observed punctate GFP signals from the split-GFP fragments targeted to any pairs of organelles among the ER, mitochondria, peroxisomes, vacuole and lipid droplets in yeast cells, which suggests that these organelles form contact sites with multiple organelles simultaneously although it is difficult to rule out the possibilities that these organelle contacts sites are artificially formed by the irreversible associations of the split-GFP probes. Importantly, split-GFP signals in the overlapped regions of the ER and mitochondria were mainly co-localized with ERMES, an authentic ER-mitochondria tethering structure, suggesting that split-GFP assembly depends on the preexisting inter-organelle contact sites. We also confirmed that the split-GFP system can be applied to detection of the ER-mitochondria contact sites in HeLa cells. We thus propose that the split-GFP system is a potential tool to observe and analyze inter-organelle contact sites in living yeast and mammalian cells.
Automated fluid delivery from multiwell plates to microfluidic devices for high-throughput experiments and microscopy
Authors: Lagoy Ross C. , Albrecht Dirk R. 
Published: April 2018

AbstractHigh-throughput biological and chemical experiments typically use either multiwell plates or microfluidic devices to analyze numerous independent samples in a compact format. Multiwell plates are convenient for screening chemical libraries in static fluid environments, whereas microfluidic devices offer immense flexibility in flow control and dynamics. Interfacing these platforms in a simple and automated way would introduce new high-throughput experimental capabilities, such as compound screens with precise exposure timing. Whereas current approaches to integrate microfluidic devices with multiwell plates remain expensive or technically complicated, we present here a simple open-source robotic system that delivers liquids sequentially through a single connected inlet. We first characterized reliability and performance by automatically delivering 96 dye solutions to a microfluidic device. Next, we measured odor dose-response curves of in vivo neural activity from two sensory neuron types in dozens of living C. elegans in a single experiment. We then identified chemicals that suppressed optogenetically-evoked neural activity, demonstrating a functional screening platform for neural modulation in whole organisms. Lastly, we automated an 85-minute, ten-step cell staining protocol. Together, these examples show that our system can automate various protocols and accelerate experiments by economically bridging two common elements of high-throughput systems: multiwell plates and microfluidics.
Association of maternal serum 25-hydroxyvitamin D concentrations in second and third trimester with risk of macrosomia
Authors: Wen Juan , Kang Congli , Wang Jiaan , Cui Xianwei , Hong Qin , Wang Xingyun , Zhu Lijun , Xu Pengfei , Fu Ziyi , You Lianghui , Wang Xing , Ji Chenbo , Guo Xirong 
Published: April 2018

AbstractWhether the maternal vitamin D deficiency is associated with infant birth weight is still an argument. Here, we performed a nested case-control study (545 women who subsequently delivered infant with macrosomia and 1090 controls) to evaluate the association of the maternal serum 25-hydroxyvitamin D [25(OH)D] concentrations with risk of macrosomia. We measured the serum 25(OH)D concentrations by enzyme immunoassays. Logistic regression analysis, receiver-operator characteristic curve analysis and graphical nomogram were used for the statistical analyses. Among women who delivered infant with macrosomia, 71.2% of the women had serum 25(OH)D concentrations <50.0 nmol/L compared with 61.1% of the control women (P < 0.001). For women with concentrations <50.0 nmol/L, they had a 33% increased risk of macrosomia compared with women whose 25(OH)D ranged from 50.0 to 74.9 nmol/L. The risk of macrosomia was significantly increased with the decreasing concentrations of serum 25(OH)D in a dose-dependent manner (P for trend = 0.001). We also observed a threshold for 25(OH)D of 50.0 nmol/L for delivering infant with macrosomia and a predictive accuracy of the 25(OH)D concentrations included panel, with an area under the ROC curve of 0.712 for delivering infant with macrosomia. In conclusion, maternal serum 25(OH)D <50.0 nmol/L is associated with delivering a macrosomic infant, and vitamin D deficiency should be monitored in pregnant women.
Preoperative Red Cell Distribution Width and 30-day mortality in older patients undergoing non-cardiac surgery: a retrospective cohort observational study
Authors: Abdullah H. R. , Sim Y. E. , Sim Y. T. , Ang A. L. , Chan Y. H. , Richards T. , Ong B. C. 
Published: April 2018

AbstractIncreased red cell distribution width (RDW) is associated with poorer outcomes in various patient populations. We investigated the association between preoperative RDW and anaemia on 30-day postoperative mortality among elderly patients undergoing non-cardiac surgery. Medical records of 24,579 patients aged 65 and older who underwent surgery under anaesthesia between 1 January 2012 and 31 October 2016 were retrospectively analysed. Patients who died within 30 days had higher median RDW (15.0%) than those who were alive (13.4%). Based on multivariate logistic regression, in our cohort of elderly patients undergoing non-cardiac surgery, moderate/severe preoperative anaemia (aOR 1.61, p = 0.04) and high preoperative RDW levels in the 3rd quartile (>13.4% and ≤14.3%) and 4th quartile (>14.3%) were significantly associated with increased odds of 30-day mortality - (aOR 2.12, p = 0.02) and (aOR 2.85, p = 0.001) respectively, after adjusting for the effects of transfusion, surgical severity, priority of surgery, and comorbidities. Patients with high RDW, defined as >15.7% (90th centile), and preoperative anaemia have higher odds of 30-day mortality compared to patients with anaemia and normal RDW. Thus, preoperative RDW independently increases risk of 30-day postoperative mortality, and future risk stratification strategies should include RDW as a factor.
Information of Complex Systems and Applications in Agent Based Modeling
Authors: Bao Lei , Fritchman Joseph C. 
Published: April 2018

AbstractInformation about a system’s internal interactions is important to modeling the system’s dynamics. This study examines the finer categories of the information definition and explores the features of a type of local information that describes the internal interactions of a system. Based on the results, a dual-space agent and information modeling framework (AIM) is developed by explicitly distinguishing an information space from the material space. The two spaces can evolve both independently and interactively. The dual-space framework can provide new analytic methods for agent based models (ABMs). Three examples are presented including money distribution, individual’s economic evolution, and artificial stock market. The results are analyzed in the dual-space, which more clearly shows the interactions and evolutions within and between the information and material spaces. The outcomes demonstrate the wide-ranging applicability of using the dual-space AIMs to model and analyze a broad range of interactive and intelligent systems.
Crocodiles Alter Skin Color in Response to Environmental Color Conditions
Authors: Merchant Mark , Hale Amber , Brueggen Jen , Harbsmeier Curt , Adams Colette 
Published: April 2018

AbstractMany species alter skin color to varying degrees and by different mechanisms. Here, we show that some crocodylians modify skin coloration in response to changing light and environmental conditions. Within the Family, Crocodylidae, all members of the genus Crocodylus lightened substantially when transitioned from dark enclosure to white enclosures, whereas Mecistops and Osteolaemus showed little/no change. The two members of the Family Gavialidae showed an opposite response, lightening under darker conditions, while all member of the Family Alligatoridae showed no changes. Observed color changes were rapid and reversible, occurring within 60–90 minutes. The response is visually-mediated and modulated by serum α-melanocyte-stimulating hormone (α-MSH), resulting in redistribution of melanosomes within melanophores. Injection of crocodiles with α-MSH caused the skin to lighten. These results represent a novel description of color change in crocodylians, and have important phylogenetic implications. The data support the inclusion of the Malayan gharial in the Family Gavialidae, and the shift of the African slender-snouted crocodile from the genus Crocodylus to the monophyletic genus Mecistops.