bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Analysis of Computed Tomography of Paranasal Sinuses in Nasal Septal Deviation
Authors: Yazici Demet 
Published: December 2018

Objectives:
Anatomic variations of paranasal sinuses are frequent among population that should be analyzed and interpreted accurately. The purpose of this study is to analyze anatomical variants and their relationships of paranasal sinuses in patients with nasal septal deviation undergoing septoplasty.

Methods:
A total number of 150 patients (74 males, 76 females) with nasal septal deviation undergoing septal surgery were included in this retrospective study. The authors analyzed the direction and the angle of the nasal septal deviation, variations of the nasal turbinates, ethmoidal air cells, paranasal sinus pneumatization, accessory pneumatization of the paranasal complex and sphenoid sinus-related structures and the Keros, optic nerve and Vidian canal classification, and relationships between these structures in the paranasal computed tomography of the patients.

Results:
The incidence of concha bullosa, Onodi cell, and anterior clinoid pneumatization were higher in patients with nasal septal deviation when compared with current literature.

Conclusion:
Physicians and surgeons dealing with the nose and maxillofacial region should be able to analyze paranasal computed tomography by themselves and must be aware of these variations during performing septal and craniomaxillofacial surgery.
GTShark: Genotype compression in large project
Authors: Deorowicz Sebastian , Danek Agnieszka 
Published: December 2018

AbstractSummaryNowadays large sequencing projects handle tens of thousands of individuals. The huge files summarizing the findings definitely require compression. We propose a tool able to compress large collections of genotypes as well as single samples in such projects to sizes not achievable to date.Availability and Implementationhttps://github.com/refresh-bio/GTSharkContactsebastian.deorowicz@polsl.plSupplementary informationSupplementary data are available at publisher’s Web site.
Fast and Flexible Sequence Induction In Spiking Neural Networks Via Rapid Excitability Changes
Authors: Pang Rich , Fairhall Adrienne 
Published: December 2018

AbstractCognitive flexibility, the adaptation of mental processing to changes in task demands, is thought to depend on biological neural networks’ ability to rapidly modulate the dynamics governing how they process information. While extensive work has elucidated how network dynamics can be reshaped by slowly occurring structural changes, e.g. the gradual modification of recurrent synaptic patterns, much less is known about how dynamics might be reconfigured over faster timescales of seconds. One compelling example of rapid and selective modulation of network dynamics potentially involved in cognitive flexibility is observed in rodent hippocampus, where short bouts of exploratory behavior cause new activity sequences to preferentially “replay” during subsequent awake rest periods without continued sensory input. Fast mechanisms for selectively biasing sequential activity through networks, however, remain unknown. Using a spiking neural network model, we asked whether a simplified version of sequence replay could arise from three biophysically plausible components: recurrent, spatially organized connectivity; homogeneous, stochastic “gating” inputs; and rapid, activity-dependent scaling of gating input strengths, based on a phenomenon known as long-term potentiation of intrinsic excitability (LTP-IE). Indeed, these enabled both forward and reverse replay of flexible sequences reflecting recent behavior, despite unchanged recurrent weights. Specifically, activation-triggered LTP-IE “tags” neurons in the recurrent network by increasing their spiking probability when gating input is applied, and the sequential ordering of spikes is reconstructed by the existing recurrent connectivity. In a proof-of-concept demonstration, we also show how LTP-IE-based sequences can implement temporary stimulus-response mappings in a straightforward manner. These results elucidate a simple yet previously unexplored combination of biological mechanisms that converge in hippocampus and suffice for fast and flexible reconfiguration of sequential network dynamics, suggesting their potential role in cognitive flexibility over rapid timescales.
Reproducibility of the correlative triad among aging, dopamine receptor availability, and cognition
Authors: Juarez Eric J. , Castrellon Jaime J. , Green Mikella A. , Crawford Jennifer L. , Seaman Kendra L. , Smith Christopher T. , Dang Linh C. , Matuskey David , Morris Evan D. , Cowan Ronald L. , Zald David H. , Samanez-Larkin Gregory R. 
Published: December 2018

AbstractThe evidence that dopamine function mediates the association between aging and cognition is one of the most cited findings in the cognitive neuroscience of aging. However, few and relatively small studies have directly examined these associations. Here we examined correlations among adult age, dopamine D2-like receptor (D2R) availability, and cognition in two cross-sectional studies of healthy human adults. Participants completed a short cognitive test battery and, on a separate day, a PET scan with either the high-affinity D2R tracer [18F]Fallypride (Study 1) or [11C]FLB457 (Study 2). Digit span, a measure of short-term memory maintenance and working memory, was the only cognitive test for which dopamine D2R availability partially mediated the age effect on cognition. In Study 1, age was negatively correlated with digit span. Striatal D2R availability was positively correlated with digit span controlling for age. The age effect on digit span was smaller when controlling for striatal D2R availability. Although other cognitive measures used here have individually been associated with age and D2R availability in prior studies, we found no consistent evidence for significant associations between low D2R availability and low cognitive performance on these measures. These results at best only partially supported the correlative triad of age, dopamine D2R availability, and cognition. While a wealth of other research in human and non-human animals demonstrates that dopamine makes critical contributions to cognition, the present studies suggest caution in interpreting PET findings as evidence that dopamine D2R loss is a primary cause of broad age-related declines in fluid cognition.
Oncogenic PIK3CA promotes cellular stemness in an allele dose-dependent manner
Authors: Madsen Ralitsa R. , Knox Rachel G. , Pearce Wayne , Lopez Saioa , Mahler-Araujo Betania , McGranahan Nicholas , Vanhaesebroeck Bart , Semple Robert K. 
Published: December 2018

AbstractThe PIK3CA gene, which encodes the p110α catalytic subunit of PI3-kinase (PI3K), is mutationally activated in cancer and in overgrowth disorders known as PIK3CA-related overgrowth spectrum (PROS). To determine the consequences of genetic PIK3CA activation in a developmental context of relevance to both PROS and cancer, we engineered isogenic human induced pluripotent stem cells (iPSCs) with heterozygous or homozygous knock-in of PIK3CAH1047R. While heterozygous iPSCs remained largely similar to wild-type cells, homozygosity for PIK3CAH1047R caused widespread, cancer-like transcriptional remodeling, partial loss of epithelial morphology, upregulation of stemness markers and impaired differentiation to all three germ layers in vitro and in vivo. Genetic analysis of PIK3CA-associated cancers revealed that 64 % had multiple oncogenic PIK3CA copies (39 %) or additional PI3K signaling pathway-activating “hits” (25 %). This contrasts with the prevailing view that PIK3CA mutations occur heterozygously in cancer. Our findings suggest that a PI3K activity threshold determines pathological consequences of oncogenic PIK3CA activation and provide the first insight into the specific role of this pathway in human pluripotent stem cells.
Differentiation of mild cognitive impairment using an entorhinal cortex-based test of VR navigation
Authors: Howett David , Castegnaro Andrea , Krzywicka Katarzyna , Hagman Johanna , Henson Richard , Rio Miguel , King John A , Burgess Neil , Chan Dennis 
Published: December 2018

AbstractThe entorhinal cortex is one of the first regions to exhibit neurodegeneration in Alzheimer’s disease, and as such identification of entorhinal cortex dysfunction may aid detection of the disease in its earliest stages. Extensive evidence demonstrates that the entorhinal cortex is critically implicated in navigation underpinned by the firing of spatially modulated neurons. This study tested the hypothesis that entorhinal-dependent navigation is impaired in pre-dementia Alzheimer’s disease.Forty-five patients with mild cognitive impairment (26 with CSF Alzheimer’s disease biomarker data: 12 biomarker-positive and 14 biomarker-negative) and 41 healthy control participants undertook an immersive virtual reality path integration test, as a measure of entorhinal-dependent navigation. Behavioural performance was correlated with MRI measures of entorhinal cortex volume, and the classification accuracy of the path integration task was compared with a battery of cognitive tests considered sensitive and specific for early Alzheimer’s Disease.Biomarker-positive patients exhibited larger errors in the navigation task than biomarker-negative patients, whose performance did not significantly differ from controls participants. Path-integration errors were negatively correlated with the volumes of the total entorhinal cortex and of its posteromedial subdivision. The path integration task demonstrated higher diagnostic sensitivity and specificity for differentiating biomarker positive versus negative patients (area under the curve = 0.90) than was achieved by the best of the cognitive tests (area under the curve = 0.57).This study demonstrates that an entorhinal cortex-based virtual reality navigation task can differentiate patients with mild cognitive impairment at low and high risk of developing dementia, with classification accuracy superior to reference cognitive tests considered to be highly sensitive to early Alzheimer’s disease. This study provides evidence that navigation tasks may aid early diagnosis of Alzheimer’s disease, and the basis of this in animal cellular and behavioural studies provides the opportunity to answer the unmet need for translatable outcome measures for comparing treatment effect across preclinical and clinical trial phases of future anti-Alzheimer’s drugs.
Neural activity in a hippocampus-like region of the teleost pallium are associated with navigation and active sensing
Authors: Fotowat H , Lee C , Jun JJ , Maler L 
Published: December 2018

AbstractNeural mechanisms underlying spatial navigation in fish are unknown and little is known, for any vertebrate, about the relationship between active sensing and the formation of spatial maps. The weakly electric fish, Gymnotus Carapo, uses their active electric sense for spatial navigation. The electric organ discharge rate (EODr) undergoes transient increases during navigation to enhance electrosensory sampling. Gymnotus also uses stereotyped forward/ backward swimming as a second form of active sensing that brings objects towards the electroreceptor-dense head region. We wirelessly recorded neural activity from the pallium of freely swimming Gymnotus. Spiking activity was sparse and occurred only during swimming. Notably, some units exhibited significant place specificity and/or association with both forms of active sensing. Our results provide the first characterization of neural activity in a hippocampal-like region of a teleost fish brain and connects active sensing via sensory sampling rate and directed movements to higher order encoding of spatial information.
Age-Related Modulations of Alpha and Gamma Brain Activities Underlying Anticipation and Distraction
Authors: ElShafei Hesham A. , Fornoni Lesly , Masson Rémy , Bertrand Olivier , Bidet-Caulet Aurélie 
Published: December 2018

AbstractAttention operates through top-down (TD) and bottom-up (BU) mechanisms. Recently, it has been shown that slow (alpha) frequencies index facilitatory and suppressive mechanisms of TD attention and faster (gamma) frequencies signal BU attentional capture. Ageing is characterized by increased behavioral distractibility, resulting from either a reduced efficiency of TD attention or an enhanced triggering of BU attention. However, only few studies have investigated the impact of ageing upon the oscillatory activities involved in TD and BU attention. MEG data were collected from 14 elderly and 14 matched young healthy human participants while performing the Competitive Attention Task. Elderly participants displayed (1) exacerbated behavioral distractibility, (2) altered TD suppressive mechanisms, indexed by a reduced alpha synchronization in task-irrelevant regions, (3) less prominent alpha peak-frequency differences between cortical regions, (4) a similar BU system activation indexed by gamma activity, and (5) a reduced activation of lateral prefrontal inhibitory control regions. These results show that the ageing-related increased distractibility is of TD origin.
Methyl ketone production byPseudomonas putidais enhanced by plant-derived amino acids
Authors: Dong Jie , Chen Yan , Benites Veronica Teixeira , Baidoo Edward E.K. , Petzold Christopher J. , Beller Harry R. , Eudes Aymerick , Scheller Henrik V. , Adams Paul D. , Mukhopadhyay Aindrila , Simmons Blake A. , Singer Steven W. 
Published: December 2018

ABSTRACTPlant biomass is an attractive source of renewable carbon for conversion to biofuels and bio-based chemicals. Conversion strategies often use a fraction of the total biomass, focusing on sugars from cellulose and hemicellulose. Strategies that use plant components such as plant-derived aromatics and amino acids have the potential to improve the efficiency of overall biomass conversion.Pseudomonas putidais a promising host for biomass conversion for its ability to metabolize a wide variety of organic compounds, including aromatics derived from lignin.P. putidawas engineered to produce medium chain methyl ketones, which are promising diesel blendstocks and potential platform chemicals, from glucose and lignin-related aromatics, 4-hydroxybenzoate (4-HB) and protocatechuate (PCA). Unexpectedly,P. putidamethyl ketone production was enhanced 2-to 5-fold compared to sugar controls whenArabidopsis thalianahydrolysates derived from engineered plants that overproduce 4-HB and PCA, whileE. coliproduction was lowered in these hydrolysates. This enhancement was more pronounced (~7-fold increase) with hydrolysates derived from non-engineered switchgrass (Panicum virgatumL.) suggesting it did not arise from overproduction of 4-HB and PCA. Global proteomic analysis of the methyl ketone-producingP. putidasuggested that plant-derived amino acids may be the source of this enhancement. Mass spectrometry-based measurements of plant-derived amino acids demonstrated a high correlation between methyl ketone production and amino acid concentration in plant hydrolysates. Amendment of glucose-containing minimal media with a defined mixture of amino acids similar to those found in the hydrolysates studied led to a 9-fold increase in methyl ketone titer (1.1 g/L).
E74 like ETS transcription factor 3 (ELF3) is a negative regulator of epithelial-mesenchymal transition in bladder carcinoma
Authors: Gondkar Kirti , Patel Krishna , Krishnappa Shoba , Patil Akkamahadevi , Nair Bipin , Sundaram Gopinath Meenakshi , Zea Tan Tuan , Kumar Prashant 
Published: December 2018

AbstractTranscription factors are known to be commonly deregulated in various cancers. The E74 like ETS transcription factor 3 (ELF3) expression is restricted to epithelial tissue. In the present study, we evaluated the role of ELF3 in the pathogenesis of bladder carcinoma (BCa) using cell line model. The cell lines with low expression of ELF3 showed increased expression of mesenchymal markers and decreased expression of epithelial markers. Immunofluorescence and immunohistochemical analysis of ELF3 showed selective expression in low-grade BCa cell lines and tumor tissues, respectively. We demonstrated that overexpression of ELF3 in UMUC3, a mesenchymal BCa cell line resulted in reduced invasion and decreased expression of mesenchymal markers. Furthermore, using publicly available data, we found that low expression of ELF3 was associated with increased risk and poor overall survival rate in BCa. In conclusion, ELF3-modulated reversal of EMT might be a useful strategy in the treatment of bladder cancer.
Phase transition and amyloid formation by a viral protein as an additional molecular mechanism of virus-induced cell toxicity
Authors: Salladini Edoardo , Debarnot Claire , Delauzun Vincent , Murrali Maria Grazia , Sutto-Ortiz Priscila , Spinelli Silvia , Pierattelli Roberta , Bignon Christophe , Longhi Sonia 
Published: December 2018

AbstractHenipaviruses are severe human pathogens responsible for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We have previously reported a biophysical characterization of the Henipavirus V proteins and shown that they interact with DDB1, a cellular protein that is a component of the ubiquitin ligase E3 complex. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquidhydrogel phase transition. By combining experimental and bioinformatics approaches, we have identified the V region responsible for this phenomenon. This region (referred to as PNT3), which falls within the long intrinsically disordered region of V, was further investigated using a combination of biophysical and structural approaches. ThioflavinT and Congo red binding assays, together with negative-staining electron microscopy studies, show that this region forms amyloid-like, β-enriched structures. Such structures are also formed in mammal cells transfected to express PNT3. Those cells also exhibit a reduced viability in the presence of a stress agent. Interestingly, mammal cells expressing a rationally designed, non-amyloidogenic PNT3 variant (PNT33A), appear to be much less sensitive to the stress agent, thus enabling the establishment of a link between fibril formation and cell toxicity. The present findings therefore pinpoint a so far never reported possible mechanism of virus-induced cell toxicity.
Analysing linear multivariate pattern transformations in neuroimaging data
Authors: Basti Alessio , Mur Marieke , Kriegeskorte Nikolaus , Pizzella Vittorio , Marzetti Laura , Hauk Olaf 
Published: December 2018

AbstractMost connectivity metrics in neuroimaging research reduce multivariate activity patterns in regions-of-interests (ROIs) to one dimension, which leads to a loss of information. Importantly, it prevents us from investigating the transformations between patterns in different ROIs. Here, we applied linear estimation theory in order to robustly estimate the linear transformations between multivariate fMRI patterns with a cross-validated Tikhonov regularisation approach. We derived three novel metrics that describe different features of these voxel-by-voxel mappings: goodness-of-fit, sparsity and pattern deformation. The goodness-of-fit describes the degree to which the patterns in an input region can be described as a linear transformation of patterns in an output region. The sparsity metric, which relies on a Monte Carlo procedure, was introduced in order to test whether the transformation mostly consists of one-to-one mappings between voxels in different regions. Furthermore, we defined a metric for pattern deformation, i.e. the degree to which the transformation rotates or rescales the input patterns. As a proof of concept, we applied these metrics to an event-related fMRI data set consisting of four subjects that has been used in previous studies. We focused on the transformations from early visual cortex (EVC) to inferior temporal cortex (ITC), fusiform face area (FFA) and parahippocampal place area (PPA). Our results suggest that the estimated linear mappings are able to explain a significant amount of variance of the three output ROIs. The transformation from EVC to ITC shows the highest goodness-of-fit, and those from EVC to FFA and PPA show the expected preference for faces and places as well as animate and inanimate objects, respectively. The pattern transformations are sparse, but sparsity is lower than would have been expected for one-to-one mappings, thus suggesting the presence of one-to-few voxel mappings. ITC, FFA and PPA patterns are not simple rotations of an EVC pattern, indicating that the corresponding transformations amplify or dampen certain dimensions of the input patterns. While our results are only based on a small number of subjects, they show that our pattern transformation metrics can describe novel aspects of multivariate functional connectivity in neuroimaging data.
Energy use and rural poverty: empirical evidence from potato farmers in northern China
Authors: Li Zihan , Gong Yazhen , Chen Kevin Z. 
Published: December 2018

Purpose
Rising energy expenditures due to more intensive use of energy in modern agriculture and increasing energy prices may affect rural households’ agricultural incomes, particularly the incomes of the rural poor in developing countries. However, the exact link between energy costs and income among the rural poor needs further empirical investigation. The purpose of this paper is to develop a deeper understanding of the relationship between energy use and family income, using household-level panel data collected from 500 potato farmers in a poor region of Northern China, where eliminating poverty by 2020 is now the top government priority.

Design/methodology/approach
The paper uses household survey data collected from six counties in a poor region in northern China in 2013 to measure the relationship between energy cost and family income. A fixed effect model is employed to estimate the relationship.

Findings
The findings indicate that potatoes play an important role in the surveyed families’ incomes, and that the energy costs of potato production have a significant negative relationship with family income. However, this negative relationship is only significant for farmers with low economic standing, such as those living below or just above the poverty line. The negative relationship between energy costs and family income is only significant for those cultivating a certain size of potato-sown area; it is insignificant for those cultivating smaller areas.

Originality/value
These findings indicate that, in general, reducing energy costs helps the poor increase their income but is not necessarily helpful to those with high economic standing or a relatively small potato-sown area. If rural development policies are to support poverty reduction and energy savings (at least in major potato production regions), interventions aimed at energy cost reduction may be effective only for the poor whose family income depends, to a relatively high degree, on potato production.