bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
Authors: Schulze Stefan , Adams Zachary , Cerletti Micaela , De Castro Rosana , Ferreira-Cerca Sébastien , Fufezan Christian , Giménez María Inés , Hippler Michael , Jevtic Zivojin , Knüppel Robert , Legerme Georgio , Lenz Christof , Marchfelder Anita , Maupin-Furlow Julie , Paggi Roberto A. , Pfeiffer Friedhelm , Poetsch Ansgar , Urlaub Henning , Pohlschroder Mechthild 
Published: June 2020

AbstractWhile many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
A dietary fatty acid counteracts neuronal mechanical sensitization
Authors: Romero Luis O. , Caires Rebeca , Nickolls Alec R. , Chesler Alexander T. , Cordero-Morales Julio F. , Vásquez Valeria 
Published: June 2020

AbstractPIEZO2 is the essential transduction channel for touch discrimination, vibration, and proprioception. Mice and humans lacking Piezo2 experience severe mechanosensory and proprioceptive deficits and fail to develop tactile allodynia. Bradykinin, a proalgesic agent released during inflammation, potentiates PIEZO2 activity. Molecules that decrease PIEZO2 function could reduce heightened touch responses during inflammation. Here, we find that the dietary fatty acid margaric acid (MA) decreases PIEZO2 function in a dose-dependent manner. Chimera analyses demonstrate that the PIEZO2 beam is a key region tuning MA-mediated channel inhibition. MA reduces neuronal action potential firing elicited by mechanical stimuli in mice and rat neurons and counteracts PIEZO2 sensitization by bradykinin. Finally, we demonstrate that this saturated fatty acid decreases PIEZO2 currents in touch neurons derived from human induced pluripotent stem cells. Our findings report on a natural product that inhibits PIEZO2 function and counteracts neuronal mechanical sensitization and reveal a key region for channel inhibition.
Leucine regulates autophagy via acetylation of the mTORC1 component raptor
Authors: Son Sung Min , Park So Jung , Stamatakou Eleanna , Vicinanza Mariella , Menzies Fiona M. , Rubinsztein David C. 
Published: June 2020

AbstractMacroautophagy (“autophagy”) is the main lysosomal catabolic process that becomes activated under nutrient-depleted conditions, like amino acid (AA) starvation. The mechanistic target of rapamycin complex 1 (mTORC1) is a well-conserved negative regulator of autophagy. While leucine (Leu) is a critical mTORC1 regulator under AA-starved conditions, how Leu regulates autophagy is poorly understood. Here, we describe that in most cell types, including neurons, Leu negatively regulates autophagosome biogenesis via its metabolite, acetyl-coenzyme A (AcCoA). AcCoA inhibits autophagy by enhancing EP300-dependent acetylation of the mTORC1 component raptor, with consequent activation of mTORC1. Interestingly, in Leu deprivation conditions, the dominant effects on autophagy are mediated by decreased raptor acetylation causing mTORC1 inhibition, rather than by altered acetylation of other autophagy regulators. Thus, in most cell types we examined, Leu regulates autophagy via the impact of its metabolite AcCoA on mTORC1, suggesting that AcCoA and EP300 play pivotal roles in cell anabolism and catabolism.
Mutually stabilizing interactions between proto-peptides and RNA
Authors: Frenkel-Pinter Moran , Haynes Jay W. , Mohyeldin Ahmad M. , C Martin , Sargon Alyssa B. , Petrov Anton S. , Krishnamurthy Ramanarayanan , Hud Nicholas V. , Williams Loren Dean , Leman Luke J. 
Published: June 2020

AbstractThe close synergy between peptides and nucleic acids in current biology is suggestive of a functional co-evolution between the two polymers. Here we show that cationic proto-peptides (depsipeptides and polyesters), either produced as mixtures from plausibly prebiotic dry-down reactions or synthetically prepared in pure form, can engage in direct interactions with RNA resulting in mutual stabilization. Cationic proto-peptides significantly increase the thermal stability of folded RNA structures. In turn, RNA increases the lifetime of a depsipeptide by >30-fold. Proto-peptides containing the proteinaceous amino acids Lys, Arg, or His adjacent to backbone ester bonds generally promote RNA duplex thermal stability to a greater magnitude than do analogous sequences containing non-proteinaceous residues. Our findings support a model in which tightly-intertwined biological dependencies of RNA and protein reflect a long co-evolutionary history that began with rudimentary, mutually-stabilizing interactions at early stages of polypeptide and nucleic acid co-existence.
Dual-comb photoacoustic spectroscopy
Authors: Friedlein Jacob T. , Baumann Esther , Briggman Kimberly A. , Colacion Gabriel M. , Giorgetta Fabrizio R. , Goldfain Aaron M. , Herman Daniel I. , Hoenig Eli V. , Hwang Jeeseong , Newbury Nathan R. , Perez Edgar F. , Yung Christopher S. , Coddington Ian , Cossel Kevin C. 
Published: June 2020

AbstractSpectrally resolved photoacoustic imaging is promising for label-free imaging in optically scattering materials. However, this technique often requires acquisition of a separate image at each wavelength of interest. This reduces imaging speeds and causes errors if the sample changes in time between images acquired at different wavelengths. We demonstrate a solution to this problem by using dual-comb spectroscopy for photoacoustic measurements. This approach enables a photoacoustic measurement at thousands of wavelengths simultaneously. In this technique, two optical-frequency combs are interfered on a sample and the resulting pressure wave is measured with an ultrasound transducer. This acoustic signal is processed in the frequency-domain to obtain an optical absorption spectrum. For a proof-of-concept demonstration, we measure photoacoustic signals from polymer films. The absorption spectra obtained from these measurements agree with those measured using a spectrophotometer. Improving the signal-to-noise ratio of the dual-comb photoacoustic spectrometer could enable high-speed spectrally resolved photoacoustic imaging.
Direct observation of independently moving replisomes in Escherichia coli
Authors: Japaridze Aleksandre , Gogou Christos , Kerssemakers Jacob W. J. , Nguyen Huyen My , Dekker Cees 
Published: June 2020

AbstractThe replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move independently from the origin to the terminus of replication along each of the two arms of the circular chromosome, providing direct support for the so-called train-track model, and against a factory model for replisomes. The origin of replication duplicates near midcell, initially splitting to random directions and subsequently towards the poles. The probability of successful segregation of chromosomes significantly decreases with increasing cell width, indicating that chromosome confinement by the cell boundary is an important driver of DNA segregation. Our findings resolve long standing questions in bacterial chromosome organization.
Heterogeneously integrated flexible microwave amplifiers on a cellulose nanofibril substrate
Authors: Zhang Huilong , Li Jinghao , Liu Dong , Min Seunghwan , Chang Tzu-Hsuan , Xiong Kanglin , Park Sung Hyun , Kim Jisoo , Jung Yei Hwan , Park Jeongpil , Lee Juhwan , Han Jung , Katehi Linda , Cai Zhiyong , Gong Shaoqin , Ma Zhenqiang 
Published: June 2020

AbstractLow-cost flexible microwave circuits with compact size and light weight are highly desirable for flexible wireless communication and other miniaturized microwave systems. However, the prevalent studies on flexible microwave electronics have only focused on individual flexible microwave elements such as transistors, inductors, capacitors, and transmission lines. Thinning down supporting substrate of rigid chip-based monolithic microwave integrated circuits has been the only approach toward flexible microwave integrated circuits. Here, we report a flexible microwave integrated circuit strategy integrating membrane AlGaN/GaN high electron mobility transistor with passive impedance matching networks on cellulose nanofibril paper. The strategy enables a heterogeneously integrated and, to our knowledge, the first flexible microwave amplifier that can output 10 mW power beyond 5 GHz and can also be easily disposed of due to the use of cellulose nanofibril paper as the circuit substrate. The demonstration represents a critical step forward in realizing flexible wireless communication devices.
Dataset of segmented nuclei in hematoxylin and eosin stained histopathology images of ten cancer types
Authors: Hou Le , Gupta Rajarsi , Van Arnam John S. , Zhang Yuwei , Sivalenka Kaustubh , Samaras Dimitris , Kurc Tahsin M. , Saltz Joel H. 
Published: June 2020

AbstractThe distribution and appearance of nuclei are essential markers for the diagnosis and study of cancer. Despite the importance of nuclear morphology, there is a lack of large scale, accurate, publicly accessible nucleus segmentation data. To address this, we developed an analysis pipeline that segments nuclei in whole slide tissue images from multiple cancer types with a quality control process. We have generated nucleus segmentation results in 5,060 Whole Slide Tissue images from 10 cancer types in The Cancer Genome Atlas. One key component of our work is that we carried out a multi-level quality control process (WSI-level and image patch-level), to evaluate the quality of our segmentation results. The image patch-level quality control used manual segmentation ground truth data from 1,356 sampled image patches. The datasets we publish in this work consist of roughly 5 billion quality controlled nuclei from more than 5,060 TCGA WSIs from 10 different TCGA cancer types and 1,356 manually segmented TCGA image patches from the same 10 cancer types plus additional 4 cancer types.
Identification of a periodontal pathogen and bihormonal cells in pancreatic islets of humans and a mouse model of periodontitis
Authors: Ilievski Vladimir , Toth Peter T. , Valyi-Nagy Klara , Valyi-Nagy Tibor , Green Stefan J. , Marattil Rosann S. , Aljewari Haider W. , Wicksteed Barton , O’Brien-Simpson Neil M. , Reynolds Eric C. , Layden Brian T. , Unterman Terry G. , Watanabe Keiko 
Published: June 2020

AbstractResults from epidemiological and prospective studies indicate a close association between periodontitis and diabetes. However the mechanisms by which periodontal pathogens influence the development of prediabetes/diabetes are not clear. We previously reported that oral administration of a periodontal pathogen, Porphyromonas gingivalis (Pg) to WT mice results in insulin resistance, hyperinsulinemia, and glucose intolerance and that Pg translocates to the pancreas. In the current study, we determined the specific localization of Pg in relation to mouse and human pancreatic α- and β-cells using 3-D confocal and immunofluorescence microscopy and orthogonal analyses. Pg/gingipain is intra- or peri-nuclearly localized primarily in β-cells in experimental mice and also in human post-mortem pancreatic samples. We also identified bihormonal cells in experimental mice as well as human pancreatic samples. A low percentage of bihormonal cells has intracellular Pg in both humans and experimental mice. Our data show that the number of Pg translocated to the pancreas correlates with the number of bihormonal cells in both mice and humans. Our findings suggest that Pg/gingipain translocates to pancreas, particularly β-cells in both humans and mice, and this is strongly associated with emergence of bihormonal cells.
Compressive Sensing for Dynamic XRF Scanning
Authors: Kourousias George , Billè Fulvio , Borghes Roberto , Alborini Antonio , Sala Simone , Alberti Roberto , Gianoncelli Alessandra 
Published: June 2020

AbstractX-Ray Fluorescence (XRF) scanning is a widespread technique of high importance and impact since it provides chemical composition maps crucial for several scientific investigations. There are continuous requirements for larger, faster and highly resolved acquisitions in order to study complex structures. Among the scientific applications that benefit from it, some of them, such as wide scale brain imaging, are prohibitively difficult due to time constraints. However, typically the overall XRF imaging performance is improving through technological progress on XRF detectors and X-ray sources. This paper suggests an additional approach where XRF scanning is performed in a sparse way by skipping specific points or by varying dynamically acquisition time or other scan settings in a conditional manner. This paves the way for Compressive Sensing in XRF scans where data are acquired in a reduced manner allowing for challenging experiments, currently not feasible with the traditional scanning strategies. A series of different compressive sensing strategies for dynamic scans are presented here. A proof of principle experiment was performed at the TwinMic beamline of Elettra synchrotron. The outcome demonstrates the potential of Compressive Sensing for dynamic scans, suggesting its use in challenging scientific experiments while proposing a technical solution for beamline acquisition software.
The correlation between family relationships and brain activity within the reward circuit in adolescents with Internet gaming disorder
Authors: Hwang Hyunchan , Hong Jisun , Kim Sun Mi , Han Doug Hyun 
Published: June 2020

AbstractDisrupted reward circuits and diminished behavioural control have been suggested as the pathophysiologies of Internet gaming disorder (IGD). Family functioning is thought to play an important role in reward-related control. We hypothesized that adolescents with IGD show disrupted patterns of family relationships, which are associated with brain activity within the reward circuit. 42 adolescents with IGD without comorbidities and 41 healthy controls were assessed for family function and psychological states using the Korean Wechsler Intelligence Scale for Children (K-WISC), Korean version of DuPaul’s attention deficit hyperactivity disorder (ADHD) Rating Scale (K-ARS), Young Internet Addiction Scale (YIAS), Children’s Depression Inventory (CDI), Beck Anxiety Inventory (BAI), and the relationship domain of the Family Environmental Scale (FES-R). Brain activity was assessed via resting-state fMRI. Adolescents with IGD showed increased K-ARS, BAI, and YIAS scores, but decreased FES-R and FES-cohesion subscale scores; YIAS scores were negatively correlated with FES-R scores. Brain connectivity from the cingulate to the striatum was decreased, positively correlated with FES-R scores, and negatively correlated with IGD severity. Adolescents with IGD showed disrupted family relationships, which was associated with the severity of the disorder, and dis-connectivity within the reward circuit.
Dynamic Network Characteristics of Power-electronics-based Power Systems
Authors: Ji Yuxi , He Wei , Cheng Shijie , Kurths Jürgen , Zhan Meng 
Published: June 2020

AbstractPower flow studies in traditional power systems aim to uncover the stationary relationship between voltage amplitude and phase and active and reactive powers; they are important for both stationary and dynamic power system analysis. With the increasing penetration of large-scale power electronics devices including renewable generations interfaced with converters, the power systems become gradually power-electronics-dominant and correspondingly their dynamical behavior changes substantially. Due to the fast dynamics of converters, such as AC current controller, the quasi-stationary state approximation, which has been widely used in power systems, is no longer appropriate and should be reexamined. In this paper, for a better description of network characteristics, we develop a novel concept of dynamic power flow and uncover an explicit dynamic relation between the instantaneous powers and the voltage vectors. This mathematical relation has been well verified by simulations on transient analysis of a small power-electronics-based power system, and a small-signal frequency-domain stability analysis of a voltage source converter connected to an infinitely strong bus. These results demonstrate the applicability of the proposed method and shed an improved light on our understanding of power-electronics-dominant power systems, whose dynamical nature remains obscure.
Irritable bowel syndrome increases the risk of chronic obstructive pulmonary disease: A retrospective cohort study
Authors: Lai Hsiang-Chun , Lin Hung-Jen , Kao Yi-Wei , Wang Kai-Hsun , Chou Jen-Wei , Shia Ben-Chang , Huang Sheng-Teng 
Published: June 2020

AbstractBoth inflammation and infection are associated with the development of irritable bowel syndrome (IBS) and chronic obstructive pulmonary disease (COPD). The purpose of this study is to further elucidate the association between IBS and COPD through a retrospective cohort study. We enrolled IBS patients diagnosed between 2000 and 2011 with follow-up for at least one year. The non-IBS patients as comparison group were selected with 1:3 matching by propensity score. Statistical analysis was utilized to assess the differences in characteristic distribution, and to compare the cumulative incidence of COPD between the IBS and non-IBS cohorts. We selected 14,021 IBS patients and 42,068 non-IBS patients for comparison. The IBS patients exhibited a significant risk to develop COPD compared with non-IBS patients. Additionally, the cumulative incidence rate of COPD in the IBS cohort increased significantly during the follow-up period of more than ten years, compared to the non-IBS cohort, based on the Kaplan-Meier analysis. The risk of COPD was also significantly decreased in those patients with more than eighteen IBS-related clinical visits. This retrospective cohort study demonstrates the significantly increased risk of COPD in patients with IBS. Therefore, early inspection and prevention of COPD is essential for patients with IBS.
Relationship between the IL-1β serum concentration, mRNA levels and rs16944 genotype in the hyperglycemic normalization of T2D patients
Authors: Iglesias Molli Andrea Elena , Bergonzi María Fernanda , Spalvieri Mónica Paula , Linari María Amelia , Frechtel Gustavo Daniel , Cerrone Gloria Edith 
Published: June 2020

AbstractTo evaluate Interleukin 1-beta (IL-1β) serum and mononuclear leucocyte mRNA levels, also rs16944 (−511C/T) genotype, in relation to hyperglycemic normalization in Type 2 diabetes (T2D) patients, we recruited 30 individuals recently T2D diagnosed with hyperglycemia studied at basal time and after 6 and 12 months of the normalization treatment. At basal time, the T polymorphic allele of the rs16944 was associated with lower IL-1β mRNA expression (p = 0.006); and higher glucose level was positive correlated to IL-1β protein levels (p = 0.015). After treatment, the individuals showed a significant decrease in glucose level (p = 0.003), but they did not express significant changes in the IL-1β serum levels. Surprisingly, we observed that the greater decreases in glucose level were associated to increased IL-1β serum levels (p = 0.040). This is the first follow-up study evaluating IL-1β mRNA expression and serum levels in hyperglycemic T2D individuals and after glycemic normalization treatment. The current results contribute to the knowledge of the relationship between inflammation and glucose metabolism in T2D.
Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys
Authors: Mallott Elizabeth K. , Borries Carola , Koenig Andreas , Amato Katherine R. , Lu Amy 
Published: June 2020

AbstractStudies in multiple host species have shown that gut microbial diversity and composition change during pregnancy and lactation. However, the specific mechanisms underlying these shifts are not well understood. Here, we use longitudinal data from wild Phayre’s leaf monkeys to test the hypothesis that fluctuations in reproductive hormone concentrations contribute to gut microbial shifts during pregnancy. We described the microbial taxonomic composition of 91 fecal samples from 15 females (n = 16 cycling, n = 36 pregnant, n = 39 lactating) using 16S rRNA gene amplicon sequencing and assessed whether the resulting data were better explained by overall reproductive stage or by fecal estrogen (fE) and progesterone (fP) concentrations. Our results indicate that while overall reproductive stage affected gut microbiome composition, the observed patterns were driven by reproductive hormones. Females had lower gut microbial diversity during pregnancy and fP concentrations were negatively correlated with diversity. Additionally, fP concentrations predicted both unweighted and weighted UniFrac distances, while reproductive state only predicted unweighted UniFrac distances. Seasonality (rainfall and periods of phytoprogestin consumption) additionally influenced gut microbial diversity and composition. Our results indicate that reproductive hormones, specifically progestagens, contribute to the shifts in the gut microbiome during pregnancy and lactation.
Diversity and function of terpene synthases in the production of carrot aroma and flavor compounds
Authors: Muchlinski Andrew , Ibdah Mwafaq , Ellison Shelby , Yahyaa Mossab , Nawade Bhagwat , Laliberte Suzanne , Senalik Douglas , Simon Philipp , Whitehead Susan R. , Tholl Dorothea 
Published: June 2020

AbstractCarrot (Daucus carota L.) is an important root vegetable crop with high nutritional value, characteristic flavor, and benefits to human health. D. carota tissues produce an essential oil that is rich in volatile terpenes and plays a major role in carrot aroma and flavor. Although terpene composition represents a critical quality attribute of carrots, little is known about the biosynthesis of terpenes in this crop. Here, we functionally characterized 19 terpene synthase (TPS) genes in an orange carrot (genotype DH1) and compared tissue-specific expression profiles and in vitro products of their recombinant proteins with volatile terpene profiles from DH1 and four other colored carrot genotypes. In addition to the previously reported (E)-β-caryophyllene synthase (DcTPS01), we biochemically characterized several TPS proteins with direct correlations to major compounds of carrot flavor and aroma including germacrene D (DcTPS7/11), γ-terpinene (DcTPS30) and α-terpinolene (DcTPS03). Random forest analysis of volatiles from colored carrot cultivars identified nine terpenes that were clearly distinct among the cultivars and likely contribute to differences in sensory quality. Correlation of TPS gene expression and terpene metabolite profiles supported the function of DcTPS01 and DcTPS03 in these cultivars. Our findings provide a roadmap for future breeding efforts to enhance carrot flavor and aroma.