bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential gene expression profile between progressive and de novo muscle invasive bladder cancer and its prognostic implication
Authors: Carrasco Raquel , Izquierdo Laura , van der Heijden Antoine G. , Lozano Juan José , Franco Marco , Ingelmo-Torres Mercedes , Roldan Fiorella L. , Llorens Montserrat , Ribal María José , Mengual Lourdes , Alcaraz Antonio 
Published: March 2021

AbstractThis study aimed to ascertain gene expression profile differences between progressive muscle-invasive bladder cancer (MIBC) and de novo MIBC, and to identify prognostic biomarkers to improve patients’ treatment. Retrospective multicenter study in which 212 MIBC patients who underwent radical cystectomy between 2000 and 2019 were included. Gene expression profiles were determined in 26 samples using Illumina microarrays. The expression levels of 94 genes were studied by quantitative PCR in an independent set of 186 MIBC patients. In a median follow-up of 16 months, 46.7% patients developed tumor progression after cystectomy. In our series, progressive MIBC patients show a worse tumor progression (p = 0.024) and cancer-specific survival (CSS) (p = 0.049) than the de novo group. A total of 480 genes were found to be differently expressed between both groups. Differential expression of 24 out of the 94 selected genes was found in an independent cohort. RBPMC2 and DSC3 were found as independent prognostic biomarkers of tumor progression and CALD1 and LCOR were identified as prognostic biomarkers of CSS between both groups. In conclusion, progressive and de novo MIBC patients show different clinical outcome and gene expression profiles. Gene expression patterns may contribute to predict high-risk of progression to distant metastasis or CSS.
Exploration for olive fruit fly parasitoids across Africa reveals regional distributions and dominance of closely associated parasitoids
Authors: Wang Xingeng , Walton Vaughn M. , Hoelmer Kim A. , Pickett Charles H. , Blanchet Arnaud , Straser Robert K. , Kirk Alan A. , Daane Kent M. 
Published: March 2021

AbstractThe olive fruit fly, Bactrocera oleae, has been a key pest of olives in Europe and North America. We conducted the largest exploration for parasitoids associated with the fly across Sub-Saharan Africa (Kenya, Namibia, and South Africa) including some of the fly’s adjoining regions (Canary Islands, Morocco, Réunion Island and Tunisia). From Sub-Saharan regions, four braconids were collected: Bracon celer, Psytallia humilis, P. lounsburyi, and Utetes africanus. Results showed that their regional dominance was related to climate niches, with P. humilis dominant in hot semi-arid areas of Namibia, P. lounsburyi dominant in more tropical areas of Kenya, and U. africanus prevalent in Mediterranean climates of South Africa. Psytallia concolor was found in the Canary Islands, Morocco and Tunisian, and the Afrotropical braconid Diachasmimorpha sp. near fullawayi on Réunion Island. Furthermore, we monitored the seasonal dynamics of the fly and parasitoids in Cape Province of South Africa. Results showed that fruit maturity, seasonal variations in climates and interspecific interactions shape the local parasitoid diversity that contribute to the low fly populations. The results are discussed with regard to ecological adaptations of closely associated parasitoids, and how their adaptations impact biocontrol.
Application of text mining to develop AOP-based mucus hypersecretion genesets and confirmation with in vitro and clinical samples
Authors: Minet Emmanuel , Haswell Linsey E. , Corke Sarah , Banerjee Anisha , Baxter Andrew , Verrastro Ivan , De Abreu e Lima Francisco , Jaunky Tomasz , Santopietro Simone , Breheny Damien , Gaça Marianna D. 
Published: March 2021

AbstractMucus hypersecretion contributes to lung function impairment observed in COPD (chronic obstructive pulmonary disease), a tobacco smoking-related disease. A detailed mucus hypersecretion adverse outcome pathway (AOP) has been constructed from literature reviews, experimental and clinical data, mapping key events (KEs) across biological organisational hierarchy leading to an adverse outcome. AOPs can guide the development of biomarkers that are potentially predictive of diseases and support the assessment frameworks of nicotine products including electronic cigarettes. Here, we describe a method employing manual literature curation supported by a focused automated text mining approach to identify genes involved in 5 KEs contributing to decreased lung function observed in tobacco-related COPD. KE genesets were subsequently confirmed by unsupervised clustering against 3 different transcriptomic datasets including (1) in vitro acute cigarette smoke and e-cigarette aerosol exposure, (2) in vitro repeated incubation with IL-13, and (3) lung biopsies from COPD and healthy patients. The 5 KE genesets were demonstrated to be predictive of cigarette smoke exposure and mucus hypersecretion in vitro, and less conclusively predict the COPD status of lung biopsies. In conclusion, using a focused automated text mining and curation approach with experimental and clinical data supports the development of risk assessment strategies utilising AOPs.
Sedimentary evolution and controlling factors of Early-Mid Miocene Deltaic systems in the Northern Pearl River Mouth Basin, South China Sea
Authors: Wang Yanru , Lin Changsong , Zhang Zhongtao , Zhang Bo , Liu Hanyao 
Published: March 2021

AbstractThe Pearl River Mouth Basin is located at the northern continental shelf of the South China Sea. Since the early Miocene, the Paleo-pearl river transported a large amount of sediments to the northwest of the basin and resulted in the formation of a large-scale river-delta depositional system, which has become an important oil and gas reservoir in the study area. In the current paper, we investigate the characteristics and evolution of fluvial-deltaic depositional systems and their controlling factors, including sea level change, tectonic subsidence and sediment supply on the basis of 3D seismic, well logging and core data. Early-Mid Miocene succession can be divided into two second-order sequences (CS1–CS2) and eight third-order sequences (S1–S8). Deltaic systems developed in S1–S2 are relatively coarse in grain size, and the delta plain deposits are dominated by thickly stacked (100–180 m) distributary channel sand bodies and interpreted as braided delta depositional system. In the early stage (S1–S2), the braided delta systems mainly distributed in the west of the Baiyun Sag, which were proceeded by a retreat to the south of the Enping Sag along with sharply rising sea level. Following the transgression of S2, the provenance of the Paleo-Pearl River extended to the coastal region of South China, and the papleoclimate changed from warm and humid to dry and cold in the early Miocene, leading to the development of transition of braided river delta to meandering river delta, which was characterized by relatively fine grain deposits. During the deposition of S3–S6, well sorted and rounded fine sandstones of deltaic front deposits accumulated in the study area. The retrogradation to accretion and subsequent progradation of these meander delta systems are attributed to the sea level change in the study area. During the deposition of S7–S8, the delta front retreated to the south of the Enping depression as a result of minor sea level rise, reduction in sediment input, and subsidence rate. This resulted in the development of a wave-controlled deltaic depositional system.
Early socialization and environmental enrichment of lactating piglets affects the caecal microbiota and metabolomic response after weaning
Authors: Saladrigas-García M. , D’Angelo M. , Ko H. L. , Traserra S. , Nolis P. , Ramayo-Caldas Y. , Folch J. M. , Vergara P. , Llonch P. , Pérez J. F. , Martín-Orúe S. M. 
Published: March 2021

AbstractThe aim of this study was to determine the possible impact of early socialization and an enriched neonatal environment to improve adaptation of piglets to weaning. We hypothesized that changes in the microbiota colonization process and in their metabolic response and intestinal functionality could help the animals face weaning stress. A total of 48 sows and their litters were allotted into a control (CTR) or an enriched treatment (ENR), in which piglets from two adjacent pens were combined and enriched with toys. The pattern of caecal microbial colonization, the jejunal gene expression, the serum metabolome and the intestinal physiology of the piglets were assessed before (-2 d) and after weaning (+ 3d). A differential ordination of caecal microbiota was observed after weaning. Serum metabolome suggested a reduced energetic metabolism in ENR animals, as evidenced by shifts in triglycerides and fatty acids, VLDL/LDL and creatine regions. The TLR2 gene showed to be downregulated in the jejunum of ENR pigs after weaning. The integration of gene expression, metabolome and microbiota datasets confirmed that differences between barren and enriched neonatal environments were evident only after weaning. Our results suggest that improvements in adaptation to weaning could be mediated by a better response to the post-weaning stress.
Real time and delayed effects of subcortical low intensity focused ultrasound
Authors: Cain Joshua A. , Visagan Shakthi , Johnson Micah A. , Crone Julia , Blades Robin , Spivak Norman M. , Shattuck David W. , Monti Martin M. 
Published: March 2021

AbstractDeep brain nuclei are integral components of large-scale circuits mediating important cognitive and sensorimotor functions. However, because they fall outside the domain of conventional non-invasive neuromodulatory techniques, their study has been primarily based on neuropsychological models, limiting the ability to fully characterize their role and to develop interventions in cases where they are damaged. To address this gap, we used the emerging technology of non-invasive low-intensity focused ultrasound (LIFU) to directly modulate left lateralized basal ganglia structures in healthy volunteers. During sonication, we observed local and distal decreases in blood oxygenation level dependent (BOLD) signal in the targeted left globus pallidus (GP) and in large-scale cortical networks. We also observed a generalized decrease in relative perfusion throughout the cerebrum following sonication. These results show, for the first time using functional MRI data, the ability to modulate deep-brain nuclei using LIFU while measuring its local and global consequences, opening the door for future applications of subcortical LIFU.
Trends and outcomes for non-elective neurosurgical procedures in Central Europe during the COVID-19 pandemic
Authors: Grassner Lukas , Petr Ondra , Warner Freda M. , Dedeciusova Michaela , Mathis Andrea Maria , Pinggera Daniel , Gsellmann Sina , Meiners Laura C. , Freigang Sascha , Mokry Michael , Resch Alexandra , Kretschmer Thomas , Rossmann Tobias , Navarro Francisco Ruiz , Gruber Andreas , Spendel Mathias , Winkler Peter A. , Marhold Franz , Sherif Camillo , Wais Jonathan P. , Rössler Karl , Pfisterer Wolfgang , Mühlbauer Manfred , Trivik-Barrientos Felipe A. , Rath Sebastian , Voldrich Richard , Krska Lukas , Lipina Radim , Kerekanic Martin , Fiedler Jiri , Kasik Petr , Priban Vladimir , Tichy Michal , Krupa Petr , Cesak Tomas , Kroupa Robert , Callo Andrej , Haninec Pavel , Pohlodek Daniel , Krahulik David , Sejkorova Alena , Sames Martin , Dvorak Josef , Suchomel Petr , Tomas Robert , Klener Jan , Juran Vilem , Smrcka Martin , Linzer Petr , Kaiser Miroslav , Hrabovsky Dusan , Jancalek Radim , Kälin Vincens , Bozinov Oliver , Niggli Cedric , Serra Carlo , Guatta Ramona , Kuhlen Dominique E. , Wanderer Stefan , Marbacher Serge , Lavé Alexandre , Schaller Karl , Esculier Clarinde , Raabe Andreas , Kramer John L. K. , Thomé Claudius , Netuka David 
Published: March 2021

AbstractThe world currently faces the novel severe acute respiratory syndrome coronavirus 2 pandemic. Little is known about the effects of a pandemic on non-elective neurosurgical practices, which have continued under modified conditions to reduce the spread of COVID-19. This knowledge might be critical for the ongoing second coronavirus wave and potential restrictions on health care. We aimed to determine the incidence and 30-day mortality rate of various non-elective neurosurgical procedures during the COVID-19 pandemic. A retrospective, multi-centre observational cohort study among neurosurgical centres within Austria, the Czech Republic, and Switzerland was performed. Incidence of neurosurgical emergencies and related 30-day mortality rates were determined for a period reflecting the peak pandemic of the first wave in all participating countries (i.e. March 16th–April 15th, 2020), and compared to the same period in prior years (2017, 2018, and 2019). A total of 4,752 emergency neurosurgical cases were reviewed over a 4-year period. In 2020, during the COVID-19 pandemic, there was a general decline in the incidence of non-elective neurosurgical cases, which was driven by a reduced number of traumatic brain injuries, spine conditions, and chronic subdural hematomas. Thirty-day mortality did not significantly increase overall or for any of the conditions examined during the peak of the pandemic. The neurosurgical community in these three European countries observed a decrease in the incidence of some neurosurgical emergencies with 30-day mortality rates comparable to previous years (2017–2019). Lower incidence of neurosurgical cases is likely related to restrictions placed on mobility within countries, but may also involve delayed patient presentation.
Associations between seven-year C-reactive protein trajectory or pack-years smoked with choroidal or retinal thicknesses in young adults
Authors: Lee Samantha Sze-Yee , Beales Darren John , Chen Fred K. , Yazar Seyhan , Alonso-Caneiro David , Mackey David A. 
Published: March 2021

AbstractInflammation and cigarette smoking predispose to macular diseases, and choroidal and retinal thinning. We explored the choroidal and retinal thicknesses in young adults against their 7-year C-reactive protein (CRP) level trajectory and pack-years smoked. Participants from the Raine study, a longitudinal cohort study, had serum CRP levels analysed at the 14-, 17-, and 20-year follow-ups. Group-based trajectory modelling was used to classify participants according to their 7-year CRP levels. At the 20-year follow-up (at 18–22 years old), participants completed questionnaires on their smoking history, and underwent optical coherence tomography imaging to obtain their choroidal and retinal thicknesses at the macula. Three CRP trajectories were identified: consistently low CRP levels (78% of sample), increasing (11%), or consistently high (11%). 340 and 1035 participants were included in the choroidal and retinal thickness analyses, respectively. Compared to those in the “Low” trajectory group, participants in the “Increasing” and “High” groups had 14–21 μm thinner choroids at most macular regions. Every additional pack-year smoked was linked with a 0.06–0.10 μm thinner retina at the inner and outer macular rings, suggesting a dose-dependent relationship between smoking and thinner retinas. These associations may suggest that an increased risk of future visual impairment or eye disease associated with these risk factors may be present since young adulthood.
Simulation study on radiation exposure of emergency medical responders from radioactively contaminated patients
Authors: Tsujiguchi Takakiyo , Suzuki Yoko , Sakamoto Mizuki , Narumi Kazuki , Ito Katsuhiro , Yasuda Hiroshi , Tokonami Shinji , Kashiwakura Ikuo 
Published: March 2021

AbstractEmergency medical responders (EMRs) who treat victims during a radiation emergency are at risk of radiation exposure. In this study, the exposure dose to EMRs treating hypothetically contaminated patients was estimated using a Monte Carlo simulation, and the findings may be useful for educating EMRs and reducing their anxiety. The Monte Carlo simulation estimated radiation doses for adult computational phantoms based on radioactive contamination conditions and radiation dosages from previous studies. At contamination conditions below the typical upper limit of general Geiger–Müller survey meters, the radiation doses to EMRs were estimated to be less than 1 μSv per hour. In cases with greater contamination due to mishandling of an intense radioactive source (hundreds of GBq), the radiation doses to EMRs could reach approximately 100 mSv per hour. These results imply that a radiological accident with a highly radioactive source could expose EMR to significant radiation that exceeds their dose limit. Thus, authorities and other parties should ensure that EMRs receive appropriate education and training regarding measures that can be taken to protect themselves from the possibility of excessive radiation exposure. The results of this study may provide EMRs with information to take appropriate protective measures, although it is also important that they not hesitate to perform lifesaving measures because of concerns regarding radiation.
Quantitative, noninvasive MRI characterization of disease progression in a mouse model of non-alcoholic steatohepatitis
Authors: Waghorn Philip A. , Ferreira Diego S. , Erstad Derek J. , Rotile Nicholas J. , Masia Ricard , Jones Chloe M. , Tu Chuantao , Sojoodi Mozhdeh , Chen Yin-ching I. , Schlerman Franklin , Wellen Jeremy , Martinez Robert V. P. , Tanabe Kenneth K. , Fuchs Bryan C. , Caravan Peter 
Published: March 2021

AbstractNon-alcoholic steatohepatitis (NASH) is an increasing cause of chronic liver disease characterized by steatosis, inflammation, and fibrosis which can lead to cirrhosis, hepatocellular carcinoma, and mortality. Quantitative, noninvasive methods for characterizing the pathophysiology of NASH at both the preclinical and clinical level are sorely needed. We report here a multiparametric magnetic resonance imaging (MRI) protocol with the fibrogenesis probe Gd-Hyd to characterize fibrotic disease activity and steatosis in a common mouse model of NASH. Mice were fed a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) to induce NASH with advanced fibrosis. Mice fed normal chow and CDAHFD underwent MRI after 2, 6, 10 and 14 weeks to measure liver T1, T2*, fat fraction, and dynamic T1-weighted Gd-Hyd enhanced imaging of the liver. Steatosis, inflammation, and fibrosis were then quantified by histology. NASH and fibrosis developed quickly in CDAHFD fed mice with strong correlation between morphometric steatosis quantification and liver fat estimated by MRI (r = 0.90). Sirius red histology and collagen quantification confirmed increasing fibrosis over time (r = 0.82). Though baseline T1 and T2* measurements did not correlate with fibrosis, Gd-Hyd signal enhancement provided a measure of the extent of active fibrotic disease progression and correlated strongly with lysyl oxidase expression. Gd-Hyd MRI accurately detects fibrogenesis in a mouse model of NASH with advanced fibrosis and can be combined with other MR measures, like fat imaging, to more accurately assess disease burden.
A scheme for enabling the ultimate speed of threshold switching in phase change memory devices
Authors: Saxena Nishant , Raghunathan Rajamani , Manivannan Anbarasu 
Published: March 2021

AbstractPhase change materials exhibit threshold switching (TS) that establishes electrical conduction through amorphous material followed by Joule heating leading to its crystallization (set). However, achieving picosecond TS is one of the key challenges for realizing non-volatile memory operations closer to the speed of computing. Here, we present a trajectory map for enabling picosecond TS on the basis of exhaustive experimental results of voltage-dependent transient characteristics of Ge2Sb2Te5 phase-change memory (PCM) devices. We demonstrate strikingly faster switching, revealing an extraordinarily low delay time of less than 50 ps for an over-voltage equal to twice the threshold voltage. Moreover, a constant device current during the delay time validates the electronic nature of TS. This trajectory map will be useful for designing PCM device with SRAM-like speed.
A feasibility study of gamma ray source finder development for multiple sources scenario based on a Monte Carlo simulation
Authors: Farzanehpoor Alwars Ali , Rahmani Faezeh 
Published: March 2021

AbstractIn this research, a rapid and accurate gamma finder system which can find orphan gamma-ray sources has been designed based on NaI(Tl) detector. By proposing complementary methods to our previous researches, an attempt has been made to provide an approach to solve the problem of 3D localization in multiple orphan gamma-ray sources scenario. Based on our previous research, the new conceptual design has been proposed and simulated using Monte Carlo MCNPX2.6 code. Afterward, in order to identify its key characteristics and features, the proposed design has been tested in several different scenarios (multiple gamma sources with various activities in different distances).
The role of bacterial urease activity on the uniformity of carbonate precipitation profiles of bio-treated coarse sand specimens
Authors: Konstantinou Charalampos , Wang Yuze , Biscontin Giovanna , Soga Kenichi 
Published: March 2021

AbstractProtocols for microbially induced carbonate precipitation (MICP) have been extensively studied in the literature to optimise the process with regard to the amount of injected chemicals, the ratio of urea to calcium chloride, the method of injection and injection intervals, and the population of the bacteria, usually using fine- to medium-grained poorly graded sands. This study assesses the effect of varying urease activities, which have not been studied systematically, and population densities of the bacteria on the uniformity of cementation in very coarse sands (considered poor candidates for treatment). A procedure for producing bacteria with the desired urease activities was developed and qPCR tests were conducted to measure the counts of the RNA of the Ure-C genes. Sand biocementaton experiments followed, showing that slower rates of MICP reactions promote more effective and uniform cementation. Lowering urease activity, in particular, results in progressively more uniformly cemented samples and it is proven to be effective enough when its value is less than 10 mmol/L/h. The work presented highlights the importance of urease activity in controlling the quality and quantity of calcium carbonate cements.
Conception and bicentric validation of the proSCANNED score, a simplified bedside prognostic score for Heart Failure patients
Authors: Duflos Claire , Solecki Kamila , Galinier Michel , Itier Romain , Roncalli Jerome , Goger Anne-Laure , Mandoraah Bara , Kalmanovich Eran , Huet Fabien , Agullo Audrey , Delseny Delphine , Macia Jean-Christophe , Leclercq Florence , Mercier Gregoire , Roubille François 
Published: March 2021

AbstractA simple and accurate prognostic tool for Heart Failure (HF) patients is critical to improve follow-up. Different risk scores are accurate but with limited clinical applicability. The current study aims to derive and validate a simple predictive tool for HF prognosis. French outpatients with stable HF of two university hospitals were included in the derivation (N = 134) or in the validation (N = 274) sample and followed up for a median of 23 months. Potential predictors were variables with known association with mortality and easily available. The proSCANNED risk score was derived using a parametric survival model on complete case data; it includes 8 binary variables and its values are 0–8. In the validation sample, the ability of the score to discriminate the 1-year vital status was moderate (AUC = 0.71, IC95% = [0.64–0.71]). However, the stratification of the score in three groups showed a good calibration for patients in the low- and medium-risk risk group. The proSCANNED score is an easy-to-use tool in clinical practice with a good discrimination, stability, and calibration sufficient to improve the medical care of patients. Other follow up studies are necessary to assess score applicability in larger populations, and its impact.