bluuebunny/crossref_metadata_2025 huggingface dataset:
An automated skin segmentation of Breasts in Dynamic Contrast-Enhanced Magnetic Resonance Imaging
Authors: Lee Chia-Yen , Chang Tzu-Fang , Chang Nai-Yun , Chang Yeun-Chung
Published: April 2018

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is used to diagnose breast disease. Obtaining anatomical information from DCE-MRI requires the skin be manually removed so that blood vessels and tumors can be clearly observed by physicians and radiologists; this requires considerable manpower and time. We develop an automated skin segmentation algorithm where the surface skin is removed rapidly and correctly. The rough skin area is segmented by the active contour model, and analyzed in segments according to the continuity of the skin thickness for accuracy. Blood vessels and mammary glands are retained, which remedies the defect of removing some blood vessels in active contours. After three-dimensional imaging, the DCE-MRIs without the skin can be used to see internal anatomical information for clinical applications. The research showed the Dice’s coefficients of the 3D reconstructed images using the proposed algorithm and the active contour model for removing skins are 93.2% and 61.4%, respectively. The time performance of segmenting skins automatically is about 165 times faster than manually. The texture information of the tumors position with/without the skin is compared by the paired t-test yielded all p < 0.05, which suggested the proposed algorithm may enhance observability of tumors at the significance level of 0.05.
Author Correction: Natural Erosion of Sandstone as Shape Optimisation
Authors: Ostanin Igor , Safonov Alexander , Oseledets Ivan
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: Shape evolution of ooids: a geometric model
Authors: Sipos András A. , Domokos Gábor , Jerolmack Douglas J.
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: The effect of foreign language in fear acquisition
Authors: García-Palacios Azucena , Costa Albert , Castilla Diana , del Río Eva , Casaponsa Aina , Duñabeitia Jon Andoni
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation
Authors: Rehman Hafiz Mamoon , Nawaz Muhammad Amjad , Shah Zahid Hussain , Ludwig-Müller Jutta , Chung Gyuhwa , Ahmad Muhammad Qadir , Yang Seung Hwan , Lee Soo In
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
Author Correction: Transitions from Ideal to Intermediate Cholesterol Levels may vary by Cholesterol Metric
Authors: Engeda Joseph C. , Holliday Katelyn M. , Hardy Shakia T. , Chakladar Sujatro , Lin Dan-Yu , Talavera Gregory A. , Howard Barbara V. , Daviglus Martha L. , Pirzada Amber , Schreiner Pamela J. , Zeng Donglin , Avery Christy L.
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper
Publisher Correction: Feed gas effect on plasma inactivation mechanism of Salmonella Typhimurium in onion and quality assessment of the treated sample
Authors: Khan Muhammad Saiful Islam , Lee Eun-Jung , Hong Seok-In , Kim Yun-Ji
Published: April 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Measurement of metabolite variations and analysis of related gene expression in Chinese liquorice (Glycyrrhiza uralensis) plants under UV-B irradiation
Authors: Zhang Xiao , Ding Xiaoli , Ji Yaxi , Wang Shouchuang , Chen Yingying , Luo Jie , Shen Yingbai , Peng Li
Published: April 2018

Plants respond to UV-B irradiation (280–315 nm wavelength) via elaborate metabolic regulatory mechanisms that help them adapt to this stress. To investigate the metabolic response of the medicinal herb Chinese liquorice (Glycyrrhiza uralensis) to UV-B irradiation, we performed liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomic analysis, combined with analysis of differentially expressed genes in the leaves of plants exposed to UV-B irradiation at various time points. Fifty-four metabolites, primarily amino acids and flavonoids, exhibited changes in levels after the UV-B treatment. The amino acid metabolism was altered by UV-B irradiation: the Asp family pathway was activated and closely correlated to Glu. Some amino acids appeared to be converted into antioxidants such as γ-aminobutyric acid and glutathione. Hierarchical clustering analysis revealed that various flavonoids with characteristic groups were induced by UV-B. In particular, the levels of some ortho-dihydroxylated B-ring flavonoids, which might function as scavengers of reactive oxygen species, increased in response to UV-B treatment. In general, unigenes encoding key enzymes involved in amino acid metabolism and flavonoid biosynthesis were upregulated by UV-B irradiation. These findings lay the foundation for further analysis of the mechanism underlying the response of G. uralensis to UV-B irradiation.
Chromobacterium spp. mediate their anti-Plasmodium activity through secretion of the histone deacetylase inhibitor romidepsin
Authors: Saraiva Raúl G. , Huitt-Roehl Callie R. , Tripathi Abhai , Cheng Yi-Qiang , Bosch Jürgen , Townsend Craig A. , Dimopoulos George
Published: April 2018

The Chromobacterium sp. Panama bacterium has in vivo and in vitro anti-Plasmodium properties. To assess the nature of the Chromobacterium-produced anti-Plasmodium factors, chemical partition was conducted by bioassay-guided fractionation where different fractions were assayed for activity against asexual stages of P. falciparum. The isolated compounds were further partitioned by reversed-phase FPLC followed by size-exclusion chromatography; high resolution UPLC and ESI/MS data were then collected and revealed that the most active fraction contained a cyclic depsipeptide, which was identified as romidepsin. A pure sample of this FDA-approved HDAC inhibitor allowed us to independently verify this finding, and establish that romidepsin also has potent effect against mosquito stages of the parasite’s life cycle. Genomic comparisons between C. sp. Panama and multiple species within the Chromobacterium genus further demonstrated a correlation between presence of the gene cluster responsible for romidepsin production and effective antiplasmodial activity. A romidepsin-null Chromobacterium spp. mutant loses its anti-Plasmodium properties by losing the ability to inhibit P. falciparum HDAC activity, and romidepsin is active against resistant parasites to commonly deployed antimalarials. This independent mode of action substantiates exploring a chromobacteria-based approach for malaria transmission-blocking.
Acoustic fine structure may encode biologically relevant information for zebra finches
Authors: Prior Nora H. , Smith Edward , Lawson Shelby , Ball Gregory F. , Dooling Robert J.
Published: April 2018

The ability to discriminate changes in the fine structure of complex sounds is well developed in birds. However, the precise limit of this discrimination ability and how it is used in the context of natural communication remains unclear. Here we describe natural variability in acoustic fine structure of male and female zebra finch calls. Results from psychoacoustic experiments demonstrate that zebra finches are able to discriminate extremely small differences in fine structure, which are on the order of the variation in acoustic fine structure that is present in their vocal signals. Results from signal analysis methods also suggest that acoustic fine structure may carry information that distinguishes between biologically relevant categories including sex, call type and individual identity. Combined, our results are consistent with the hypothesis that zebra finches can encode biologically relevant information within the fine structure of their calls. This study provides a foundation for our understanding of how acoustic fine structure may be involved in animal communication.
A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer
Authors: Wang QuanQiu , Li Li , Xu Rong
Published: April 2018

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths. It is estimated that about half the cases of CRC occurring today are preventable. Recent studies showed that human gut microbiota and their collective metabolic outputs play important roles in CRC. However, the mechanisms by which human gut microbial metabolites interact with host genetics in contributing CRC remain largely unknown. We hypothesize that computational approaches that integrate and analyze vast amounts of publicly available biomedical data have great potential in better understanding how human gut microbial metabolites are mechanistically involved in CRC. Leveraging vast amount of publicly available data, we developed a computational algorithm to predict human gut microbial metabolites for CRC. We validated the prediction algorithm by showing that previously known CRC-associated gut microbial metabolites ranked highly (mean ranking: top 10.52%; median ranking: 6.29%; p-value: 3.85E-16). Moreover, we identified new gut microbial metabolites likely associated with CRC. Through computational analysis, we propose potential roles for tartaric acid, the top one ranked metabolite, in CRC etiology. In summary, our data-driven computation-based study generated a large amount of associations that could serve as a starting point for further experiments to refute or validate these microbial metabolite associations in CRC cancer.
Detecting liver fibrosis with Gd-EOB-DTPA-enhanced MRI: A confirmatory study
Authors: Verloh Niklas , Utpatel Kirsten , Haimerl Michael , Zeman Florian , Beyer Lukas , Fellner Claudia , Brennfleck Frank , Dahlke Marc H , Stroszczynski Christian , Evert Matthias , Wiggermann Philipp
Published: April 2018

Strong correlations between the grade of fibrosis and cirrhosis, classified using the Ishak scoring system, and the uptake characteristics of Gd-EOB-DTPA with the relative enhancement (RE) of the liver parenchyma have been reported. To confirm the results of a retrospective analysis, patients undergoing liver surgery were prospectively examined with Gd-EOB-DTPA-enhanced liver 3 Tesla MRI to determine the degree of liver fibrosis. Correlations between the grade of fibrosis and cirrhosis, classified using the Ishak scoring system, and RE were investigated and compared with those derived from an initial retrospective study. After validating the cut-off values in the retrospective study (Ishak ≥ 1, RE-cut-off 0.90; Ishak ≥ 2, RE-cut-off 0.79; Ishak ≥ 4, RE-cut-off 0.60; and Ishak = 6, RE-cut-off 0.47), we showed that Gd-EOB-DTPA has a high sensitivity (≥86%) and a high positive predictive value (≥86%). These results support the use of Gd-EOB-DTPA-enhanced liver MRI as a non-invasive method for determining the degree of liver fibrosis and cirrhosis.
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

Fecal 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

The 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

We 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

To 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

Despite 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

Establishing 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

We 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

The 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

By 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

Functional 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

High-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

Whether 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

Increased 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

Information 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

Many 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.
The mechanism of short-term monocular deprivation is not simple: separate effects on parallel and cross-oriented dichoptic masking
Authors: Baldwin Alex S. , Hess Robert F.
Published: April 2018

Short-term deprivation of the input to one eye increases the strength of its influence on visual perception. This effect was first demonstrated using a binocular rivalry task. Incompatible stimuli are shown to the two eyes, and their competition for perceptual dominance is then measured. Further studies used a combination task, which measures the contribution of each eye to a fused percept. Both tasks show an effect of deprivation, but there have been inconsistencies between them. This suggests that the deprivation causes multiple effects. We used dichoptic masking to explore this possibility. We measured the contrast threshold for detecting a grating stimulus presented to the target eye. Thresholds were elevated when a parallel or cross-oriented grating mask was presented to the other eye. This masking effect was reduced by depriving the target eye for 150 minutes. We tested fourteen subjects with normal vision, and found individual differences in the magnitude of this reduction. Comparing the reduction found in each subject between the two masks (parallel vs. cross-oriented), we found no correlation. This indicates that there is not a single underlying effect of short-term monocular deprivation. Instead there are separate effects which can have different dependencies, and be probed by different tasks.
Extramitochondrial Assembly of Mitochondrial Targeting Signal Disrupted Mitochondrial Enzyme Aldehyde Dehydrogenase
Authors: Noree Chalongrat
Published: April 2018

Supramolecular assembly of metabolic enzymes has been studied both in vivo and in vitro for nearly a decade. Experimental evidence has suggested a close relationship between enzymatic activity and enzyme assembly/disassembly. However, most cases were studied with the cytosolic enzymes. Here, I report the evidence for a mitochondrial enzyme with its ability in forming visible intracellular structures. By removing the mitochondrial targeting sequence, yeast mitochondrial enzyme aldehyde dehydrogenase (Ald4p) exhibits reversible supramolecular assembly in the cytoplasm, thus creating a useful system for further characterization of the regulatory factors that modulate the assembly/disassembly of this mitochondrial enzyme.
Transient adhesion in a non-fully detached contact
Authors: Liu Zheyu , Lu Hongyu , Zheng Yelong , Tao Dashuai , Meng Yonggang , Tian Yu
Published: April 2018

Continuous approaching and detaching displacement usually occurs in an adhesion test. Here, we found a transient adhesion force at the end of a non-fully detached contact. This force occurred when the nominal detaching displacement was less than the traditional quasi-static theory predicted zero force point. The transient adhesion force was ascribed to interfacial adhesion hysteresis, which was caused by the cracking process of the contact and the deformation competition between the sphere and supporting spring. Results indicated that the testing of adhesion can be significantly affected by different combinations of stiffnesses of the contact objects and the supporting spring cantilever. This combination should be carefully designed in an adhesion test. All these results enabled increased understanding of the nature of adhesion and can guide the design of adhesive actuators.
Heterogeneity Analysis and Diagnosis of Complex Diseases Based on Deep Learning Method
Authors: Li Xiong , Liu Liyue , Zhou Juan , Wang Che
Published: April 2018

Understanding genetic mechanism of complex diseases is a serious challenge. Existing methods often neglect the heterogeneity phenomenon of complex diseases, resulting in lack of power or low reproducibility. Addressing heterogeneity when detecting epistatic single nucleotide polymorphisms (SNPs) can enhance the power of association studies and improve prediction performance of complex diseases diagnosis. In this study, we propose a three-stage framework including epistasis detection, clustering and prediction to address both epistasis and heterogeneity of complex diseases based on deep learning method. The epistasis detection stage applies a multi-objective optimization method to find several candidate sets of epistatic SNPs which contribute to different subtypes of complex diseases. Then, a K-means clustering algorithm is used to define subtypes of the case group. Finally, a deep learning model has been trained for disease prediction based on graphics processing unit (GPU). Experimental results on pure and heterogeneous datasets show that our method has potential practicality and can serve as a possible alternative to other methods. Therefore, when epistasis and heterogeneity exist at the same time, our method is especially suitable for diagnosis of complex diseases.
The salience of self, not social pain, is encoded by dorsal anterior cingulate and insula
Authors: Perini Irene , Gustafsson Per A. , Hamilton J. Paul , Kämpe Robin , Zetterqvist Maria , Heilig Markus
Published: April 2018

The human neural correlates of social rejection have attracted significant research interest, but remain subject to vigorous debate. Specifically, it has been proposed that a matrix of brain regions overlapping with the classical pain matrix, and including the dorsal anterior cingulate cortex (dACC) and the anterior insular cortex (AI) is critical for processing of social rejection. The present study expands on this conceptualization, by showing that these areas are involved in processing of self-relevant social evaluation, irrespective of valence. Forty healthy adolescents (N = 20 females) were tested in a magnetic resonance imaging (MRI) scanner. We used a novel paradigm that balanced participants’ experience of rejection and acceptance. In addition, the paradigm also controlled for whether the social judgment was towards the participants or towards other fictitious players. By creating a “self” and “other” distinction, we show that right AI and dACC are involved in processing the salience of being judged by others, irrespective of the quality of this judgment. This finding supports the idea that these regions are not specific to social rejection or even to pain or metaphorically painful experiences, but activate to self-relevant, highly salient information.
Acetylcholine and necroptosis are players in follicular development in primates
Authors: Du Yongrui , Bagnjuk Konstantin , Lawson Maralee S. , Xu Jing , Mayerhofer Artur
Published: April 2018

Acetylcholine (ACh) in the ovary and its actions were linked to survival of human granulosa cells in vitro and improved fertility of rats in vivo. These effects were observed upon experimental blockage of the ACh-degrading enzyme (ACH esterase; ACHE), by Huperzine A. We now studied actions of Huperzine A in a three-dimensional culture of macaque follicles. Because a form of programmed necrotic cell death, necroptosis, was previously identified in human granulosa cells in vitro, we also studied actions of necrostatin-1 (necroptosis inhibitor). Blocking the breakdown of ACh by inhibiting ACHE, or interfering with necroptosis, did not improve the overall follicle survival, but promoted the growth of macaque follicles from the secondary to the small antral stage in vitro, which was correlated with oocyte development. The results from this translational model imply that ovarian function and fertility in primates may be improved by pharmacological interference with ACHE actions and necroptosis.
Highly selective and sensitive optical probe for Fe3+ based on a water-soluble squarylium dye
Authors: Xu Zongguang , Jiang Mengying , Zhang Chen , Mei Jinfeng , Li Zhongyu , Xu Song , Wang Liping
Published: April 2018

A highly selective and sensitive water-soluble optical probe based on a squarylium dye, 2,3,3-trimethyl-3H-indolenine-5-sulfonate squaraine (SQ) has been successfully synthesized.
Bio-guided isolation of plant growth regulators from allelopathic plant-Codonopsis pilosula: phyto-selective activities and mechanisms
Authors: Xie Min , Liu Jingkun , Yan Zhiqiang , Li Xiuzhuang , Yang Xiaoyan , Jin Hui , Su Anxiang , Qin Bo
Published: April 2018

Bio-guided isolation of the aerial waste part of typical allelopathic plant-Codonopsis pilosulaled to six active compounds being produced.
Performance evaluation of zero-valent iron nanoparticles (NZVI) for high-concentration H2S removal from biogas at different temperatures
Authors: Su Lianghu , Liu Chenwei , Liang Kangkang , Chen Yudong , Zhang Longjiang , Li Xiaolin , Han Zhihua , Zhen Guangyin , Chai Xiaoli , Sun Xu
Published: April 2018

Performances of zero-valent iron nanoparticles for high-concentration H2S removal from biogas at different temperatures were evaluated.
Dense and thin 13X membranes on porous α-Al2O3 tubes: preparation, structure and deep purification of oxygenated compounds from gaseous olefin flow
Authors: Zhou Yongxian , Chen Wei , Wang Pengfei , Zhang Yimin
Published: April 2018

Dense and thin 13X molecular sieve membranes on porous α-Al2O3 tubes were successfully fabricated by a combination of 3-aminopropyl triethoxy silane surface modification and vacuum pre-coating sol for purifying trace oxygenated compounds from gaseous olefins.
Giant magnetic coercivity in Fe3C-filled carbon nanotubes
Authors: Liu Dan , Zhu Jie , Ivaturi Sameera , He Yi , Wang Shanling , Wang Jiayu , Zhang Sijie , Willis Maureen A. C. , Boi Filippo S.
Published: April 2018

One of the major challenges in the synthesis of ferromagnetically filled carbon nanotubes (CNTs) is the achievement of high coercivities. Here we report an anomalously high coercivity observed in Fe3C filled CNTs.
Effects of surface roughness on the self-diffusion dynamics of a single polymer
Authors: Li Jiaxiang , Ding Mingming , Zhang Ran , Shi Tongfei
Published: April 2018

We employ molecular dynamics simulations to simulate the diffusion dynamics of a single polymer adsorbed on surfaces with different roughnesses, which are characterized by the separation distance between obstacles and the height of obstacles.
A fluorescence and colorimetric dual-mode assay of alkaline phosphatase activity via destroying oxidase-like CoOOH nanoflakes
Authors: Liu Shi Gang , Han Lei , Li Na , Xiao Na , Ju Yan Jun , Li Nian Bing , Luo Hong Qun
Published: April 2018

A fluorescence and colorimetric dual-mode assay of alkaline phosphatase activity was developed using a CoOOH nanoflake/o-phenylenediamine (OPD) sensing system.
A sensitive electrochemical sensor for ofloxacin based on a graphene/zinc oxide composite film
Authors: Si Xiaojing , Wei Youli , Wang Chaolin , Li Li , Ding Yaping
Published: April 2018

Herein, a facile and novel preparation strategy based on electrochemical techniques for the fabrication of an electrodeposited graphene (GR) and zinc oxide (ZnO) nanocomposite-modified electrode (ZnO/GR/GCE) was developed to determine ofloxacin.
Driving dimethyl carbonate synthesis from CO2 and methanol and production of acetylene simultaneously using CaC2
Authors: Zhang Zhaofu , Liu Shuaishuai , Zhang Lujun , Yin Shuai , Yang Guanying , Han Buxing
Published: April 2018

The synthesis of dimethyl carbonate (DMC) from CO2 and methanol is a very interesting reaction, but is thermodynamically limited.
Decorating an individual living cell with a shell of controllable thickness by cytocompatible surface initiated graft polymerization
Authors: Wang Guan , Zhang Kai , Wang Yindian , Zhao Changwen , He Bin , Ma Yuhong , Yang Wantai
Published: April 2018

A polymeric shell of controllable-thickness was synthesized on a living yeast cell by visible light-induced graft polymerization.
Strategies toward realization of unsupported transition metal–boron donor–acceptor complexes: an insight from theory
Authors: Borthakur Bitupon , Das Sandeep , Phukan Ashwini K.
Published: April 2018

Pre-pyramidalization of the boron center is found to be a necessary condition for the realization of unsupported metal–boron dative bond.
Structure, magnetic and optical properties of Sr3RE2(Ge3O9)2 cyclogermanates (RE = La–Gd)
Authors: Chufarov Alexander Yu. , Lipina Olga A. , Surat Ludmila L. , Melkozerova Marina A. , Baklanova Yana V. , Enyashin Andrey N. , Tyutyunnik Alexander P. , Kellerman Dina G. , Zubkov Vladimir G.
Published: April 2018

A new group of cyclogermanates has been characterized using XRD, DFT calculations, photoluminescence spectroscopy and magnetic study.
Novel carbon polymorphs with cumulative double bonds in three-dimensional sp–sp2 hybrid framework
Authors: Liu Lingyu , Hu Meng , Liu Chao , Liang Xiaowei , Pan Yilong , Ying Pan , Zhao Zhisheng , Gao Guoying , He Julong , Tian Yongjun
Published: April 2018

Two new three-dimensional microporous carbon allotropes consisting of whorl chains connected by cumulative double bonds in a sp–sp2 hybrid framework have been proposed in this study.