bluuebunny/crossref_metadata_2025_split huggingface dataset:
microRNA and Metabolite Signatures Linked to Early Consequences of Lethal Radiation
Authors: Chakraborty Nabarun , Gautam Aarti , Holmes-Hampton Gregory P. , Kumar Vidya P. , Biswas Shukla , Kumar Raina , Hamad Dana , Dimitrov George , Olabisi Ayodele O. , Hammamieh Rasha , Ghosh Sanchita P. 
Published: March 2020

AbstractLethal total body irradiation (TBI) triggers multifactorial health issues in a potentially short time frame. Hence, early signatures of TBI would be of great clinical value. Our study aimed to interrogate microRNA (miRNA) and metabolites, two biomolecules available in blood serum, in order to comprehend the immediate impacts of TBI. Mice were exposed to a lethal dose (9.75 Gy) of Cobalt-60 gamma radiation and euthanized at four time points, namely, days 1, 3, 7 and 9 post-TBI. Serum miRNA libraries were sequenced using the Illumina small RNA sequencing protocol, and metabolites were screened using a mass spectrometer. The degree of early impacts of irradiation was underscored by the large number of miRNAs and metabolites that became significantly expressed during the Early phase (day 0 and 1 post-TBI). Radiation-induced inflammatory markers for bone marrow aplasia and pro-sepsis markers showed early elevation with longitudinal increment. Functional analysis integrating miRNA-protein-metabolites revealed inflammation as the overarching host response to lethal TBI. Early activation of the network linked to the synthesis of reactive oxygen species was associated with the escalated regulation of the fatty acid metabolism network. In conclusion, we assembled a list of time-informed critical markers and mechanisms of significant translational potential in the context of a radiation exposure event.
Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment
Authors: Rachlin Audrey , Mayo Mark , Webb Jessica R. , Kleinecke Mariana , Rigas Vanessa , Harrington Glenda , Currie Bart J. , Kaestli Mirjam 
Published: March 2020

AbstractMelioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.
Semi-CAM: A semi-supervised deconvolution method for bulk transcriptomic data with partial marker gene information
Authors: Dong Li , Kollipara Avinash , Darville Toni , Zou Fei , Zheng Xiaojing 
Published: March 2020

AbstractDeconvolution of bulk transcriptomics data from mixed cell populations is vital to identify the cellular mechanism of complex diseases. Existing deconvolution approaches can be divided into two major groups: supervised and unsupervised methods. Supervised deconvolution methods use cell type-specific prior information including cell proportions, reference cell type-specific gene signatures, or marker genes for each cell type, which may not be available in practice. Unsupervised methods, such as non-negative matrix factorization (NMF) and Convex Analysis of Mixtures (CAM), in contrast, completely disregard prior information and thus are not efficient for data with partial cell type-specific information. In this paper, we propose a semi-supervised deconvolution method, semi-CAM, that extends CAM by utilizing marker information from partial cell types. Analysis of simulation and two benchmark data have demonstrated that semi-CAM outperforms CAM by yielding more accurate cell proportion estimations when markers from partial/all cell types are available. In addition, when markers from all cell types are available, semi-CAM achieves better or similar accuracy compared to the supervised method using signature genes, CIBERSORT, and the marker-based supervised methods semi-NMF and DSA. Furthermore, analysis of human chlamydia-infection data with bulk expression profiles from six cell types and prior marker information of only three cell types suggests that semi-CAM achieves more accurate cell proportion estimations than CAM.
Perioperative symptomatic venous thromboembolism after immediate chemoprophylaxis in patients with pelvic and lower-extremity fractures
Authors: Lee Jin Kyu , Koo Ja Wook , Jeong Soo-Young , Choi Sihoon , Park Ki-Chul , Hwang Kyu-Tae 
Published: March 2020

AbstractThe purpose of this study was to investigate the incidence of symptomatic venous thromboembolism (VTE) after chemoprophylaxis in patients with pelvic and lower-extremity fractures, and to identify risk factors for VTEs in this subgroup of patients. To detect VTE, multi-detector computed tomography (CT) angiography was performed. Of 363 patients assessed, the incidence of symptomatic VTE was 12.4% (45 patients), and the incidence of symptomatic PE was 5.2% (19 patients). For the risk-factor analysis, a higher Charlson comorbidity index (p = 0.037), and a history of external fixator application (p = 0.007) were associated with increased VTE risk. Among patients who had VTE, male sex (p = 0.017), and above-the-knee fractures (p = 0.035) were associated with increased pulmonary embolism (PE) risk. In conclusions, the incidence of VTE in post-traumatic patients is not low after chemoprophylaxis. Risk factors for VTE and PE are different among patients with pelvic and lower-extremity fractures.
Application of random forest based approaches to surface-enhanced Raman scattering data
Authors: Seifert Stephan 
Published: March 2020

AbstractSurface-enhanced Raman scattering (SERS) is a valuable analytical technique for the analysis of biological samples. However, due to the nature of SERS it is often challenging to exploit the generated data to obtain the desired information when no reporter or label molecules are used. Here, the suitability of random forest based approaches is evaluated using SERS data generated by a simulation framework that is also presented. More specifically, it is demonstrated that important SERS signals can be identified, the relevance of predefined spectral groups can be evaluated, and the relations of different SERS signals can be analyzed. It is shown that for the selection of important SERS signals Boruta and surrogate minimal depth (SMD) and for the analysis of spectral groups the competing method Learner of Functional Enrichment (LeFE) should be applied. In general, this investigation demonstrates that the combination of random forest approaches and SERS data is very promising for sophisticated analysis of complex biological samples.
Improving the drug-likeness of inspiring natural products - evaluation of the antiparasitic activity against Trypanosoma cruzi through semi-synthetic and simplified analogues of licarin A
Authors: Morais Thiago R. , Conserva Geanne A. Alves , Varela Marina T. , Costa-Silva Thais A. , Thevenard Fernanda , Ponci Vitor , Fortuna Ana , Falcão Amílcar C. , Tempone Andre G. , Fernandes João Paulo S. , Lago João Henrique G. 
Published: March 2020

AbstractNeolignan licarin A (1) was isolated from leaves of Nectandra oppositifolia (Lauraceae) and displayed activity against trypomastigote forms of the etiologic agent of American trypanosomiasis, Trypanosoma cruzi. Aiming for the establishment of SAR, five different compounds (1a – 1e) were prepared and tested against T. cruzi. The 2-allyl derivative of licarin A (1d) exhibited higher activity against trypomastigotes of T. cruzi (IC50 = 5.0 μM and SI = 9.0), while its heterocyclic derivative 1e displayed IC50 of 10.5 μM and reduced toxicity against NCTC cells (SI > 19.0). However, these compounds presented limited oral bioavailability estimation (<85%, Papp <1.0 × 10−6 cm/s) in parallel artificial membrane permeability assays (PAMPA) due to excessive lipophilicity. Based on these results, different simplified structures of licarin A were designed: vanillin (2), vanillyl alcohol (3), isoeugenol (4), and eugenol (5), as well as its corresponding methyl (a), acetyl (b), O-allyl (c), and C-allyl (d) analogues. Vanillin (2) and its acetyl derivative (2b) displayed expressive activity against intracellular amastigotes of T. cruzi with IC50 values of 5.5 and 5.6 μM, respectively, and reduced toxicity against NCTC cells (CC50 > 200 μM). In addition, these simplified analogues showed a better permeability profile (Papp > 1.0 × 10−6 cm/s) on PAMPA models, resulting in improved drug-likeness. Vanillyl alcohol acetyl derivative (3b) and isoeugenol methyl derivative (4a) displayed activity against the extracellular forms of T. cruzi (trypomastigotes) with IC50 values of 5.1 and 8.8 μM respectively. Based on these results, compounds with higher selectivity index against extracellular forms of the parasite (1d, 1e, 3d, and 4a) were selected for a mechanism of action study. After a short incubation period (1 h) all compounds increased the reactive oxygen species (ROS) levels of trypomastigotes, suggesting cellular oxidative stress. The ATP levels were increased after two hours of incubation, possibly involving a high energy expenditure of the parasite to control the homeostasis. Except for compound 4a, all compounds induced hyperpolarization of mitochondrial membrane potential, demonstrating a mitochondrial imbalance. Considering the unique mitochondria apparatus of T. cruzi and the lethal alterations induced by structurally based on licarin A, these compounds are interesting hits for future drug discovery studies in Chagas disease.
Examining the association between serum phosphate levels and leukocyte telomere length
Authors: Yang Zhe-Yu , Kao Tung-Wei , Peng Tao-Chun , Chen Yuan-Yuei , Yang Hui-Fang , Wu Chen-Jung , Chen Wei-Liang 
Published: March 2020

AbstractAccelerated telomere attrition is related to various diseases, and multiple factors have been reported to influence telomere length. However, little attention has focused on the relationship between serum phosphate levels and mean telomere length. The purpose of this study was to explore the relationship between serum phosphate levels and mean telomere length in the US general population. A total of 7,817 participants from the 1999–2002 NHANES were included. The association between serum phosphate levels and mean telomere length was investigated using regression models. A remarkably positive relationship between serum phosphate levels and mean telomere length emerged after adjustments were made for covariates. The adjusted β coefficient of serum phosphate levels for mean telomere length was 0.038 (95% confidence intervals (CIs), 0.022 to 0.095, p = 0.002). A longer telomere length was observed in participants with serum phosphate levels in the highest quartiles, and a dose-dependent association was observed. Our study demonstrated that higher quartiles of phosphate had a remarkable correlation with longer telomere length.
EDN1 gene potentially involved in the development of acute mountain sickness
Authors: Yu Jie , Liu Chuan , Zhang Chen , Bian ShiZhu , Yang Jie , Zhang JiHang , Gao XuBin , Qiu YouZhu , Huang Lan 
Published: March 2020

AbstractPrevious investigations have indicated that environmental and genetic factors collectively contribute to the development of acute mountain sickness (AMS), but whether the EDN1 gene is involved in AMS remains to be elucidated. A total of 356 healthy male soldiers who had not traveled to high altitudes in the previous 12 months were enrolled in our study. All participants were taken by plane from 500 m (Chengdu in Sichuan Province) to a 3700 m highland (Lhasa) within 2 hours. Clinical data were collected within 24 hours, and pulmonary function parameters were completed simultaneously. Genotypes were obtained by using iMLDR genotyping assays. A total of 237 soldiers (66.57%) presented AMS symptoms, including headache, dizziness, gastrointestinal upset and fatigue. Soldiers with AMS showed an increase in heart rate (HR), plasma tryptophan and serotonin, and a decrease in SaO2, FEV1, PEF, FVC, V75, V50, V25 and MMF (all P < 0.01). Notably, allele T in single nucleotide polymorphism (SNP) rs2070699 showed a positive correlation with the occurrence of AMS. A general linear regression analysis showed that rs2060799, Mean Arterial Pressure (MAP), SaO2, FVC, tryptophan and serotonin were independent predictors for the occurrence of AMS. Importantly, the area under the curve (AUC) values for tryptophan (0.998), serotonin (0.912) and FVC (0.86) had diagnostic specificity and sensitivity. Our results demonstrated that AMS is accompanied by changes in lung function parameters, increased plasma tryptophan and serotonin levels, and that the EDN1 polymorphism is a potential risk factor for AMS.
Targeted Drug Delivery of Microbubble to Arrest Abdominal Aortic Aneurysm Development: A Simulation Study Towards Optimized Microbubble Design
Authors: Shamloo Amir , Ebrahimi Sina , Amani Ali , Fallah Famida 
Published: March 2020

AbstractAbdominal aortic aneurysm (AAA) is an irreversible bulge in the artery with higher prevalence among the elderlies. Increase of the aneurysm diameter by time is a fatal phenomenon which will lead to its sidewall rupture. Invasive surgical treatments are vital in preventing from AAA development. These approaches however have considerable side effects. Targeted drug delivery using microbubbles (MBs) has been recently employed to suppress the AAA growth. The present study is aimed to investigate the surface adhesion of different types of drug-containing MBs to the inner wall of AAA through ligand-receptor binding, using fluid-structure interaction (FSI) simulation by using a patient CT-scan images of the vascular system. The effect of blood flow through AAA on MBs delivery to the intended surface was also addressed. For this purpose, the adherence of four types of MBs with three different diameters to the inner surface wall of AAA was studied in a patient with 40-mm diameter aneurysm. The effects of the blood mechanical properties on the hematocrit (Hct) percentage of patients suffering from anemia and diabetes were studied. Moreover, the impact of variations in the artery inlet velocity on blood flow was addressed. Simulation results demonstrated the dependency of the surface density of MBs (SDM) adhered on the AAA lumen to the size and the type of MBs. It was observed that the amount of SDM due to adhesion on the AAA lumen for one of the commercially-approved MBs (Optison) with a diameter of 4.5 μm was higher than the other MBs. Furthermore, we have shown that the targeted drug delivery to the AAA lumen is more favorable in healthy individuals (45% Hct) compared to the patients with diabetes and anemia. Also, it was found that the targeted drug delivery method using MBs on the patients having AAA with complicated aneurysm shape and negative inlet blood flow velocity can be severely affected.
The Size-Value Compatibility Effect
Authors: Hasegawa Kunihiro 
Published: March 2020

AbstractThis study aimed to examine the relationship between an object’s physical size and judgements of its value. Two preregistered experiments were performed to explore a size-value compatibility effect. Two images of Japanese-yen coins with different values but similar actual sizes (10-yen and 100-yen) were manipulated for size and presented side-by-side on a computer screen. Participants judged which coin was larger or smaller based on the images. Results revealed that size judgements were slower and less accurate when the lower-value coin was presented as larger than the higher-value coin, compared to when the lower-value coin was presented as smaller. This effect was observed even after participants had been allowed to examine the physical coins prior to the experiment to judge their actual size. This finding suggests that participants perceived the coins’ values based on their sizes, indicating it may be difficult for many people to stop thinking ‘better is bigger’.
The “gift effect” on functional brain connectivity. Inter-brain synchronization when prosocial behavior is in action
Authors: Balconi Michela , Fronda Giulia 
Published: March 2020

AbstractThe gift exchange represents a moment that characterizes interpersonal interactions. In particular, research in psychological and neuroscientific fields aimed to observe the social function of gift exchange. Specifically, the present study aimed to investigate the effects of prosocial behavior, experienced during gift exchange, on individuals’ cognitive performance and brain activity. To this aim, behavioral performance and neural activity of 15 dyads of participants, with a consolidated friendship, were collected during the execution of an attentional cooperative task before or after a gift exchange. Individuals’ brain activity was recorded through the use of Functional Near Infrared Spectroscopy (fNIRS) in hyperscanning. Results showed an increase of perceived cooperation and cognitive performance, in terms of accuracy (ACC), after gift exchange. The increase of interpersonal tuning and cooperation was also shown by neural activity with an increase of oxygenated hemoglobin (O2Hb) intra-brain and inter-brain connectivity in the dorsolateral prefrontal cortex (DLPFC) following the gift exchange. Moreover, from ConIndex analysis emerged an increase of inter-brain connectivity compared to intra-brain in DLPFC area. The present study, therefore, highlights how prosocial behavior can have positive effects on cognitive performance improvement and interpersonal relationships and neural coordination strengthen, increasing intra and inter-brain connectivity mechanisms.
Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture
Authors: Cummings Lisa A. , Hoogestraat Daniel R. , Rassoulian-Barrett Sara L. , Rosenthal Christopher A. , Salipante Stephen J. , Cookson Brad T. , Hoffman Noah G. 
Published: March 2020

AbstractOptimal clinical decision-making depends on identification of clinically relevant organisms present in a sample. Standard microbiological culture may fail to identify unusual or fastidious organisms and can misrepresent relative abundance of sample constituents. Culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We used next-generation 16S rRNA gene sequencing (NGS16S) to determine how often cultivatable organisms in complex polymicrobial samples are not reported by standard culture. Twenty consecutive bronchoalveolar lavage (BAL) samples were plated to standard and additional media; bacteria were identified by NGS16S analysis of DNA extracted directly from samples or from washed culture plates. 96% of organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up provides an incomplete assessment of microbial constituents. Direct NGS16S correlated well with standard culture, identifying the same predominant organism in 50% of samples. When predominant organisms differed, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions for this specimen. NGS16S identified more organisms per sample and allowed identification of fastidious organisms, while culture was better at capturing organisms when bacterial load was low, and allowed incidental recovery of non-bacterial pathogens. Molecular and culture-based methods together detect more organisms than either method alone.
Analyses of air pollution control measures and co-benefits in the heavily air-polluted Jinan city of China, 2013–2017
Authors: Cui Liangliang , Zhou Jingwen , Peng Xiumiao , Ruan Shiman , Zhang Ying 
Published: March 2020

AbstractChina has made great efforts in air pollution control since 2013. However, there is a lack of evaluation of environmental, health and economic co-benefits associated with the national and local air pollution control measures at a city level. We analyzed local air pollution control policies and implementation in Jinan, one of the most heavily air-polluted cities in China between 2013 and 2017. We assessed the changes in exhaust emissions, air quality, mortality and morbidity of associated specific-diseases, and related economic benefits. We also projected the future scenarios of PM2.5 concentration dropped to 15 μg/m3. There were significant decreases in exhaust emissions of SO2 and NOx in Jinan during the study period. Annual reductions in ambient air pollution were 72.6% for SO2, 43.1% for PM2.5, and 34.2% for PM10. A total of 2,317 (95%CI: 1,533–2,842) premature deaths and 15,822 (95%CI: 8,734–23,990) related morbidity cases had been avoided in 2017, leading to a total of US$ 317.7 million (95%CI: 227.5–458.1) in economic benefits. Decreasing PM2.5 concentrations to 15 μg/m3 would result in reductions of 70% in total PM2.5-related non-accidental mortality and 95% in total PM2.5-related morbidity, which translates into US$ 1,289.5 million (95%CI: 825.8–1,673.6) in economic benefits. The national and local air pollution control measures have brought significant environmental, health and economic benefits to a previously heavy polluted Chinese city.
Vaginal metabolome: towards a minimally invasive diagnosis of microbial invasion of the amniotic cavity in women with preterm labor
Authors: Vicente-Muñoz Sara , Cobo Teresa , Puchades-Carrasco Leonor , Sánchez-García Ana B. , Agustí Núria , Palacio Montse , Pineda-Lucena Antonio , Gratacós Eduard 
Published: March 2020

AbstractMicrobial invasion of the amniotic cavity (MIAC) is only identified by amniocentesis, an invasive procedure that limits its clinical translation. Here, we aimed to evaluate whether the vaginal metabolome discriminates the presence/absence of MIAC in women with preterm labor (PTL) and intact membranes. We conducted a case-control study in women with symptoms of PTL below 34 weeks who underwent amniocentesis to discard MIAC. MIAC was defined as amniotic fluid positive for microorganisms identified by specific culture media. The cohort included 16 women with MIAC and 16 control (no MIAC). Both groups were matched for age and gestational age at admission. Vaginal fluid samples were collected shortly after amniocentesis. Metabolic profiles were analyzed by nuclear magnetic resonance (NMR) spectroscopy and compared using multivariate and univariate statistical analyses to identify significant differences between the two groups. The vaginal metabolomics profile of MIAC showed higher concentrations of hypoxanthine, proline, choline and acetylcholine and decreased concentrations of phenylalanine, glutamine, isoleucine, leucine and glycerophosphocholine. In conclusion, metabolic changes in the NMR-based vaginal metabolic profile are able to discriminate the presence/absence of MIAC in women with PTL and intact membranes. These metabolic changes might be indicative of enhanced glycolysis triggered by hypoxia conditions as a consequence of bacterial infection, thus explaining the utilization of alternative energy sources in an attempt to replenish glucose.