bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition of CaOx crystals byNeolamarckia cadamba: Anin vivoapproach
Authors: Prathibhakumari P.V , Prasad G. 
Published: January 2018

AbstractThe objective of the study was to find out the effectiveness of the methanol fruit extract ofN. cadambaon calcium oxalate induced nephrolithiasis in wistar albino rats. Animals were divided into nine groups (n=4) in which group 1 as control, group II as antilithiatic control and group III as lithiatic control. Dose for the methanol fruit extract was selected for the study as 200 and 400mg/kg body weight of fruit extract. Group IV and V were considered as post treatment groups and group VI to IX were co treatment groups. Ethylene glycol in drinking water was given to group II - IX for the induction of renal calculi. All the stone forming constituents such as urea, uric acid and creatinine were reduced significantly (p<0.01) in the extract treated groups. Calcium, oxalate and phosphorous concentrations in kidney were found to be diminished by the supplementation of extract. ICP-MS analysis, Histopathology, microcrystal study and pizzalato’s staining confirmed the efficacy of the fruit extract. In conclusion, the results suggested that the fruit extract is endowed with the property of an antilithiatic drug.
Neural engagement with online educational videos predicts learning performance for individual students
Authors: Cohen Samantha S. , Madsen Jens , Touchan Gad , Robles Denise , Lima Stella F. A. , Henin Simon , Parra Lucas C. 
Published: January 2018

AbstractOnline educational materials are largely disseminated through videos, and yet there is little understanding of how these videos engage students and fuel academic success. We hypothesized that components of the electroencephalogram (EEG), previously shown to reflect video engagement, would be predictive of academic performance in the context of educational videos. Two groups of subjects watched educational videos in either an intentional learning paradigm, in which they were aware of an upcoming test, or in an incidental learning paradigm, in which they were unaware that they would be tested. “Neural engagement” was quantified by the inter-subject correlation (ISC) of the EEG that was evoked by the videos. In both groups, students with higher neural engagement retained more information. Neural engagement also discriminated between attentive and inattentive video viewing. These results suggest that this EEG metric is a marker of the stimulus-related attentional mechanisms necessary to retain information. In the future, EEG may be used as a tool to design and assess online educational content.
Neuromagnetic signatures of the spatiotemporal transformation for manual pointing
Authors: Blohm G. , Alikhanian H. , Gaetz W. , Goltz H.C. , DeSouza J.F.X. , Cheyne D.O. , Crawford J.D. 
Published: January 2018

AbstractMovement planning involves transforming the sensory goal representation into a command in motor coordinates. Surprisingly, the real-time dynamics of sensorimotor transformations at the whole brain level remain unknown, in part due to the spatiotemporal limitations of fMRI and neurophysiological recordings. Here, we used magnetoencephalography (MEG) during pro-/anti-wrist pointing to determine (1) the cortical areas involved in transforming visual signals into appropriate hand motor commands, and (2) how this transformation occurs in real time, both within and across the regions involved. We computed sensory, motor, and sensorimotor indices in 16 bilateral brain regions for direction coding based on hemispherically lateralized de/synchronization in the α (7-15Hz) and β (15-35Hz) bands. We found a visuomotor progression, from pure sensory codes in ‘early’ occipital-parietal areas, to a temporal transition from sensory to motor coding in the majority of parietal-frontal sensorimotor areas, to a pure motor code, in both the α and β bands. Further, the timing of these transformations revealed a top-down pro/anti cue influence that propagated ‘backwards’ from frontal through posterior cortical areas. These data directly demonstrate a progressive, real-time transformation both within and across the entire occipital-parietal-frontal network that follows specific rules of spatial distribution and temporal order.
qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps
Authors: van Zundert Gydo C.P. , Hudson Brandi M. , Keedy Daniel A. , Fonseca Rasmus , Heliou Amelie , Suresh Pooja , Borrelli Kenneth , Day Tyler , Fraser James S. , van den Bedem Henry 
Published: January 2018

AbstractProteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. We found that up to 29 % of a dataset of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multi-temperature crystallography could therefore augment the structure-based drug design toolbox.
Idiosyncratic, retinotopic bias in face identification modulated by familiarity
Authors: di Oleggio Castello Matteo Visconti , Taylor Morgan , Cavanagh Patrick , Ida Gobbini M. 
Published: January 2018

AbstractThe perception of gender and age of unfamiliar faces is reported to vary idiosyncratically across retinal locations such that, for example, the same androgynous face may appear to be male at one location but female at another. Here we test spatial heterogeneity for the recognition of theidentityof personally familiar faces in human participants. We found idiosyncratic biases that were stable within participants and that varied more across locations for low as compared to high familiar faces. These data suggest that like face gender and age, face identity is processed, in part, by independent populations of neurons monitoring restricted spatial regions and that the recognition responses vary for the same face across these different locations. Moreover, repeated and varied social interactions appear to lead to adjustments of these independent face recognition neurons so that the same familiar face is eventually more likely to elicit the same recognition response across widely separated visual field locations. We provide a mechanistic account of this reduced retinotopic bias based on computational simulations.Significance statementIn this work we tested spatial heterogeneity for the recognition of personally familiar faces. We found retinotopic biases that varied more across locations for low as compared to highly familiar faces. The retinotopic biases were idiosyncratic and stable within participants. Our data suggest that, like face gender and age, face identity is processed by independent populations of neurons monitoring restricted spatial regions and that recognition may vary for the same face at these different locations. Unlike previous findings, our data and computational simulation address the effects of learning and show how increased familiarity modifies the representation of face identity in face-responsive cortical areas. This new perspective has broader implications for understanding how learning optimizes visual processes for socially salient stimuli.
Priority effects and non-hierarchical competition shape species composition in a complex grassland community
Authors: Uricchio Lawrence H. , Daws S. Caroline , Spear Erin R. , Mordecai Erin A. 
Published: January 2018

AbstractNiche and fitness differences control the outcome of competition, but determining their relative importance in invaded communities – which may be far from equilibrium – remains a pressing concern. Moreover, it is unclear whether classic approaches for studying competition, which were developed predominantly for pairs of interacting species, will fully capture dynamics in complex species assemblages. We parameterized a population dynamic model using competition experiments of two native and three exotic species from a grassland community. We found evidence for minimal fitness differences or niche differences between the native species, leading to slow replacement dynamics and priority effects, but large fitness advantages allowed exotics to unconditionally invade natives. Priority effects driven by strong interspecific competition between exotic species drove single-species dominance by one of two exotic species in 80% of model outcomes, while a complex mixture of non-hierarchical competition and coexistence between native and exotic species occurred in the remaining 20%. Fungal infection, a commonly hypothesized coexistence mechanism, had weak fitness effects, and is unlikely to substantially affect coexistence. In contrast to previous work on pairwise outcomes in largely native-dominated communities, our work supports a role for nearly-neutral dynamics and priority effects as drivers of species composition in invaded communities.
A MinION-based pipeline for fast and cost-effective DNA barcoding
Authors: Srivathsan Amrita , Baloğlu Bilgenur , Wang Wendy , Tan Wei Xin , Bertrand Denis , Ng Amanda Hui Qi , Boey Esther Jia Hui , Koh Jayce Jia Yu , Nagarajan Niranjan , Meier Rudolf 
Published: January 2018

ABSTRACTDNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well-equipped molecular laboratory, is time-consuming, and/or expensive. We here address these issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and demonstrate that one flowcell can generate barcodes for ∼500 specimens despite high base-call error rates of MinION™. The pipeline overcomes the errors by first summarizing all reads for the same tagged amplicon as a consensus barcode. These barcodes are overall mismatch-free but retain indel errors that are concentrated in homopolymeric regions. We thus complement the barcode caller with an optional error correction pipeline that uses conserved amino-acid motifs from publicly available barcodes to correct the indel errors. The effectiveness of this pipeline is documented by analysing reads from three MinION™ runs that represent three different stages of MinION™ development. They generated data for (1) 511 specimens of a mixed Diptera sample, (2) 575 specimens of ants, and (3) 50 specimens of Chironomidae. The run based on the latest chemistry yielded MinION barcodes for 490 specimens which were assessed against reference Sanger barcodes (N=471). Overall, the MinION barcodes have an accuracy of 99.3%-100% and the number of ambiguities ranges from <0.01-1.5% depending on which correction pipeline is used. We demonstrate that it requires only 2 hours of sequencing to gather all information that is needed for obtaining reliable barcodes for most specimens (>90%). We estimate that up to 1000 barcodes can be generated in one flowcell and that the cost of a MinION barcode can be <USD 2.
Dynamic combination of sensory and reward information under time pressure
Authors: Farashahi Shiva , Ting Chih-Chung , Kao Chang-Hao , Wu Shih-Wei , Soltani Alireza 
Published: January 2018

AbstractWhen making choices, collecting more information is beneficial but comes at the cost of sacrificing time that could be allocated to making other potentially rewarding decisions. To investigate how the brain balances these costs and benefits, we conducted a series of novel experiments in humans and simulated various computational models. Under six levels of time pressure, subjects made decisions either by integrating sensory information over time or by dynamically combining sensory and reward information over time. We found that during sensory integration, time pressure reduced performance as the deadline approached, and choice was more strongly influenced by the most recent sensory evidence. By fitting performance and reaction time with various models we found that our experimental results are more compatible with leaky integration of sensory information with an urgency signal or a decision process based on stochastic transitions between discrete states modulated by an urgency signal. When combining sensory and reward information, subjects spent less time on integration than optimally prescribed when reward decreased slowly over time, and the most recent evidence did not have the maximal influence on choice. The suboptimal pattern of reaction time was partially mitigated in an equivalent control experiment in which sensory integration over time was not required, indicating that the suboptimal response time was influenced by the perception of imperfect sensory integration. Meanwhile, during combination of sensory and reward information, performance did not drop as the deadline approached, and response time was not different between correct and incorrect trials. These results indicate a decision process different from what is involved in the integration of sensory information over time. Together, our results not only reveal limitations in sensory integration over time but also illustrate how these limitations influence dynamic combination of sensory and reward information.
Graphene-oxide quenching-based molecular beacon imaging of exosome-mediated transfer of neurogenic miR-193a on microfluidic platform
Authors: Oh Hyun Jeong , Park Hyejin , Yoon Dayoung , Chung Seok , Hwang Do Won , Lee Dong Soo 
Published: January 2018

ABSTRACTA microRNA (miR-193a) was found to be transferred in the exosomes of differentiated neural progenitors to undifferentiated clones. Graphene-oxide (GO) quenching-based molecular beacon was developed to detect RNAs in living cells and tissues quickly and sensitively. Here, we applied GO quencher-based molecular beacon sensor to visualize neurogenic miR-193a levels delivered via exosome during cell-non-autonomous neurogenesis of neural progenitor cells on microfluidic platform. Fluorescence signals of FAM-labeled peptide nucleic acid (PNA) against miR-193a quenched by GO nanosheets (FAM-PNA193a-GO) were recovered in undifferentiated recipient cells differentiated to the neuronal lineage by exosome-mediated neurogenesis 3 days after co-culture with differentiated donor cells. We propose that molecular beacon imaging using PNA-GO complex can be used to visualize individual cellular expression of mature microRNAs revealing their precise spatial localization and temporal sequences by the intercellular exosome delivery of messages to undergo processes such as cell-non-autonomous neurogenesis.
Attention periodically samples competing stimuli during binocular rivalry
Authors: Davidson Matthew James , Alais David , Tsuchiya Naotsugu , van Boxtel Jeroen J.A. 
Published: January 2018

AbstractThe attentional sampling hypothesis suggests that attention rhythmically enhances sensory processing when attending to a single (~8 Hz), or multiple (~4 Hz) objects. Here we investigated using binocular rivalry whether attention samples sensory representations that are not part of the conscious percept, during competition for perceptual dominance. When crossmodally cued toward a conscious image, subsequent changes in consciousness occurred at ~8 Hz, consistent with rates of undivided attentional sampling. However, when attention was cued toward the suppressed image, changes in consciousness slowed to ~3.5 Hz, indicating the division of attention away from the conscious visual image. In the electroencephalogram, we found that at 3.5 and 8 Hz, the strength of inter-trial phase coherence over fronto-temporal and parieto-occipital regions correlated with behavioral measures of changes in perception. When cues were not task-relevant, these effects disappeared, confirming that perceptual changes were dependent upon the allocation of attention, and that attention can flexibly sample away from a conscious image in a task-dependent manner.
Profile of Molecular Subtypes of Breast Cancer Among Bangladeshi Women - Audit of Initial Experience
Authors: Rahman Md. Zillur , Karim Anwarul 
Published: January 2018

AbstractBackgroundReceptor status and molecular subtyping of breast cancer are crucial for patient management. We present here our initial experience on the status of different molecular subtypes and clinicopathological characteristics of invasive breast carcinomas in Bangladeshi population especially in Chittagong zone.Materials and methodsA total of 59 histopathologically confirmed cases of invasive ductal carcinoma were selected for this study. Fifteen out of 59 cases were reported as HER2 equivalent and could not be categorized into any subtype because of the lack of availability of fluorescence in situ hybridization. The remaining 44 cases were distributed into different molecular subtypes and then the clinicopathological characteristics were compared for each molecular subtype.ResultsAge ranges from 24-70 years with a mean age of 43.95 years. Most of the patients were in 41-50 years age group. Among the 44 cases, most common subtype was HER2/neu amplification (13 cases, 29.55%). Luminal A, luminal B and basal like subtypes were 11 (25%), 10 (22.73%) and 10 (22.73%) respectively. The mean tumor size was 3.46 cm and the highest mean tumor size was in basal-like subtype (4.01cm). Twenty five out of 59 cases (42.37%) showed axillary lymph node metastasis. Lowest axillary lymph node metastasis was found in luminal A subtype (3/11=27.27%).ConclusionHER2/neu amplification subtype was found to be more common in this region. Luminal A subtype was found to be more favorable in comparison to the other subtypes in terms of axillary lymph node metastasis.
Meta-analyses identify differentially expressed microRNAs in Parkinson’s disease
Authors: Schulz Jessica , Takousis Petros , Wohlers Inken , Itua Ivie O G , Dobricic Valerija , Rücker Gerta , Binder Harald , Middleton Lefkos , Ioannidis John P A , Perneczky Robert , Bertram Lars , Lill Christina M 
Published: January 2018

ABSTRACTObjectiveMicroRNA-mediated (dys)regulation of gene expression has been implicated in Parkinson’s disease (PD), although results of microRNA expression studies remain inconclusive. We aimed to identify microRNAs that show consistent differential expression across all published expression studies in PD.MethodsWe performed a systematic literature search on microRNA expression studies in PD and extracted data from eligible publications. After stratification for brain, blood, and cerebrospinal fluid (CSF)-derived specimen we performed meta-analyses across microRNAs assessed in three or more independent datasets. Meta-analyses were performed using effect-size and p-value based methods, as applicable.ResultsAfter screening 599 publications we identified 47 datasets eligible for meta-analysis. On these, we performed 160 meta-analyses on microRNAs quantified in brain (n=125), blood (n=31), or CSF samples (n=4). Twenty-one meta-analyses were performed using effect sizes. We identified 13 significantly (Bonferroni-adjusted α=3.13×10-4) differentially expressed microRNAs in brain (n=3) and blood (n=10) with consistent effect directions across studies. The most compelling findings were with hsa-miR-132-3p (p=6.37×10-5), hsa-miR-497-5p (p=1.35×10-4), and hsa-miR-133b (p=1.90×10-4) in brain, and with hsa-miR-221-3p (p=4.49×10-35), hsa-miR-214-3p (p=2.00×10-34), and hsa-miR-29c-3p (p=3.00×10-12) in blood. No significant signals were found in CSF. Analyses of GWAS data for target genes of brain microRNAs showed significant association (α=9.40×10-5) of genetic variants in nine loci.InterpretationWe identified several microRNAs that showed highly significant differential expression in PD. Future studies may assess the possible role of the identified brain miRNAs in pathogenesis and disease progression as well as the potential of the top blood microRNAs as biomarkers for diagnosis, progression or prediction of PD.
Understanding the role of alterations in cortical D1 receptor sensitivity in shaping working memory maintenance through mesocortical dynamics
Authors: Reneaux Melissa , Gupta Rahul 
Published: January 2018

AbstractThe dopamine (DA) hypothesis of cognitive deficits suggests that too low or too high extracellular DA concentration in the prefrontal cortex (PFC) can severely impair the working memory (WM) maintenance during delay period. Thus, there exists only an optimal range of DA where the sustained-firing activity, the neural correlate of WM maintenance, in the cortex possesses optimal firing frequency as well as robustness against noisy distractions. Empirical evidences demonstrate changes even in the D1 receptor (D1R)-sensitivity to extracellular DA, collectively manifested through D1R density and DA-binding affinity, in the PFC under neuropsychiatric conditions such as ageing and schizophrenia. However, the impact of alterations in the cortical D1R-sensitivity on WM maintenance has yet remained poorly addressed. Using a quantitative neural mass model of the prefronto-mesoprefrontal system, the present study reveals that higher D1R-sensitivity may not only effectuate shrunk optimal DA range but also shift of the range to lower concentrations. Moreover, higher sensitivity may significantly reduce the WM-robustness even within the optimal DA range and exacerbates the decline at abnormal DA levels. These findings project important clinical implications, such as dosage precision and variability of DA-correcting drugs across patients, and failure in acquiring healthy WM maintenance even under drug-controlled normal cortical DA levels.