bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Outcomes Associated with Fluid Overload in Critically Ill Pediatric Patients
Authors: El-Nawawy Ahmed , Moustafa Azza A , Antonios Manal A M , Atta May M 
Published: June 2019

Abstract

Background
Fluid overload (FO) has been accused as being one of the ICU problems affecting morbidity and mortality. The aim of the study was to assess the effect and critical threshold of FO that is related to mortality.

Methods
This prospective observational study was conducted in a pediatric ICU. All patients admitted (n = 203) during 12 months with a length of stay more than 48 h were recruited.

Results
FO was found to be related to mortality (p = 0.025) but was not proved to be an independent risk factor of fatal outcome by the logistic regression model. This raises the suspicion about any cause—effect relationship between FO and mortality. Even though, FO was statistically a fair discriminator of death (AUC = 0.655, p = 0.0008) and a cutoff level of FO was set at 7%. Kaplan–Meier curve showed that cumulative of survival differed significantly between groups of patients with FO more and less than 7% (p = 0.002)

Conclusion
Frequent and accurate monitoring of FO is crucial among critically ill patients. The present study suggested a threshold of 7% FO beyond which a more conservative regimen of fluid administration might improve patients’ outcome.
Ultrastructure of the midgut epithelium in three species of Macrobiotidae (Tardigrada: Eutardigrada: Parachela)
Authors: Rost-Roszkowska M , Janelt K , Poprawa I 
Published: June 2019

Abstract
Three species of Macrobiotidae, Macrobiotus polonicus, Macrobiotus diversus and Macrobiotus pallarii, were selected for analysis of the fine structure of the midgut epithelium. They are gonochoric and carnivorous species that live in wet terrestrial and freshwater environments. The ultrastructure of the midgut epithelium of the investigated Macrobiotidae species was analysed in both males and females. Their digestive system is composed of fore- and hindguts that are covered by a cuticle, and the middle region, termed the midgut. It is lined with a simple epithelium that is formed by digestive cells that have a distinct brush border. Crescent-shaped cells that form an anterior ring in the border between the fore- and midgut were detected. The ultrastructure of the intestinal epithelium of the examined species differs slightly depending on sex. The digestive cells of the posterior segment of the intestine contain numerous lipid droplets, which are the reserve material. We concluded that the digestive cells of the Macrobiotidae midgut are responsible for its intracellular digestion owing to endocytosis. They also participate in the extracellular digestion owing to merocrine secretion (exocytosis). However, the midgut is not the main organ that accumulates reserve material. Additionally, the midgut epithelium does not participate in oogenesis.
A prospective analysis of circulating plasma metabolomics and ovarian cancer risk
Authors: Zeleznik Oana A. , Eliassen A. Heather , Kraft Peter , Poole Elizabeth M. , Rosner Bernard , Jeanfavre Sarah , Deik Amy , Bullock Kevin , Hitchcock Daniel , Avila-Pancheco Julian , Clish Clary B. , Tworoger Shelley S. 
Published: June 2019

AbstractWe assessed the association of pre-diagnostic plasma metabolites (N=420) with ovarian cancer risk. We included 252 cases and 252 matched controls from the Nurses’ Health Studies. Multivariable logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI) comparing the 90th-10thpercentile in metabolite levels, using permutation tests to account for testing multiple correlated hypotheses. Weighted gene co-expression network analysis (WGCNA) modules (n=10) and metabolite set enrichment analysis (MSEA; n=23) were also evaluated. Pseudouridine had the strongest statistical association with ovarian cancer risk overall (OR=2.56, 95%CI=1.48-4.45; p=0.001/adjusted-p=0.15). C36:2 phosphatidylcholine (PC) plasmalogen had the strongest statistical association with lower risk (OR=0.11, 95%CI=0.03-0.35; p<0.001/adjusted-p=0.06) and pseudouridine with higher risk (OR=9.84, 95%CI=2.89-37.82; p<0.001/adjusted-p=0.07) of non-serous tumors. Seven WGCNA modules and 15 classes were associated with risk at FDR≤0.20. Triacylglycerols (TAGs) showed heterogeneity by tumor aggressiveness (case-only heterogeneity-p<0.0001). TAG association with risk overall and serous tumors differed by acyl carbon content and saturation. Pseudouridine may be a novel risk factor for ovarian cancer. TAGs may also be important, particularly for rapidly fatal tumors, with associations differing by structural features. Validation in independent prospective studies and complementary experimental work to understand biological mechanisms is needed.
Mendelian Randomization Analysis Dissects the Relationship between NAFLD, T2D, and Obesity and Provides Implications to Precision Medicine
Authors: Liu Zhipeng , Zhang Yang , Graham Sarah , Pique-Regi Roger , Dong Xiaocheng Charlie , Chen Y. Eugene , Willer Cristen , Liu Wanqing 
Published: June 2019

ABSTRACTBackgroundNon-alcoholic fatty liver disease (NAFLD) is epidemiologically correlated with both type 2 diabetes (T2D) and obesity. However, the causal inter-relationships among the three diseases have not been completely investigated.AimWe aim to explore the causal relationships among the three diseases.Design and methodsWe performed a genome-wide association study (GWAS) on fatty liver disease in ∼400,000 UK BioBank samples. Using this data as well as the largest-to-date publicly available summary-level GWAS data, we performed a two-sample bidirectional Mendelian Randomization (MR) analysis. This analysis tested the causal inter-relationship between NAFLD, T2D, and obesity, as well as the association between genetically driven NAFLD (with two well-established SNPs at the PNPLA3 and TM6SF2 loci) and glycemic and lipidemic traits, respectively. Transgenic mice expressing the human PNPLA3 I148I (TghPNPLA3-I148I) and PNPLA3 I148M (TghPNPLA3-I148M) isoforms were used to further validate the causal effects.ResultsWe found that genetically instrumented hepatic steatosis significantly increased the risk for T2D (OR=1.3, 95% CI: [1.2, 1.4],p=8.3e-14) but not the intermediate glycemic phenotypes at the Bonferroni-adjusted level of significance (p<0.002). There was a moderate, but significant causal association between genetically driven hepatic steatosis and decreased risk for BMI (β=- 0.027 SD, 95%CI: [−0.043, −0.01],p=1.3e-4), but an increased risk for WHRadjBMI (Waist-Hip Ratio adjusted for BMI) (β=0.039 SD, 95%CI: [0.023, 0.054],p=8.2e-7), as well as a decreased level for total cholesterol (β=-0.084 SD, 95%CI [−0.13, −0.036],p=6.8e-4), but not triglycerides (β=0.02 SD, 95%CI [−0.023, 0.062],p=0.36). The reverse MR analyses suggested that genetically driven T2D (OR=1.1, 95% CI: [1.0, 1.2],p=1.7e-3), BMI (OR=2.3, 95% CI: [2.0, 2.7],p=1.4e-25) and WHRadjBMI (OR=1.5, 95% CI: [1.3, 1.8],p=1.1e-6) causally increase the NAFLD risk. In the animal study, as compared to the TghPNPLA3-I148I controls, the TghPNPLA3-I148M mice developed higher fasting glucose level and reduced glucose clearance. Meanwhile, the TghPNPLA3-I148M mice demonstrated a reduced body weight, increased central to peripheral fat ratio, decreased circulating total cholesterol as compared to the TghPNPLA3-I148I controls.ConclusionThis large-scale bidirectional MR study suggests that lifelong, genetically driven NAFLD is a causal risk factor for T2D (hence potentially a “NAFLD-driven T2D” subtype) and central obesity (or “NAFLD-driven obesity” subtype), but protects against overall obesity; while genetically driven T2D, obesity, and central obesity also causally increase the risk of NAFLD, hence a “metabolic NAFLD”. This causal relationship revealed new insights into disease subtypes and provided novel hypotheses for precision treatment or prevention for the three diseases.
A new colorectal cancer risk prediction model incorporating family history, personal and environmental factors
Authors: Zheng Yingye , Hua Xinwei , Win Aung K. , MacInnis Robert J. , Gallinger Steven , Marchand Loic Le , Lindor Noralane M. , Baron John A. , Hopper John L. , Dowty James G. , Antoniou Antonis C. , Zheng Jiayin , Jenkins Mark A. , Newcomb Polly A. 
Published: June 2019

AbstractPurposeReducing colorectal cancer (CRC) incidence and mortality through early detection would improve efficacy if targeted. A CRC risk-prediction model incorporating personal, family, genetic and environmental risk factors could enhance prediction.MethodsWe developed risk-prediction models using population-based CRC cases (N=4,445) and controls (N=3,967) recruited by the Colon Cancer Family Registry Cohort (CCFRC). A familial risk profile (FRP) was calculated to summarize individuals’ risk based on their CRC family history, family structure, germline mutation probability in major susceptibility genes, and a polygenic component. Using logistic regression, we developed risk models including individuals’ FRP or a binary CRC family-history (FH), and risk factors collected at recruitment. Model validation used follow-up data for population-(N=12,052) and clinic-based (N=5,584) relatives with no cancer history at recruitment, assessing calibration (E/O) and discrimination (AUC).ResultsThe E/O (95% confidence interval [CI]) for FRP models for population-based relatives were 1.04 (0.74-1.45) and 0.86 (0.64-1.20) for men and women, and for clinic-based relatives 1.15 (0.87-1.58) and 1.04 (0.76-1.45). The age-adjusted AUC (95% CI) for FRP models in population-based relatives were 0.69 (0.60-0.78) and 0.70 (0.62-0.77), and for clinic-based relatives 0.77 (0.69-0.84) and 0.68 (0.60-0.76). The incremental values of AUC (95% CI) for FRP over FH models for population-based relatives were 0.08 (0.01-0.15) and 0.10 (0.04-0.16), and for clinic-based relatives 0.11 (0.05-0.17) and 0.11 (0.06-0.17).ConclusionThe FRP-based model and FH-based model calibrate well in both settings. The FRP-based model provided better risk-prediction and discrimination than the FH-based model. A detailed family history may be useful for targeted risk-based screening and clinical management.
Genomic and phenotypic comparison of environmental and patient-derived isolates ofPseudomonas aeruginosasuggest that antimicrobial resistance is rare within the environment
Authors: Ramsay Kay A , Wardell Samuel J T , Patrick Wayne M , Brockway Ben , Reid David W , Winstanley Craig , Bell Scott C , Lamont Iain L 
Published: June 2019

AbstractPatient-derived isolates of the opportunistic pathogenPseudomonas aeruginosaare frequently resistant to antibiotics due to the presence of sequence variants in resistance-associated genes. However, the frequency of antibiotic resistance and of resistance-associated sequence variants in environmental isolates ofP. aeruginosahas not been well studied. Antimicrobial susceptibility testing (ciprofloxacin, ceftazidime, meropenem, tobramycin) of environmental (n=50) and cystic fibrosis (n=42)P. aeruginosaisolates was carried out. Following whole genome sequencing of all isolates, twenty-five resistance-associated genes were analysed for the presence of likely function-altering sequence variants. Environmental isolates were susceptible to all antibiotics with one exception, whereas patient-derived isolates had significant frequencies of resistance to each antibiotic and a greater number of likely resistance-associated genetic variants. These findings indicate that the natural environment does not act as a reservoir of antibiotic-resistantP. aeruginosa, supporting a model in which antibiotic susceptible environmental bacteria infect patients and develop resistance during infection.Author Contributions
NoRCE: Non-coding RNA Sets Cis Enrichment Tool
Authors: Olgun Gulden , Nabi Afshan , Tastan Oznur 
Published: June 2019

AbstractSummaryWhile some non-coding RNAs (ncRNAs) are assigned to critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic spatial proximity can lead to a functional association. Based on this idea, we present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. NoRCE allows incorporating other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information. NoRCE repository provides several data, such as cell-line specific TAD boundaries, functional gene sets, and expression data for coding and ncRNAs specific to cancer for the analysis. Additionally, users can utilize their custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. NoRCE is a platform-independent, user-friendly, comprehensive R package that could be used to gain insight into the functional importance of a list of any type of interesting ncRNAs. Users can run the pipeline in a single function; also, the tool offers flexibility to conduct the users’ preferred analysis in a single base and design their pipeline. It is available in Bioconductor and https://github.com/guldenolgun/NoRCE.
Plasticity in auditory categorization is supported by differential engagement of the auditory-linguistic network
Authors: Bidelman Gavin M. , Walker Breya 
Published: June 2019

ABSTRACTTo construct our perceptual world, the brain categorizes variable sensory cues into behaviorally-relevant groupings. Categorical representations are apparent within a distributed fronto-temporo-parietal brain network but how this neural circuitry is shaped by experience remains undefined. Here, we asked whether speech (and music) categories might be formed within different auditory-linguistic brain regions depending on listeners’ auditory expertise. We recorded EEG in highly skilled (musicians) vs. novice (nonmusicians) perceivers as they rapidly categorized speech and musical sounds. Musicians showed perceptual enhancements across domains, yet source EEG data revealed a double dissociation in the neurobiological mechanisms supporting categorization between groups. Whereas musicians coded categories in primary auditory cortex (PAC), nonmusicians recruited non-auditory regions (e.g., inferior frontal gyrus, IFG) to generate category-level information. Functional connectivity confirmed nonmusicians’ increased left IFG involvement reflects stronger routing of signal from PAC directed to IFG, presumably because sensory coding is insufficient to construct categories in less experienced listeners. Our findings establish auditory experience modulates specific engagement and inter-regional communication in the auditory-linguistic network supporting CP. Whereas early canonical PAC representations are sufficient to generate categories in highly trained ears, less experienced perceivers broadcast information downstream to higher-order linguistic brain areas (IFG) to construct abstract sound labels.
Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking
Authors: McGough Sarah F. , Johansson Michael A. , Lipsitch Marc , Menzies Nicolas A. 
Published: June 2019

AbstractDelays in case reporting are common to disease surveillance systems, making it difficult to track diseases in real-time. “Nowcast” approaches attempt to estimate the complete case counts for a given reporting date, using a time series of case reports that is known to be incomplete due to reporting delays. Modeling the reporting delay distribution is a common feature of nowcast approaches. However, many nowcast approaches ignore a crucial feature of infectious disease transmission—that future cases are intrinsically linked to past reported cases—and are optimized to a single application, which may limit generalizability. Here, we present a Bayesian approach, NobBS (Nowcasting by Bayesian Smoothing) capable of producing smooth and accurate nowcasts in multiple disease settings. We test NobBS on dengue in Puerto Rico and influenza-like illness (ILI) in the United States to examine performance and robustness across settings exhibiting a range of common reporting delay characteristics (from stable to time-varying), and compare this approach with a published nowcasting package. We show that introducing a temporal relationship between cases considerably improves performance when the reporting delay distribution is time-varying, and we identify trade-offs in the role of moving windows to accurately capture changes in the delay. We present software implementing this new approach (R package “NobBS”) for widespread application.SignificanceAchieving accurate, real-time estimates of disease activity is challenged by delays in case reporting. However, approaches that seek to estimate cases in spite of reporting delays often do not consider the temporal relationship between cases during an outbreak, nor do they identify characteristics of robust approaches that generalize to a wide range of surveillance contexts with very different reporting delays. Here, we present a smooth Bayesian nowcasting approach that produces accurate estimates that capture the time evolution of the epidemic curve and outperform a previous approach in the literature. We assess the performance for two diseases to identify important features of the reporting delay distribution that contribute to the model’s performance and robustness across surveillance settings.
De novoβ-alanine synthesis in α-proteobacteria involves a β-alanine synthase from the uracil degradation pathway
Authors: López-Sámano Mariana , Lozano-Aguirre Beltrán Luis Fernando , Sánchez-Thomas Rosina , Dávalos Araceli , Villaseñor Tomás , García-García Jorge Donato , García-de los Santos Alejandro 
Published: June 2019

Abstractβ-alanine synthesis in bacteria occurs by the decarboxylation of L-aspartate as part of the pantothenate synthesis pathway. In the other two domains of life we find different pathways for β-alanine formation, such as sources from spermine in plants, uracil in yeast and by transamination reactions in insects and mammals. There are also promiscuous decarboxylases that can decarboxylate aspartate. Several bioinformatics studies about the conservation of pantothenate synthesis pathway performed on bacteria, archaea and eukaryotes, have shown a partial conservation of the pathway. As a part of our work, we performed an analysis of the prevalence of reported β-alanine synthesis pathways in 204 genomes of alpha-proteobacteria, with a focus on theRhizobialesorder. The aim of this work was to determine the enzyme or pathway used to synthetize β-alanine inRhizobium etliCFN42. Our bioinformatics analysis showed that this strain encodes the pyrimidine degradation pathway in its genome. We obtained a β-alanine synthase (amaB)mutant that was a β-alanine auxotroph. Complementation with the cloned gene restored the wild type phenotype. Biochemical analysis confirmed that the recombinant AmaB catalyzed the formation of β-alanine from 3-Ureidopropionic acidin vitro. Here we show a different way in bacteria to produce this essential metabolite.ImportanceSince the pioneer studies of Cronan (1980) on β-alanine synthesis inE. coli, it has been assumed that the decarboxilation of aspartate by the L-aspartate-α-decarboxylase it’s the main enzymatic reaction for β-alanine synthesis in bacteria. Forty years later, while we were studying the pantothenic acid synthesis in rhizobia, we demonstrate that a numerous and diverse group of bacteria classified as α-proteobacteria synthesize β-alaninede novousing β-alanine synthase, the last enzyme from the reductive pathway for uracil degradation.Additionally, there is a growing interest in β-amino acid due to its remarkable pharmaceuticals properties as hypoglycemic, antiketogenic and anti-fungal agents.
SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies
Authors: Toki Naoko , Takahashi Hazuki , Zucchelli Silvia , Gustincich Stefano , Carninci Piero 
Published: June 2019

AbstractSINEUPs are long non-coding RNAs (lncRNAs) that contain a SINE element, which up-regulate the translation of target mRNA and have been studied in a wide range of applications for biological and therapeutic tools, although the molecular mechanism is unclear. Here, we focused on the kinetic distribution of target mRNAs and SINEUP RNAs by performing co-transfection of expression vectors for these transcripts into human embryonic normal kidney cells (HEK293T/17) to investigate the network of translational regulation. The results showed that co-localization of target mRNAs and SINEUP RNAs in the cytoplasm was one of the key phenomena. We identified PTBP1 and HNRNPK as essential RNA binding proteins. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhanced target mRNA translation. These findings will promote a better understanding of the mechanisms on the fate of regulatory RNAs implicated in efficient protein translation.
Identification of nutrient deficiency in bean plants by prompt chlorophyll fluorescence measurements and Artificial Neural Networks
Authors: Aleksandrov Vladimir 
Published: June 2019

AbstractThe deficiency of macro (N, P, S, Ca, Mg and K) and micro (Zn, Cu, B, Mo, Cl, Mn and Fe) minerals has a major effect on plant development. The lack of some nutrient minerals especially of nitrogen, potassium, calcium, phosphorus and iron is a huge problem for agriculture and early warning and prevention of the problem will be very useful for agro-industry. Methods currently used to determine nutritional deficiency in plants are soil analysis, plant tissue analysis, or combined methods. But these methods are slow and expensive. In this study, a new method for determining nutrient deficiency in plants based on the prompt fluorescence of chlorophyll a is proposed. In this paper bean plants are grown on a complete nutrient solution (control) were compared with those grown in a medium, which lacked one of these elements - N, P, K, Ca and Fe. In this article the mineral deficiency in nutrient solution was evaluated by the stress response of the plants estimated by leaves photosynthetic activity. The photosynthetic activity was estimated by analysis of the chlorophyll fluorescence using JIP-test approach that reflects functional activity of Photosystems I and II and of electron transfer chain between them, as well as the physiological state of the photosynthetic apparatus as whole. Next the fluorescence transient recorded from plants grown in nutrient solution with deficiency of N, P, K, Ca and Iron, as an input data in Artificial Neural Network was used. This ANN was train to recognise deficiency of N, P, K, Ca and Iron in bean plants. The results obtained were of high recognition accuracy. The ANN of fluorescence transient was presented as a possible approach to identify/predict the nutrient deficiency using the fast chlorophyll fluorescence records.