bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-Depth Characterization of Monocyte-Derived Macrophages using a Mass Cytometry-Based Phagocytosis Assay
Authors: Schulz Daniel , Severin Yannik , Zanotelli Vito Riccardo Tomaso , Bodenmiller Bernd 
Published: February 2019

AbstractPhagocytosis is a process in which target cells or particles are engulfed and taken up by other cells, typically professional phagocytes; this process is crucial in many physiological processes and disease states. The detection of targets for phagocytosis is directed by a complex repertoire of cell surface receptors. Pattern recognition receptors directly detect targets for binding and uptake, while opsonic and complement receptors detect objects coated by soluble factors. However, the importance of single and combinatorial surface marker expression across different phenotypes of professional phagocytes is not known. Here we developed a novel mass cytometry-based phagocytosis assay that enables the simultaneous detection of phagocytic events in combination with up to 40 other protein markers. We applied this assay to distinct monocyte derived macrophage (MDM) populations and found that prototypic M2-like MDMs phagocytose more E. coli than M1-like MDMs. Surface markers such as CD14, CD206, and CD163 rendered macrophages phagocytosis competent, but only CD209 directly correlated with the amount of particle uptake. Similarly, M2-like MDMs also phagocytosed more cancer cells than M1-like MDMs but, unlike M1-like MDMs, were insensitive to anti-CD47 opsonization. Our approach facilitates the simultaneous study of single-cell phenotypes, phagocytic activity, signaling and transcriptional events in complex cell mixtures.
Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
Authors: Luedin Samuel M. , Liechti Nicole , Cox Raymond P. , Danza Francesco , Frigaard Niels-Ulrik , Posth Nicole R. , Pothier Joël F. , Roman Samuele , Storelli Nicola , Wittwer Matthias , Tonolla Mauro 
Published: February 2019

AbstractBlooms of purple sulfur bacteria (PSB) are important drivers of the global sulfur cycling oxidizing reduced sulfur in intertidal flats and stagnant water bodies. Since the discovery of PSB Chromatium okenii in 1838, it has been found that this species is characteristic of for stratified, sulfidic environments worldwide and its autotrophic metabolism has been studied in depth since. We describe here the first high-quality draft genome of a large-celled, phototrophic, γ-proteobacteria of the genus Chromatium isolated from the stratified alpine Lake Cadagno, C. okenii strain LaCa. Long read technology was used to assemble the 3.78 Mb genome that encodes 3,016 protein-coding genes and 67 RNA genes. Our findings are discussed from an ecological perspective related to Lake Cadagno. Moreover, findings of previous studies on the phototrophic and the proposed chemoautotrophic metabolism of C. okenii were confirmed on a genomic level. We additionally compared the C. okenii genome with other genomes of sequenced, phototrophic sulfur bacteria from the same environment. We found that biological functions involved in chemotaxis, movement and S-layer-proteins were enriched in strain LaCa. We describe these features as possible adaptions of strain LaCa to rapidly changing environmental conditions within the chemocline and the protection against phage infection during blooms. The high quality draft genome of C. okenii strain LaCa thereby provides a basis for future functional research on bioconvection and phage infection dynamics of blooming PSB.
Antimicrobial and inflammatory properties of South African clinical Lactobacillus isolates and vaginal probiotics
Authors: Chetwin Emily , Manhanzva Monalisa T. , Abrahams Andrea G. , Froissart Remy , Gamieldien Hoyam , Jaspan Heather , Jaumdally Shameem Z. , Barnabas Shaun L. , Dabee Smritee , Happel Anna-Ursula , Bowers Desiree , Davids Lester , Passmore Jo-Ann S. , Masson Lindi 
Published: February 2019

AbstractBacterial vaginosis (BV) causes genital inflammation and increased HIV acquisition risk. The standard-of-care for BV, antibiotic therapy, is associated with high recurrence rates. Probiotics may improve treatment outcomes, although substantial heterogeneity in efficacy has been observed during clinical trials. To evaluate the potential to improve existing probiotics, we compared the inflammatory and antimicrobial (adhesion, H2O2, D-lactate and L-lactate production) characteristics of 23 vaginal Lactobacillus isolates from South African women, commercial vaginal probiotics (L. casei rhamnosus, L. acidophilus) and 4 reference strains. All lactobacilli induced inflammatory cytokine production by genital epithelial cells and produced D-lactate. Of six isolates assessed, five suppressed inflammatory responses to Gardnerella vaginalis. Although the L. acidophilus probiotic was the most adherent, many clinical isolates produced greater amounts of H2O2, D-lactate and L-lactate than the probiotics. The most L-lactate and H2O2 were produced by L. jensenii (adjusted p = 0.0091) and L. mucosae (adjusted p = 0.0308) species, respectively. According to the characteristics evaluated, the top 10 isolates included 4 L. jensenii, 2 L. crispatus, 1 L. mucosae, 1 L. vaginalis and the L. acidophilus probiotic. There is potential to develop an improved vaginal probiotic using clinical Lactobacillus isolates. Inflammatory profiles are critical to evaluate as some isolates induced substantial cytokine production.
DNA demethylation is associated with malignant progression of lower-grade gliomas
Authors: Nomura Masashi , Saito Kuniaki , Aihara Koki , Nagae Genta , Yamamoto Shogo , Tatsuno Kenji , Ueda Hiroki , Fukuda Shiro , Umeda Takayoshi , Tanaka Shota , Takayanagi Shunsaku , Otani Ryohei , Nejo Takahide , Hana Taijun , Takahashi Satoshi , Kitagawa Yosuke , Omata Mayu , Higuchi Fumi , Nakamura Taishi , Muragaki Yoshihiro , Narita Yoshitaka , Nagane Motoo , Nishikawa Ryo , Ueki Keisuke , Saito Nobuhito , Aburatani Hiroyuki , Mukasa Akitake 
Published: February 2019

AbstractTo elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively. This cohort included 24 matched pairs of initial lower-grade gliomas and recurrent tumors, most of which showed malignant progression. Nearly half of IDH-mutant glioblastomas that had progressed from lower-grade gliomas exhibited characteristic partial DNA demethylation in previously methylated genomic regions of their corresponding initial tumors, which had the glioma CpG island methylator phenotype (G-CIMP). In these glioblastomas, cell cycle-related genes, RB and PI3K-AKT pathway genes were frequently altered. Notably, late-replicating domain was significantly enriched in the demethylated regions that were mostly located in non-regulatory regions, suggesting that the loss of DNA methylation during malignant transformation may involve mainly passive demethylation due to a delay in maintenance of methylation during accelerated cell division. Nonetheless, a limited number of genes including IGF2BP3, which potentially drives cell proliferation, were presumed to be upregulated due to demethylation of their promoter. Our data indicated that demethylation of the G-CIMP profile found in a subset of recurrent gliomas reflects accelerated cell divisions accompanied by malignant transformation. Oncogenic genes activated by such epigenetic change represent potential therapeutic targets.
Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth
Authors: Yheskel Matanel , Lakhia Ronak , Cobo-Stark Patricia , Flaten Andrea , Patel Vishal 
Published: February 2019

AbstractAutosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of renal failure. We have recently shown that inhibiting miR-17~92 is a potential novel therapeutic approach for ADPKD. However, miR-17~92 is a polycistronic cluster that encodes microRNAs (miRNAs) belonging to the miR-17, miR-18, miR-19 and miR-25 families, and the relative pathogenic contribution of these miRNA families to ADPKD progression is unknown. Here we performed an in vivo anti-miR screen to identify the miRNA drug targets within the miR-17~92 miRNA cluster. We designed anti-miRs to individually inhibit miR-17, miR-18, miR-19 or miR-25 families in an orthologous ADPKD model. Treatment with anti-miRs against the miR-17 family reduced cyst proliferation, kidney-weight-to-body-weight ratio and cyst index. In contrast, treatment with anti-miRs against the miR-18, 19, or 25 families did not affect cyst growth. Anti-miR-17 treatment recapitulated the gene expression pattern observed after miR-17~92 genetic deletion and was associated with upregulation of mitochondrial metabolism, suppression of the mTOR pathway, and inhibition of cyst-associated inflammation. Our results argue against functional cooperation between the various miR-17~92 cluster families in promoting cyst growth, and instead point to miR-17 family as the primary therapeutic target for ADPKD.
Deletion of BSG1 in Chlamydomonas reinhardtii leads to abnormal starch granule size and morphology
Authors: Findinier Justin , Laurent Sylvain , Duchêne Thierry , Roussel Xavier , Lancelon-Pin Christine , Cuiné Stéphan , Putaux Jean-Luc , Li-Beisson Yonghua , D’Hulst Christophe , Wattebled Fabrice , Dauvillée David 
Published: February 2019

AbstractChlamydomonas reinhardtii represents an ideal model microbial system to decipher starch metabolism. In this green algae, in cells growing in photosynthetic conditions, starch mainly accumulates as a sheath surrounding the pyrenoid while in cells subjected to a nutrient starvation, numerous starch granules are filling up the plastid stroma. The mechanisms underlying and regulating this switch from photosynthetic to storage starch metabolisms are not known. In this work, we have isolated a Chlamydomonas mutant strain containing a deletion in chromosome 2 which displays abnormal starch granule distribution. Under nitrogen starvation, this strain contains an additional starch granules population. These granules are twice as big as the wild-type granules and display characteristics of photosynthetic starch. Genetic and functional complementation analyses allowed us to identify the gene responsible for this original phenotype which was called BSG1 for “Bimodal Starch Granule”. Possible roles of BSG1 in starch metabolism modifications during the transition from photosynthetic to starved growth conditions are discussed.
Oxidation stability of Ti3C2Tx MXene nanosheets in solvents and composite films
Authors: Habib Touseef , Zhao Xiaofei , Shah Smit A. , Chen Yexiao , Sun Wanmei , An Hyosung , Lutkenhaus Jodie L. , Radovic Miladin , Green Micah J. 
Published: February 2019

AbstractTi3C2Tx belongs to the family of MXenes, 2D materials with an attractive combination of functional properties suitable for applications such as batteries, supercapacitors, and strain sensors. However, the fabrication of devices and functional coatings based on Ti3C2Tx remains challenging as they are prone to chemical degradation by their oxidation to TiO2. In this paper, we examine the oxidation of Ti3C2Tx in air, liquid, and solid media via conductivity measurements to assess the shelf life of Ti3C2Tx MXenes. The oxidation of Ti3C2Tx was observed in all the media used in this study, but it is fastest in liquid media and slowest in solid media (including polymer matrices). We also show that the conventional indicators of MXene oxidation, such as changes in color and colloidal stability, are not always reliable. Finally, we demonstrate the acceleration of oxidation under exposure to UV light.
Impflücken und Impfnebenwirkungen – eine aktuelle Übersicht
Authors: Bogdan Christian 
Published: February 2019

AbstractThe success of vaccination programs is jeopardized by gaps in vaccine coverage of the target population. These are frequently due to a lack of awareness, but also result from misconceptions of adverse effects of vaccines. Subject of this article are the current vaccination rates of children, adolescents and adults as well as of medical personnel in Germany, the reporting and surveillance system for adverse effects of vaccines, the magnitude of registered permanent vaccine-induced damages and the possible immunological mechanisms underlying vaccine-triggered autoimmune diseases.
Impact of Social Media on Current Medical Conferences
Authors: Lin Jennifer An-Jou , Hsu Angela Ting-Wei , Huang Jung-Ju , Daniel Bassem W. , Lee Che-Hsiung , Kwon Soo-Ha , Tang Evelyn Ting-Hsuan , Chu Cheng-Feng , Chien Cheng-An Tony , Chuang David Chwei-Chin , Lu Johnny Chuieng-Yi , Koshima Isao , Wang Zeng-Tao , Hao Liwen , Chen Chao , Chang Tommy Nai-Jen 
Published: February 2019

Background Medical conferences are forums for research, continuing medical education, and networking. Social media is increasingly used for communication and networking due to its low cost and ability to overcome large distances. This study investigates the impact that social media brings to the current conference system.
Methods There are three parts of this study: (1) comparing two similar brachial plexus injuries (BPIs) courses without (2009) and with (2017) social media support, and the participants' feedback; (2) sharing our experiences in the management of the 2018 International Course on SuperMicrosurgery (ICSM) conference; and (3) evaluating the studies from the social media platform International Microsurgery Club (IMC), for the consensus pertaining to social media and conference system.
Results With the help of social media, international attendance increased during the 2017 BPI conference compared with the 2009 BPI course (25 nationalities in 2009 vs. 35 in 2017). At least 23% obtained their meeting information through social media. Live surgery was the overall main attraction (79%). The 2018 ICSM meeting revealed that video posts increased attendance; videos that were the most effective in attracting (viewership) were either short or pertained to surgical procedures. Facebook, Messenger, and WeChat smartphone applications were effective for immediate communication and troubleshooting among the participants. From the IMC polls, 78% believe that the social media and the conference complemented each other. 97% attended the conference to update their skills and knowledge.
Conclusion Social media is a quick and economic tool in promoting medical conferences and instant messenger systems offer immediate communication amongst associates. Despite the popularity of social media, the conference still has its irreplaceable role. The combination of the conference and the social media enhances the training and education of microsurgeons.
Predictors of Substance use Treatment Initiation and Engagement among Adult and Adolescent Medicaid Recipients
Authors: Lind Bonnie K. , McCarty Dennis , Gu Yifan , Baker Robin , John McConnell K. 
Published: February 2019

Background It is important to understand patterns and predictors of initiation and engagement in treatment for Medicaid-covered individuals with substance use disorders because Medicaid is a major source of payment for addiction treatment in the United States. Our analysis examined similarities and differences in predictors between adults and adolescents. Methods An analysis of Oregon Medicaid claims data for the time period January 2010 through June 2015 assessed rates of substance use and of treatment initiation and engagement using the Healthcare Effectiveness Data and Information Set (HEDIS) definitions. The analysis included individuals aged 13–64 with a new alcohol and other drug dependence diagnosis who met the HEDIS enrollment criteria and did not have cancer. We created 4 logistic regression models to assess treatment initiation and engagement, separately for adults (ages 18–64) and adolescents (ages 13–17). Independent predictors included age, gender, race, the interaction of gender and race, urban/rural residence, presence of any chronic disease, a psychiatric diagnosis, or a pain diagnosis. Results Among adults, odds of initiation were lower in white males than in nonwhite males, white females, and nonwhite females. Conversely, among adolescents, odds of initiation were higher in white males than in the other gender/race groups. Predictors of initiation also went in opposite directions for presence of a psychiatric diagnosis (negative in adults, positive in adolescents) and urban residence (positive in adults, negative in adolescents). We found similar patterns in models of engagement, although for engagement those with a psychiatric diagnosis had lower odds of engagement in both adults and adolescents. Conclusions Predictors of treatment initiation and engagement for alcohol and drug use disorders differed between adults and adolescents on Medicaid. A better understanding of these differences will enable development of targeted treatment programs that are effective within age groups.
Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data
Authors: Khater Ismail M , Meng Fanrui , Nabi Ivan Robert , Hamarneh Ghassan 
Published: February 2019

Abstract

Motivation
Network analysis and unsupervised machine learning processing of single-molecule localization microscopy of caveolin-1 (Cav1) antibody labeling of prostate cancer cells identified biosignatures and structures for caveolae and three distinct non-caveolar scaffolds (S1A, S1B and S2). To obtain further insight into low-level molecular interactions within these different structural domains, we now introduce graphlet decomposition over a range of proximity thresholds and show that frequency of different subgraph (k = 4 nodes) patterns for machine learning approaches (classification, identification, automatic labeling, etc.) effectively distinguishes caveolae and scaffold blobs.

Results
Caveolae formation requires both Cav1 and the adaptor protein CAVIN1 (also called PTRF). As a supervised learning approach, we applied a wide-field CAVIN1/PTRF mask to CAVIN1/PTRF-transfected PC3 prostate cancer cells and used the random forest classifier to classify blobs based on graphlet frequency distribution (GFD). GFD of CAVIN1/PTRF-positive (PTRF+) and -negative Cav1 clusters showed poor classification accuracy that was significantly improved by stratifying the PTRF+ clusters by either number of localizations or volume. Low classification accuracy (&lt;50%) of large PTRF+ clusters and caveolae blobs identified by unsupervised learning suggests that their GFD is specific to caveolae. High classification accuracy for small PTRF+ clusters and caveolae blobs argues that CAVIN1/PTRF associates not only with caveolae but also non-caveolar scaffolds. At low proximity thresholds (50–100 nm), the caveolae groups showed reduced frequency of highly connected graphlets and increased frequency of completely disconnected graphlets. GFD analysis of single-molecule localization microscopy Cav1 clusters defines changes in structural organization in caveolae and scaffolds independent of association with CAVIN1/PTRF.

Supplementary information
Supplementary data are available at Bioinformatics online.
Temporal network alignment via GoT-WAVE
Authors: Aparício David , Ribeiro Pedro , Milenković Tijana , Silva Fernando 
Published: February 2019

Abstract

Motivation
Network alignment (NA) finds conserved regions between two networks. NA methods optimize node conservation (NC) and edge conservation. Dynamic graphlet degree vectors are a state-of-the-art dynamic NC measure, used within the fastest and most accurate NA method for temporal networks: DynaWAVE. Here, we use graphlet-orbit transitions (GoTs), a different graphlet-based measure of temporal node similarity, as a new dynamic NC measure within DynaWAVE, resulting in GoT-WAVE.

Results
On synthetic networks, GoT-WAVE improves DynaWAVE’s accuracy by 30% and speed by 64%. On real networks, when optimizing only dynamic NC, the methods are complementary. Furthermore, only GoT-WAVE supports directed edges. Hence, GoT-WAVE is a promising new temporal NA algorithm, which efficiently optimizes dynamic NC. We provide a user-friendly user interface and source code for GoT-WAVE.

Availability and implementation
http://www.dcc.fc.up.pt/got-wave/

Supplementary information
Supplementary data are available at Bioinformatics online.
Theoretical Expression for the Evolution of Genomic Island of Speciation: From Its Birth to Preservation
Authors: Sakamoto T. , Innan H. 
Published: February 2019

AbstractEcological speciation could be driven by divergent selection that works to maintain phenotypes that are adaptive to each niche. In its early stages, genetic divergence (or FST) can be maintained around the target sites of divergent selection, while in other regions, genetic variation can be mixed by gene flow or migration. Such regions of elevated genetic divergence are called genomic islands of speciation. In this work, we theoretically consider the evolutionary process of a genomic island of speciation, from its birth to stable preservation. Under a simple two-population model, we use a diffusion approach to obtain analytical expressions for the probability of initial establishment of a locally adaptive allele, the reduction of genetic variation due to the spread of the adaptive allele, and the process to the development of a sharp peak of divergence. Our result would be useful to understand how genomes evolve through ecological speciation with gene flow.
A dataset to explore kinase control of environmental stress responsive transcription
Authors: Mace Kieran , Krakowiak Joanna , El-Samad Hana , Pincus David 
Published: February 2019

ABSTRACTCells respond to changes in environmental conditions by activating signal transduction pathways and gene expression programs. Here we present a dataset to explore the relationship between environmental stresses, kinases, and global gene expression in yeast. We subjected 28 drug-sensitive kinase mutants to 10 environmental conditions in the presence of inhibitor and performed mRNA deep sequencing. With these data, we reconstructed canonical stress pathways and identified examples of crosstalk among pathways. The data also implicated numerous kinases in novel environment-specific roles. However, rather than regulating dedicated sets of target genes, individual kinases tuned the magnitude of induction of the environmental stress response (ESR) – a gene expression signature shared across the set of perturbations – in environment-specific ways. This suggests that the ESR integrates inputs from multiple sensory kinases to modulate gene expression and growth control. As an example, we provide experimental evidence that the high osmolarity glycerol pathway is a constitutive negative regulator of protein kinase A, a known inhibitor of the ESR. These results elaborate the central axis of cellular stress response signaling.