bluuebunny/crossref_metadata_2025_split huggingface dataset:
Liquid-chromatography retention order prediction for metabolite identification
Authors: Bach Eric , Szedmak Sandor , Brouard Céline , Böcker Sebastian , Rousu Juho 
Published: July 2018

AbstractMotivationLiquid Chromatography (LC) followed by tandem Mass Spectrometry (MS/MS) is one of the predominant methods for metabolite identification. In recent years, machine learning has started to transform the analysis of tandem mass spectra and the identification of small molecules. In contrast, LC data is rarely used to improve metabolite identification, despite numerous published methods for retention time prediction using machine learning.ResultsWe present a machine learning method for predicting the retention order of molecules; that is, the order in which molecules elute from the LC column. Our method has important advantages over previous approaches: We show that retention order is much better conserved between instruments than retention time. To this end, our method can be trained using retention time measurements from different LC systems and configurations without tedious pre-processing, significantly increasing the amount of available training data. Our experiments demonstrate that retention order prediction is an effective way to learn retention behaviour of molecules from heterogeneous retention time data. Finally, we demonstrate how retention order prediction and MS/MS-based scores can be combined for more accurate metabolite identifications when analyzing a complete LC-MS/MS run.Availability and implementationImplementation of the method is available at https://version.aalto.fi/gitlab/bache1/retention_order_prediction.git.
A Curated Cancer Clinical Outcomes Database (C3OD) for accelerating patient recruitment in cancer clinical trials
Authors: Mudaranthakam Dinesh Pal , Thompson Jeffrey , Hu Jinxiang , Pei Dong , Chintala Shanthan Reddy , Park Michele , Fridley Brooke L , Gajewski Byron , Koestler Devin C , Mayo Matthew S 
Published: July 2018

Abstract
Data used to determine patient eligibility for cancer clinical trials often come from disparate sources that are typically maintained by different groups within an institution, use differing technologies, and are stored in different formats. Collecting data and resolving inconsistencies across sources increase the time it takes to screen eligible patients, potentially delaying study completion. To address these challenges, the Biostatistics and Informatics Shared Resource at The University of Kansas Cancer Center developed the Curated Cancer Clinical Outcomes Database (C3OD). C3OD merges data from the electronic medical record, tumor registry, bio-specimen and data registry, and allows querying through a single unified platform. By centralizing access and maintaining appropriate controls, C3OD allows researchers to more rapidly obtain detailed information about each patient in order to accelerate eligibility screening. This case report describes the design of this informatics platform as well as initial assessments of its reliability and usability.
Microbiology Comment Nudge Improves Pneumonia Prescribing
Authors: Musgrove Mary A , Kenney Rachel M , Kendall Ronald E , Peters Michael , Tibbetts Robert , Samuel Linoj , Davis Susan L 
Published: July 2018

Abstract

Background
Systematic and behavioral interventions are needed to improve antibiotic use for common conditions like pneumonia.

Methods
Single pretest, post-test quasi-experiment in a 4-hospital health system in metropolitan Detroit, Michigan. Hospitalized patients treated with anti-methicillin-resistant Staphylococcus aureus and antipseudomonal antibiotics for respiratory infections from August 1, 2015, through January 31, 2016, and August 1, 2016, through January 31, 2017, were eligible for inclusion. Beginning in May 2016, respiratory cultures with no dominant organism growth and no Pseudomonas sp. or Staphylococcus aureus were reported by the clinical microbiology laboratory as “commensal respiratory flora only: No S. aureus/MRSA [methicillin-resistant Staphylococcus aureus] or P. [Pseudomonas] aeruginosa.” Before intervention, these were reported as “commensal respiratory flora.” The primary end point was de-escalation or discontinuation of anti-methicillin-resistant Staphylococcus aureus or antipseudomonal therapy. Secondary clinical and safety outcomes included nephrotoxicity and in-hospital, all-cause mortality.

Results
Two hundred ten patients were included in the study. De-escalation/discontinuation was more commonly performed in the intervention group (39% vs 73%, P &lt; .001). After adjusting for APACHE II and Charlson Comorbidity Index, the intervention comment was associated with a 5.5-fold increased odds of de-escalation (adjusted odds ratio, 5.5; 95% confidence interval, 2.8–10.7). Acute kidney injury was reduced in the intervention phase (31% vs 14%, P = .003). No difference in all-cause mortality was detected between the groups (30% vs 18%, P = .052).

Conclusion
A simple, behavioral nudge in microbiology reporting increased de-escalation and discontinuation of unnecessary broad-spectrum antibiotics. This highlights the importance of clear, persuasive communication of diagnostic testing in improving antibiotic prescribing behaviors.
Polydatin suppresses VEGF‐induced angiogenesis through binding with VEGF and inhibiting its receptor signaling
Authors: Hu Wei-Hui , Wang Huai-You , Kong Xiang-Peng , Xiong Qing-Ping , Poon Karman Ka-Man , Xu Li , Duan Ran , Chan Gallant Kar-Lun , Dong Tina Ting-Xia , Tsim Karl Wah-Keung 
Published: July 2018

ABSTRACTPolydatin, also called piceid, is a stilbenoid glucoside of a resveratrol derivative. It derives mainly from the root and rhizome of Polygonum cuspidatum Sieb. et Zucc. Although the role of P. cuspidatum root in angiogenesis has been reported, the active chemical or chemicals responsible for such function is not known. Here, polydatin was proposed to bind VEGF, which therefore altered the functions of VEGF in angiogenesis. Several lines of evidence supported the pharmaceutical effects of polydatin in VEGF‐induced angiogenesis. In human umbilical vein endothelial cells, polydatin inhibited VEGF‐stimulated cell proliferation, cell migration, and tube formation. Moreover, polydatin showed suppressive effects on the subintestinal vessel formation in zebrafish embryos. In signaling cascades, polydatin application attenuated VEGF‐induced phosphorylations of VEGF receptor 2 and JNK. Moreover, the VEGF‐induced phosphorylations of Akt, eNOS, and Erk were significantly decreased in the presence of polydatin. In parallel, the formation of reactive oxygen species, triggered by VEGF, was markedly decreased under polydatin application. Thus, our results supported the angiogenic roles of polydatin, as well as its signaling mechanism in blocking VEGF‐mediated responses. The current study provides support for the possible development of polydatin as a potential therapeutic agent for treatment and prevention of angiogenesis‐related diseases.—Hu, W.‐H., Wang, H.‐Y., Kong, X.‐P., Xiong, Q.‐P., Poon, K. K.‐M., Xu, L., Duan, R., Chan, G. K.‐L., Dong, T. T.‐X., Tsim, K. W.‐K. Polydatin suppresses VEGF‐induced angiogenesis through binding with VEGF and inhibiting its receptor signaling. FASEB J. 33, 532–544 (2019). www.fasebj.org
Taking a Dive: Experiments in Deep Learning for Automatic Ontology-based Annotation of Scientific Literature
Authors: Manda Prashanti , Beasley Lucas , Mohanty Somya D. 
Published: July 2018

I.AbstractText mining approaches for automated ontology-based curation of biological and biomedical literature have largely focused on syntactic and lexical analysis along with machine learning. Recent advances in deep learning have shown increased accuracy for textual data annotation. However, the application of deep learning for ontology-based curation is a relatively new area and prior work has focused on a limited set of models.Here, we introduce a new deep learning model/architecture based on combining multiple Gated Recurrent Units (GRU) with a character+word based input. We use data from five ontologies in the CRAFT corpus as a Gold Standard to evaluate our model’s performance. We also compare our model to seven models from prior work. We use four metrics - Precision, Recall, F1 score, and a semantic similarity metric (Jaccard similarity) to compare our model’s output to the Gold Standard. Our model resulted in a 84% Precision, 84% Recall, 83% F1, and a 84% Jaccard similarity. Results show that our GRU-based model outperforms prior models across all five ontologies. We also observed that character+word inputs result in a higher performance across models as compared to word only inputs.These findings indicate that deep learning algorithms are a promising avenue to be explored for automated ontology-based curation of data. This study also serves as a formal comparison and guideline for building and selecting deep learning models and architectures for ontology-based curation.
Computer Assisted Localization of a Heart Arrhythmia
Authors: Vogl Chris , Zheng Peng , Seslar Stephen P. , Aravkin Aleksandr Y. 
Published: July 2018

AbstractWe consider the problem of locating a point-source heart arrhythmia using data from a standard diagnostic procedure, where a reference catheter is placed in the heart, and arrival times from a second diagnostic catheter are recorded as the diagnostic catheter moves around within the heart.We model this situation as a nonconvex feasibility problem, where given a set of arrival times, we look for a source location that is consistent with the available data. We develop a new optimization approach and fast algorithm to obtain online proposals for the next location to suggest to the operator as she collects data. We validate the procedure using a Monte Carlo simulation based on patients’ electrophysiological data. The proposed procedure robustly and quickly locates the source of arrhythmias without any prior knowledge of heart anatomy.
In Vitro Potentiation of Carbapenems with Tannic Acid Against Carbapenemase Producing Enterobacteriaceae: Exploring Natural Products as Potential Carbapenemase Inhibitors
Authors: Somboro Anou M. , Sekyere John Osei , Amoako Daniel G. , Kumalo Hezekiel M. , Khan René , Bester Linda A. , Essack Sabiha Y. 
Published: July 2018

AbstractResistance to antibiotics is increasing worldwide, necessitating urgent action to sustain the efficacy of existing antibiotics in clinical use. We show that tannic acid (TA) in combination with carbapenems can reduce and/or reverse the minimum inhibitory concentrations (MICs) of carbapenems to susceptible values in Enterobacteriaceae that express class A and B carbapenemases. MICs of carbapenems in the presence and absence of TA and other efflux pump inhibitors, TA-carbapenemases inhibition assays and computational studies were undertaken to determine the effect of TA on carbapenem susceptibility in Enterobacteriaceae. TA had the greatest effect on metallo-β-lactamases (MBLs) followed by class A serine-β-lactamases (SBLs). Antibiotic susceptibility testing showed that TA reversed the MICs of MBLs to susceptible values whilst substantially reducing the MICs of SBLs (class A). Tolerable cytotoxicity effect was observed for the concentrations tested. TA inhibited enzymes with a marked difference between ≈50% inhibition (IC50) for NDM-1 and KPC-2. Computational studies including molecular docking, molecular dynamics simulations and binding free energy calculations showed that TA interact with both MBLs and SBLs hydrophobic sites. Moreover, TA had a stronger binding affinity for MBLs than SBLs as the MBLs, specifically VIM-1 and NDM-1, interact with a larger number of their catalytic active-site residues than that of OXA- 48 and KPC-2. These in vitro evaluations together with computational simulation explain the potentiating effect of TA toward carbapenems against carbapenem-resistance enterobacteriaceae. This study proposes TA as a promising adjuvant for MBLs and SBLs.
Asymmetric Diversification of Mating Pheromones in Fission Yeast
Authors: Seike Taisuke , Shimoda Chikashi , Niki Hironori 
Published: July 2018

AbstractIn fungi, mating between partners critically depends on the molecular recognition of two peptidyl mating pheromones by their respective receptors. The fission yeastSchizosaccharomyces pombehas two mating types, Plus (P) and Minus (M), which secrete two different mating pheromones: P-factor recognized by Mam2, and M-factor recognized by Map3, respectively. Our recent study demonstrated that a few mutations in both M-factor and Map3 can trigger reproductive isolation, a cause of speciation, inS. pombe. Here we explored the mechanism underlying reproductive isolation through genetic changes of pheromones and receptors. We investigated the diversity of genes encoding the pheromones and their receptor in 150S. pombewild strains. Whereas the amino acid sequences of M-factor and Map3 were completely conserved, those of P-factor and Mam2 were very diverse. In addition, the P-factor gene contained varying numbers of tandem repeats of P-factor (4–8 repeats). We also explored the recognition specificity of pheromones betweenS. pombe(Sp) and its close relativeSchizosaccharomyces octosporus(So). So-M-factor did not have an effect onS. pombeP-cells, but So-P-factor had a partial effect onS. pombeM-cells, allowing them to mate successfully. Thus, recognition of M-factor seems to be tight, whereas that of P-factor is relatively loose. Moreover, diversity of P-factor and Mam2 might be due to a P-factor-specific peptidase. Overall, the asymmetric system for pheromone recognition in yeasts seems to allow flexible adaptation to mutational changes in the combination of pheromone and receptor while maintaining tight recognition for mating partners.
Reconstitution of mammalian Cleavage Factor II involved in 3’ processing of mRNA precursors
Authors: Schäfer Peter , Tüting Christian , Schönemann Lars , Kühn Uwe , Treiber Thomas , Treiber Nora , Ihling Christian , Graber Anne , Keller Walter , Meister Gunter , Sinz Andrea , Wahle Elmar 
Published: July 2018

AbstractCleavage factor II (CF II) is a poorly characterized component of the multi-protein complex catalyzing 3’ cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5’ kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.
Multi-protein Bridging Factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting
Authors: Wang Jiyu , Zhou Jie , Yang Qidi , Grayhack Elizabeth J. 
Published: July 2018

AbstractStalled ribosomes in bacteria frameshift, but stalled ribosomes in eukaryotes do not frameshift and abort translation, suggesting that eukaryote-specific mechanisms might prevent frameshifting. We show that the conserved eukaryotic/archaeal protein Mbf1 acts with ribosomal proteins Rps3/uS3 and eukaryotic Asc1/RACK1 to prevent frameshifting at inhibitory CGA-CGA codon pairs inSaccharomyces cerevisiae. Mutations inRPS3that allow frameshifting implicate eukaryotic conserved residues near the mRNA entry site. Mbf1 and Rps3 cooperate to maintain the reading frame of stalled ribosomes, while Asc1 mediates distinct events that result in aborted translation. Frameshifting occurs through a +1 shift with a CGA codon in the P site and involves competition between codons entering the A site, implying that the wobble interaction of the P site codon destabilizes translation elongation. Thus, eukaryotes have evolved unique mechanisms involving both a universally conserved ribosome component and two eukaryotic-specific proteins to maintain the reading frame at ribosome stalls.
Yap/Taz-TEAD ACTIVITY LINKS MECHANICAL CUES TO CELL PROGENITOR BEHAVIOR DURING HINDBRAIN SEGMENTATION
Authors: Voltes Adrià , Hevia Covadonga F , Dingare Chaitanya , Calzolari Simone , Terriente Javier , Norden Caren , Lecaudey Virginie , Pujades Cristina 
Published: July 2018

SUMMARYCells perceive their microenvironment through chemical and physical cues. However, how mechanical signals are interpreted during embryonic tissue deformation resulting in specific cell behaviors is largely unexplored. The Yap/Taz family of transcriptional co-activators has emerged as an important regulator of tissue growth and regeneration, responding to physical cues from the extracellular matrix, cell shape and actomyosin cytoskeleton. In this work, we unveiled the role of Yap/Taz-TEAD activity as sensor of mechanical signals in the regulation of the progenitor behavior of boundary cells during hindbrain compartmentalization. Monitoringin vivoYap/Taz-activity during hindbrain segmentation we discovered that boundary cells respond to mechanical cues in a cell-autonomous manner through Yap/Taz-TEAD activity. Cell-lineage analysis revealed that Yap/Taz-TEAD boundary cells decrease their proliferative activity when Yap/Taz-TEAD ceased, preceding changes of cell fate: from proliferating progenitors to differentiated neurons. Functional experiments demonstrated the pivotal role of Yap/Taz-TEAD signaling in maintaining the progenitor features in the hindbrain boundary cell population.
Distinct and sequential re-replication barriers ensure precise genome duplication
Authors: Zhou Yizhuo , Pozo Pedro N. , Oh Seeun , Stone Haley M. , Cook Jeanette Gowen 
Published: July 2018

AbstractAchieving complete and precise genome duplication requires that each genomic segment be replicated only once per cell division cycle. Protecting large eukaryotic genomes from re-replication requires an overlapping set of molecular mechanisms that prevent the first DNA replication step, the DNA loading of MCM helicase complexes to license replication origins. Previous reports have defined many such origin licensing inhibition mechanisms, but the temporal relationships among them are not clear, particularly with respect to preventing re-replication in G2 and M phases. Using a combination of mutagenesis, biochemistry, and single cell analyses in human cells, we define a new mechanism that prevents re-replication through hyperphosphorylation of the essential MCM loading protein, Cdt1. We demonstrate that Cyclin A/CDK1 hyperphosphorylates Cdt1 to inhibit MCM re-loading in G2 phase. The mechanism of inhibition is to block Cdt1 binding to MCM independently of other known Cdt1 inactivation mechanisms such as Cdt1 degradation during S phase or Geminin binding. Moreover, we provide evidence that protein phosphatase 1-dependent Cdt1 dephosphorylation at the mitosis-to-G1 phase transition re-activates Cdt1. We propose that multiple distinct, non-redundant licensing inhibition mechanisms act in a series of sequential relays through each cell cycle phase to ensure precise genome duplication.Author SummaryThe initial step of DNA replication is loading the DNA helicase, MCM, onto DNA during the first phase of the cell division cycle. If MCM loading occurs inappropriately onto DNA that has already been replicated, then cells risk DNA re-replication, a source of endogenous DNA damage and genome instability. How mammalian cells prevent any sections of their very large genomes from re-replicating is still not fully understood. We found that the Cdt1 protein, one of the critical MCM loading factors, is inhibited specifically in late cell cycle stages through a mechanism involving protein phosphorylation. This phosphorylation prevents Cdt1 from binding MCM; when Cdt1 can’t be phosphorylated MCM is inappropriately re-loaded onto DNA and cells are prone to re-replication. When cells divide and transition into G1 phase, Cdt1 is then dephosphorylated to re-activate it for MCM loading. Based on these findings we assert that the different mechanisms that cooperate to avoid re-replication are not redundant, but rather distinct mechanisms are dominant in different cell cycle phases. These findings have implications for understanding how genomes are duplicated precisely once per cell cycle and shed light on how that process is perturbed by changes in Cdt1 levels or phosphorylation activity.
mRNP architecture in translating and stress conditions reveals an ordered pathway of mRNP compaction
Authors: Khong Anthony , Parker Roy 
Published: July 2018

ABSTRACTStress granules (SGs) are non-translating mRNP assemblies that form during stress. Herein, we use multiple smFISH probes for specific mRNAs to examine their SG recruitment and spatial organization. We observed that ribosome run-off is required for SG entry with long ORF mRNAs being delayed in SG accumulation, revealing SG transcriptome changes over time. Moreover, mRNAs are ~20X compacted from an expected linear length when translating and compact ~2 fold further in a stepwise manner beginning at the 5’ end during ribosome run-off. Surprisingly, the 5’ and 3’ ends of the examined mRNAs were separated in non-stress conditions, but in non-translating conditions, the ends of AHNAK and DYNC1H1 mRNAs become close, suggesting the closed-loop model of mRNPs preferentially forms on non-translating mRNAs. These results suggest translation inhibition triggers a mRNP reorganization that brings ends closer, which has implications for the regulation of mRNA stability and translation by 3’ UTR elements and the poly(A) tail.
Hidden in plain sight - highly abundant and diverse planktonic freshwater Chloroflexi
Authors: Mehrshad Maliheh , Salcher Michaela M. , Okazaki Yusuke , Nakano Shin-ichi , Šimek Karel , Andrei Adrian-Stefan , Ghai Rohit 
Published: July 2018

AbstractBackgroundRepresentatives of the phylum Chloroflexi, though reportedly highly abundant (up to 30% of total prokaryotes) in the extensive deep water habitats of both marine (SAR202) and freshwater (CL500-11), remain uncultivated and uncharacterized. There are few metagenomic studies on marine Chloroflexi representatives, while the pelagic freshwater Chloroflexi community is largely unknown except for a single metagenome-assembled genome of CL500-11.ResultsHere we provide the first extensive examination of the community composition of this cosmopolitan phylum in a range of pelagic habitats (176 datasets) and highlight the impact of salinity and depth on their phylogenomic composition. Reconstructed genomes (53 in total) provide a perspective on the phylogeny, metabolism and distribution of three novel classes and two family-level taxa within the phylum Chloroflexi. We unraveled a remarkable genomic diversity of pelagic freshwater Chloroflexi representatives that thrive not only in the hypolimnion as previously suspected, but also in the epilimnion. Our results suggest that the lake hypolimnion provides a globally stable habitat reflected in lower species diversity among hypolimnion specific CL500-11 and TK10 clusters in distantly related lakes compared to a higher species diversity of the epilimnion specific SL56 cluster. Cell volume analyses show that the CL500-11 are amongst the largest prokaryotic cells in the water column of deep lakes and with a biomass:abundance ratio of two they significantly contribute to the deep lake carbon flow. Metabolic insights indicate participation of JG30-KF-CM66 representatives in the global cobalamin production via cobinamide to cobalamin salvage pathway.ConclusionsExtending phylogenomic comparisons to brackish and marine habitats suggests salinity as the major influencer of the community composition of the deep-dwelling Chloroflexi in marine (SAR202) and freshwater (CL500-11) habitats as both counterparts thrive in intermediate brackish salinity however, freshwater habitats harbor the most phylogenetically diverse community of pelagic Chloroflexi representatives that reside both in epi- and hypolimnion.