bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negligible Risk of Acute Renal Failure Among Hospitalized Patients After Contrast-Enhanced Imaging With Iodinated Versus Gadolinium-Based Agents
Authors: Gorelik Yuri , Yaseen Hiba , Heyman Samuel N. , Khamaisi Mogher 
Published: November 2018

Introduction
The potential adverse renal outcome among patients undergoing iodine-based contrast-enhanced computerized tomography (CT) has been questioned recently, given the caution undertaken in patients' selection, hydration protocols, and the low radiocontrast volume, used with advanced imaging equipment.

Materials and Methods
This study is a retrospective assessment of renal outcome in 12,580 hospitalized patients undergoing contrast-enhanced CT, compared with 754 patients subjected to gadolinium-based magnetic resonance imaging, with subsequent propensity matching for clinical characteristics and potential risk factors.

Results
The risk of postcontrast acute kidney injury (PC-AKI) was found to be negligible as compared with patients undergoing enhanced magnetic resonance imaging studies, before and after propensity matching (8% vs 7.3% rate of AKI in the nonmatched iodine-based contrast agents [IBCAs] and gadolinium-based contrast agents [GBCAs], respectively, P = 0.3, and 7% in the matched IBCA group, P = 0.9), including comparisons among subgroups with well-defined risk factors such as chronic renal failure, diabetes, older age, and hypertension. However, lower systolic blood pressure before imaging was associated with higher risk to develop PC-AKI after IBCA administration but not with GBCA (for systolic blood pressure lower than 110 mm Hg, odds ratio for AKI after IBCA was 1.49; 95% confidence interval, 1.16–1.88, and after GBCA; odds ratio, 0.12; 95% confidence interval, 0.003–0.73).

Conclusions
With the current precautions undertaken, the real-life risk of PC-AKI among inpatients undergoing CT is insignificant. Possible reasons for the diverse impact of blood pressure on the propensity to develop acute kidney failure after iodine-based but not gadolinium-based enhancement imaging are discussed.
Catecholamine modulation of evidence accumulation during perceptual decision formation; a randomised trial
Authors: Loughnane Gerard M. , Brosnan Méadhbh B. , Barnes Jessica J.M. , Dean Angela , Nandam L. Sanjay , O’Connell Redmond G. , Bellgrove Mark A. 
Published: November 2018

AbstractRecent behavioural modelling and pupillometry studies suggest that neuromodulatory arousal systems play a role in regulating decision formation but neurophysiological support for these observations is lacking. We employed a randomised, double-blinded, placebo-controlled, crossover design to probe the impact of pharmacological enhancement of catecholamine levels on perceptual decision making. Catecholamine levels were manipulated using the clinically relevant drugs methylphenidate (MPH) and atomoxetine (ATM) and their effects were compared to those of citalopram (CIT), and placebo (PLA). Participants performed a classic EEG oddball paradigm which elicits the P3b, a centro-parietal potential that has been shown to trace evidence accumulation, under each of the four drug conditions. We found that MPH and ATM administration shortened RTs to the oddball targets. The neural basis of this behavioural effect was an earlier P3b peak latency, driven specifically by an increase in its build-up rate without any change in its time of onset or peak amplitude. This study provides neurophysiological evidence for the catecholaminergic enhancement of a discrete aspect of human decision making, i.e. evidence accumulation. Our results also support theoretical accounts suggesting that catecholamines may enhance cognition via increases in neural gain.
Single-cell whole-brain imaging and network analysis provide evidence of the three-stage hypothesis of addiction
Authors: Kimbrough Adam , Lurie Daniel J. , Collazo Andres , Kreifeldt Max , Sidhu Harpreet , D’Esposito Mark , Contet Candice , George Olivier 
Published: November 2018

SummaryThree main theories of the neurobiology of addiction have been proposed: (1) incentive salience mediated by a brainstem-striatal network, (2) habit mediated by a cortico-striato-thalamic network, and (3) hedonic allostasis mediated by an extended amygdala network. Efforts have been made to reconcile these theories within a three-stage model, but the relevance of each theory remains controversial. We tested the validity of each theory with a single dataset using unbiased single-cell whole-brain imaging and data-driven analyses of neuronal activity in a mouse model of alcohol use disorder. Abstinence in alcohol dependent mice decreased brain modularity and resulted in clustering of brain regions that correspond to each stage of the three-stage theory of addiction. Furthermore, we identified several brain regions whose activity highly predicted addiction-like behaviors and “hub” regions that may drive neural activation during abstinence. These results validate the three-stage theory of addiction and identify potential target regions for future study.
Evidence for absence of bilateral transfer of olfactory learned information in Apis dorsata and Apis mellifera
Authors: Vijaykumar Meenakshi , Mogily Sandhya , Dutta-Gupta Aparna , Joseph Joby 
Published: November 2018

AbstractCapacity and condition under which lateral transfer of olfactory memory is possible in insects are still debated. Here we present evidence consistent with lack of ability to transfer olfactory associative memory in two species of honeybees, Apis mellifera and Apis dorsata in a PER associative conditioning paradigm where the untrained antenna is blocked by an insulating coat. We show that the olfactory system on each side of the bee can learn and retrieve independently and the retrieval using the antenna on the side contralateral to the trained one is not affected by the training. Recreating the paradigm in which the memory on the contralateral side has been reported at three hours after training we see that the memory is available on the contralateral side immediately after training and moreover, training with trained side antenna coated with insulator does not prevent learning, pointing to a possible insufficiency of block of odor stimuli in this paradigm. Bee does not learn the odor stimuli applied to one side alone as a stimulus different from odor presented to both sides. Moreover the behaviour of the bee as a whole can be predicted if the sides are assumed to learn and store independently and the organism as a whole is able to retrieve the memory if either of the sides have learned.Summary StatementThe two halves of honeybee brain store and retrieve olfactory associative memories independently.
Strengths and potential pitfalls of hay-transfer for ecological restoration revealed by RAD-seq analysis in floodplainArabisspecies
Authors: Dittberner Hannes , Becker Christian , Jiao Wen-Biao , Schneeberger Korbinian , Hölzel Norbert , Tellier Aurélien , de Meaux Juliette 
Published: November 2018

AbstractAchieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay-transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious flood-plain speciesArabis nemorensisis co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relativeArabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay-transfer maintains genetic diversity for both species. Additionally, inA. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. InA. nemorensis,transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay-transfer on genetic diversity also depend on the genetic makeup of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay-transfer for habitat restoration and emphasize the importance of pre-restoration characterization of micro-geographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, i.e. maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained fromde novoand reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.
A century of decline: loss of genetic diversity in a southern African lion-conservation stronghold
Authors: Dures Simon G. , Carbone Chris , Loveridge Andrew J. , Maude Glyn , Midlane Neil , Aschenborn Ortwin , Gottelli Dada 
Published: November 2018

AbstractAimThere is a dearth of evidence that determines the genetic diversity of populations contained within present-day protected areas compared with their historic state prior to large-scale species declines, making inferences about a species’ conservation genetic status difficult to assess. The aim of this paper is to demonstrate the use of historic specimens to assess the change in genetic diversity over a defined spatial area.LocationLike other species, African lion populations (Panthera leo) are undergoing dramatic contractions in range and declines in numbers, motivating the identification of a number of lion conservation strongholds across East and southern Africa. We focus on one such stronghold, the Kavango-Zambezi transfrontier conservation area (KAZA) of Botswana, Namibia, Zambia and Zimbabwe.MethodsWe compare genetic diversity between historical museum specimens, collected during the late 19th and early 20th century, with samples from the modern extant population. We use 16 microsatellite markers and sequence 337 base pairs of the hypervariable control region (HVR1) of the mitochondrial genome. We use bootstrap resampling to allow for comparisons between the historic and modern data.ResultsWe show that the genetic diversity of the modern population was reduced by 12% to 17%, with a reduction in allelic diversity of approximately 15%, compared to historic populations, in addition to having lost a number of mitochondrial haplotypes. We also identify reduced allelic diversity and a number of ‘ghost alleles’ in the historical samples no longer present in the extant population.Main ConclusionsWe argue a rapid decline in allelic richness after 1895 suggests the erosion of genetic diversity coincides with the rise of a European colonial presence and the outbreak of rinderpest in the region. Our results support the need to improved connectivity between protected areas in order to prevent further loss of genetic diversity in the region.
The study of hormonal metabolism of Trincadeira and Syrah cultivars indicates new roles of salicylic acid, jasmonates, ABA and IAA during grape ripening and upon infection with Botrytis cinerea
Authors: Coelho João , Almeida-Trapp Marilia , Pimentel Diana , Soares Flávio , Reis Pedro , Rego Cecília , Mithöfer Axel , Fortes Ana Margarida 
Published: November 2018

Hormones play an important role in fruit ripening and in response to biotic stress. Nevertheless, analyses of hormonal profiling during plant development and defense are scarce. In this work, changes in hormonal metabolism in grapevine (Vitis vinifera) were compared between a susceptible (Trincadeira) and a tolerant (Syrah) variety during grape ripening and upon infection with Botrytis cinerea. Infection of grapes with the necrotrophic pathogen Botrytis cinerea leads to significant economic losses worldwide.Peppercorn-sized fruits were infected in the field and mock-treated and infected berries were collected at green, veraison and harvest stages for hormone analysis and targeted qPCR analysis of genes involved in hormonal metabolism and signaling. Results indicate a substantial reprogramming of hormonal metabolism during grape ripening and in response to fungal attack. Syrah and Trincadeira presented differences in the metabolism of abscisic acid (ABA), indole-3-acetic acid (IAA) and jasmonates during grape ripening that may be connected to fruit quality. On the other hand, high basal levels of salicylic acid (SA), jasmonates and IAA at an early stage of ripening, together with activated SA, jasmonates and IAA signaling, likely enable a fast defense response leading to grape resistance/ tolerance towards B. cinerea.The balance among the different phytohormones seems to depend on the ripening stage and on the intra-specific genetic background and may be fundamental in providing resistance or susceptibility. In addition, this study indicated the involvement of SA and IAA in defense against necrotrophic pathogens and gains insights into possible strategies for conventional breeding and/or gene editing aiming at improving grape quality and grape resistance against Botrytis cinerea.
A phenome-wide approach to identify causal risk factors for deep vein thrombosis
Authors: Constantinescu Andrei-Emil , Bull Caroline J , Goudswaard Lucy J , Zheng Jie , Elsworth Benjamin , Timpson Nicholas J , Moore Samantha F , Hers Ingeborg , Vincent Emma E 
Published: November 2018

SummaryBackgroundDeep vein thrombosis (DVT) is the formation of a blood clot in a deep vein. DVT can lead to a venous thromboembolism (VTE), the combined term for DVT and pulmonary embolism, a leading cause of death and disability worldwide. Despite the prevalence and associated morbidity of DVT, the underlying causes are not well understood.ObjectiveTo leverage publicly available genetic summary association statistics to identify causal risk factors for DVT.Methods & ResultsWe conducted a Mendelian randomization phenome-wide association study (MR-PheWAS) using genetic summary association statistics for 973 exposures and DVT (6,767 cases and 330,392 controls in UK Biobank). There was evidence for a causal effect of 57 exposures on DVT risk, including previously reported risk factors (e.g. body mass index - BMI and height) and novel risk factors (e.g. hyperthyroidism, chronic obstructive pulmonary disease (COPD) and varicose veins). As the majority of identified risk factors were adiposity-related, we explored the molecular link with DVT by undertaking a two-sample MR mediation analysis of BMI-associated circulating proteins on DVT risk. Our results indicate that circulating neurogenic locus notch homolog protein 1 (NOTCH1), inhibin beta C chain (INHBC) and plasminogen activator inhibitor 1 (PAI-1) influence DVT risk, with PAI-1 mediating the BMI-DVT relationship.ConclusionUsing a phenome-wide approach, we provide putative causal evidence that hyperthyroidism, varicose veins, COPD and BMI enhance the risk of DVT. The circulating protein PAI-1 has furthermore a causal role in DVT aetiology and is involved in mediating the BMI-DVT relationship.
On the impact of chemo-mechanically induced phenotypic transitions in gliomas
Authors: Mascheroni Pietro , Lopez Alfonso Juan Carlos , Kalli Maria , Stylianopoulos Triantafyllos , Meyer-Hermann Michael , Hatzikirou Haralampos 
Published: November 2018

ABSTRACTTumor microenvironment is a critical player in glioma progression and novel therapies for its targeting have been recently proposed. In particular, stress-alleviation strategies act on the tumor by reducing its stiffness, decreasing solid stresses and improving blood perfusion. However, these microenvironmental changes trigger chemo-mechanically induced cellular phenotypic transitions whose impact on therapy outcomes is not completely understood. In this work, we perform experiments to analyze the effects of mechanical compression on migration and proliferation of two glioma cell lines. From these experiments, we derive a mathematical model of glioma progression focusing on cellular phenotypic plasticity. The model reveals a trade-off between tumor infiltration and cellular content as a consequence of stress-alleviation approaches. We discuss how these findings can improve the current understanding of glioma/microenvironment interactions, and suggest strategies to improve therapeutic outcomes.
A Computational Framework for DNA Sequencing-Based Microscopy
Authors: Hoffecker Ian T. , Yang Yunshi , Bernardinelli Giulio , Orponen Pekka , Högberg Björn 
Published: November 2018

AbstractBarcoded DNA polony amplification techniques provide a means to impart a unique sequence identity onto specific locations of a surface wafer or chip. We describe a method whereby micro-scale spatial information such as the relative positions of biomolecules on a surface can be transferred to a sequence-based format and reconstructed into images without the use of conventional optics. The principle is based on the pair-wise association of uniquely tagged and spatially adjacenct polonies. The network of polonies connected by shared borders forms a graph whose topology can be reconstructed from a set of edges derived from pairs of barcodes associated with each other during a polony crosslinking phase, the sequences of which could be determined by isolation of the DNA and next-gen sequencing. We developed a mathematical and computational framework for this principle called Polony Adjacency Reconstruction for Spatial Inference and Topology and show that Euclidean spatial data may be partially stored and transmitted in the form of untethered graph topology. This effect may be exploited to form images by transferring molecular information from a surface of interest, which we demonstrated in silico by reconstructing images formed from stochastic transfer of hypothetical red, green, and blue molecular markers. The theory developed here could serve as a guide for a highly automated, multiplexable, and potentially super resolution imaging method based on molecular information encoding and transmission.
The CIC-DUX4 fusion oncoprotein drives metastasis and tumor growth via distinct downstream regulatory programs and therapeutic targets in sarcoma
Authors: Okimoto Ross A. , Wu Wei , Nanjo Shigeki , Olivas Victor , Lin Yone K. , Oyama Rieko , Kondo Tadashi , Bivona Trever G. 
Published: November 2018

AbstractTranscription factor fusion genes create oncoproteins that drive oncogenesis, and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. CIC-DUX4 is a transcription factor fusion that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We show that increased expression of ETV4 and CCNE1 occurs via neo-morphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We demonstrate a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4 tumors sensitive to inhibition of the CCNE-CDK2 complex, highlighting a therapeutic strategy for CIC-DUX4 tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically-aberrant transcriptional regulator, with therapeutic implications.
Variability of soybean response to rhizobia inoculant, Vermicompost, and a legume-specific fertilizer blend in Siaya County of Kenya
Authors: Mathenge Catherine , Thuita Moses , Masso Cargele , Gweyi-Onyango Joseph , Vanlauwe Bernard 
Published: November 2018

AbstractRhizobia inoculation can increase soybean yield, but its performance is influenced by soybean genotype, rhizobia strains, environment, and crop management among others. The objective of the study was to assess soybean response to rhizobia inoculation when grown in soils amended with urea or Vermicompost to improve nitrogen levels. Two greenhouse experiments and one field trial at two sites were carried out. The first greenhouse experiment included soils from sixty locations, sampled from smallholder farms in Western Kenya. The second greenhouse experiment consisted of one soil selected from soils used in the first experiment where inoculation response was poor. The soil was amended with Vermicompost or urea. In the two greenhouse experiments, Legumefix® (inoculant) + Sympal (legume fertilizer blend) were used as a standard package. Results from the second greenhouse experiment were then validated in the field. In the first greenhouse trial, soybean response to inoculation was significantly affected by soil fertility based on nodule fresh weight and shoot biomass. Soils with low nitrogen had low to no response to inoculation. After amendment, nodule fresh weight, nodule effectiveness, nodule occupancy, and shoot dry biomass were greater in the treatment amended with Vermicompost than those amended with urea (Legumefix® + Sympal + Vermicompost and Legumefix® + Sympal + urea). Under field conditions, trends were similar to the second experiment for nodulation, nodule occupancy, and nitrogen uptake resulting in significantly greater grain yields (475, 709, 856, 880, 966 kg ha−1) after application of Vermicompost at 0, 37, 74, 111, and 148 kg N ha−1, respectively. It was concluded that soybean nodulation and biological nitrogen fixation in low fertility soils would not be suppressed by organic amendments like Vermicompost up to 148 kg N ha−1.
Interrogation of genes controlling biofilm formation using CRISPR interference in Pseudomonas fluorescens
Authors: Noirot-Gros Marie-Francoise , Forrester Sara , Malato Grace , Larsen Peter E. , Noirot Philippe 
Published: November 2018

ABSTRACTBacterial biofilm formation involves multigenic signaling and regulatory pathways that control the transition from motile to sessile lifestyle, production of extracellular polymeric matrix, and maturation of the biofilm complex 3D structure. Biofilms are extensively studied because of their importance in biomedical, ecological and industrial settings. Genetic approaches based on gene inactivation are powerful for mechanistic studies but often are labor intensive, limiting systematic gene surveys to the most tractable bacterial hosts. Here, we adapted the CRISPR interference (CRISPRi) system for use in P. fluorescens. We found that CRISPRi is applicable to three genetically and physiologically diverse species, SBW25, WH6 and Pf0-1 and affords extended periods of time to study complex phenotypes such as cell morphology, motility and biofilm formation. In SBW25, CRISPRi-mediated silencing of the GacA/S two-component system and genes regulated by cylic-di-GMP produced phenotypes similar to those previously described after gene inactivation in various Pseudomonas. Combined with detailed confocal microscopy of biofilms, our study also revealed novel phenotypes associated with biofilm architecture and extracellular matrix biosynthesis as well as the potent inhibition of SBW25 biofilm formation mediated by the PFLU1114 protein. Thus, CRISPRi is a reliable and scalable approach to interrogate gene networks in the diverse P. fluorescens group.