bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified neurocognitive model of the anterior temporal lobe contributions to semantics, language, social behaviour & face recognition
Authors: Ding Junhua , Chen Keliang , Liu Haoming , Huang Lin , Chen Yan , Lv Yingru , Yang Qing , Guo Qihao , Han Zaizhu , Lambon Ralph Matthew. A. 
Published: August 2019

AbstractThe anterior temporal lobes (ATL) have become a key brain region of interest in cognitive and clinical neuroscience. Contemporary explorations are founded upon neuropsychological investigations of semantic dementia (SD) that describe the patients’ selective semantic impairment and the variations in their language, behavioural and face recognition abilities. The purpose of this investigation was to generate a single unified model which captures the known cognitive-behavioural variations in SD, and integrates with the considerable database on healthy semantic function and other patient groups. A new analytical approach was able to capture the graded neuropsychological differences and map these to the patients’ distribution of frontotemporal atrophy. Multiple regression and principal component analyses confirmed that the degree of generalised semantic impairment was related to the patients’ total, bilateral ATL atrophy. Verbal production and word-finding abilities were related to total ATL atrophy as well as to the balance of left>right ATL atrophy. Behavioural apathy was found to relate positively to the degree of orbitofrontal atrophy and negatively to total temporal volumes. Disinhibited behaviour was related to right ATL and orbitofrontal atrophy and face recognition to right ATL volumes. Rather than positing mutually-exclusive sub-categories, the data-driven model repositions semantics, language, social behaviour and face recognition into a continuous frontotemporal neurocognitive space.
Evolutionary dynamics of microbial communities in bioelectrochemical systems
Authors: Szydlowski Lukasz , Sorokin Anatoly , Vasieva Olga , Boerner Susan , Fedorovich Veyacheslav , Goryanin Igor 
Published: August 2019

SUMMARYBio-electrochemical systems can generate electricity by virtue of mature microbial consortia that gradually and spontaneously optimize performance. To evaluate selective enrichment of these electrogenic microbial communities, five, 3-electrode reactors were inoculated with microbes derived from rice wash wastewater and incubated under a range of applied potentials. Reactors were sampled over a 12-week period and DNA extracted from anodal, cathodal, and planktonic bacterial communities was interrogated using a custom-made bioinformatics pipeline that combined 16S and metagenomic samples to monitor temporal changes in community composition. Some genera that constituted a minor proportion of the initial inoculum dominated within weeks following inoculation and correlated with applied potential. For instance, the abundance ofGeobacterincreased from 423-fold to 766-fold between −350 mV and −50 mV, respectively. Full metagenomic profiles of bacterial communities were obtained from reactors operating for 12 weeks. Functional analyses of metagenomes revealed metabolic changes between different species of the dominant genus,Geobacter, suggesting that optimal nutrient utilization at the lowest electrode potential is achieved via genome rearrangements and a strong inter-strain selection, as well as adjustment of the characteristic syntrophic relationships. These results reveal a certain degree of metabolic plasticity of electrochemically active bacteria and their communities in adaptation to adverse anodic and cathodic environments.
Astrocytes modulate baroreceptor reflex sensitivity at the level of the nucleus of the solitary tract
Authors: Mastitskaya Svetlana , Turovsky Egor , Marina Nephtali , Theparambil Shefeeq M. , Hadjihambi Anna , Ramage Andrew G. , Gourine Alexander V. , Hosford Patrick S. 
Published: August 2019

AbstractAstrocytes play an important role in cardiovascular reflex integration at the level of the nucleus tractus solitarii (NTS). Existing reports from brainstem slice preparations suggest that astrocytes here respond to input from the solitary tract by increasing intracellular calcium. However, the physiological significance of this neuron-astrocyte signaling in vivo remains unknown. Here, we report that stimulation of the vagus nerve in an anesthetized rat induced rapid [Ca2+]i increases in astrocytes transduced to express calcium sensor GCaMP6. The receptors involved were determined using brainstem-derived astroglial cell cultures were loaded with [Ca2+] indicator Fura-2. 5-HT (10 µM) caused robust increases in [Ca2+]i, and pharmacological interrogation revealed the expression of functional 5-HT2A receptors. This observation was confirmed in vivo: intravenous administration of ketanserin decreased the magnitude of [Ca2+]i responses, induced by vagal afferent simulation, by ∼50%. However, the response was completely blocked by topical application of the AMPA receptor antagonist CNQX alone. To investigate the role of astrocyte-neuron communication, the vesicular release in the NTS astrocytes was blocked by virally driven expression of a dominant-negative SNARE protein in vivo. This increased baroreflex sensitivity in awake animals, which was also observed in anesthetized animals after topical application of the P2Y1 receptor antagonist MDS-2500 to the NTS. We hypothesize that NTS astrocytes respond to incoming afferent release of glutamate and this response is modulated by 5-HT originating from vagal afferents or other sources. ATP is then released, which acts on inhibitory interneurons via P2Y1 receptors and thus modulates the expression of cardiovascular reflexes.Significance statementCardiorespiratory nuclei in the brainstem integrate cardiovascular sensory information to optimise tissue perfusion and blood gas concentrations. We describe experimental evidence that NTS astrocytes participate in setting the baroreflex sensitivity by release of ATP acting on P2Y1 receptors on inhibitory interneurons. Activation of astrocytes is partly under control of 5-HT co-released with glutamate from vagal afferents, which allows modulation of autonomic response to high frequency/duration of afferent stimulation by monitoring extra-synaptic 5-HT acting on glial 5-HT2A receptors. This could represent a signaling pathway that is activated under pathological conditions and is responsible for baroreflex impairment in conditions that result in astrogliosis, for example from systemic inflammatory response or chronic hypoxia/hypercapnia.
Variations in the coverage of biological soil crusts along a gradient of aridity in the center-west of argentina
Authors: Navas Romero A.L , Herrera Moratta M.A. , Vento B. , Rodriguez R.A. , Martínez Carretero E.E. 
Published: August 2019

AbstractThe biological soil crusts (biocrust) play a fundamental role in the arid and semiarid areas of South America. However, little attention has been paid to the distribution and coverage of them. In Argentina, studies about biocrust are still scarce. The goal of this contribution is to analyze the coverage of the biocrust and each of the functional component along a gradient of aridity in the center-west of Argentina. The gradient included three differentiated sites: semiarid, arid, and hyperarid sites. The coverage was recorded using the Point-quadrat method on 30 transects through a gradient consisting of three sites: semiarid, arid, and hyper-arid sites. The arid site was the system with the highest coverage of biocrust followed by the hyper-arid site. The semiarid site had the lowest values of coverage and showed significant differences among the three systems were found. Cyanobacteria’s dominate in the hyper-arid site. On the other hand, cyanobacteria and lichens were dominant in the arid site. The coverage of studied organisms showed variations in the semiarid site. These results support the idea that the coverage has a strong relationship with the features of the studied ecosystem and the environmental factors both at a mesoscale and a microscale in a determined community.
Cross-Species association statistics for genome-wide studies of host and parasite polymorphism data
Authors: Märkle Hanna , Tellier Aurélien , John Sona 
Published: August 2019

AbstractUncovering the genes governing host-parasite coevolutionary interactions is of importance for disease management. The increasing availability of host and parasite full genome-data allows for cross-species genome-wide association studies based on the genomic data of in-fected hosts and their associated parasite strains sampled from natural populations (i.e. natural co-GWAs). Such studies focus on searching for cross-species allelic associations between pairs of host and parasite SNPs. We aim to quantify the power of natural co-GWAs to pinpoint loci under coevolution with respect to the intrinsic complexities of coevolutionary systems, such as the genetic specificity of the interaction and the temporal allele frequency changes resulting from the interaction. Therefore, we develop the cross-species association (CSA) and the cross-species prevalence (CSP) indices, the latter additionally incorporating genomic data from uninfected hosts. To provide an assessment of the statistical power of these indices, we analytically derive their genome-wide False Discovery Rates (FDR) based on the neutral site-frequency spectrum of the host and the parasite population. Using two coevolutionary models, we investigate under which parameter regimes these indices pin-point the coevolving loci. Under trench warfare dynamics, CSA and CSP are very accurate in pinpointing the loci under coevolution, while under arms race dynamics the power is limited especially for gene-for-gene interactions. Furthermore, we reveal that the combination of both indices across time samples is an indicator for the specificity of the interaction. Our results provide novel insights into the power and biological interpretation of natural cross-species association studies.
Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods
Authors: Charles Adam S. , Song Alexander , Gauthier Jeff L. , Pillow Jonathan W. , Tank David W. 
Published: August 2019

AbstractThe past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes large-scale, systematic validation impossible. Here we provide a new framework for evaluating TPM methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets. We verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this access to in silico ground truth to perform direct comparisons between different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. Overall, by leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.
Nrf1 is endowed with a dominant tumor-repressing effect onto the Wnt/β-Catenin-dependent and -independent signaling networks in the human liver cancer
Authors: Chen Jiayu , Wang Meng , Ru Xufang , Xiang Yuancai , Ren Yonggang , Liu Xiping , Qiu Lu , Zhang Yiguo 
Published: August 2019

ABSTRACTOur previous work revealed that Nrf1α exerts a tumor-repressing effect because its genomic loss (to yieldNrf1α−/−) results in oncogenic activation of Nrf2 and target genes. Interestingly, β-catenin is concurrently activated by loss of Nrf1α in a way similar to β-catenin-driven liver tumor. However, a presumable relationship between Nrf1 and β-catenin is not as yet established. Here, we demonstrate that Nrf1 enhanced ubiquitination of β-catenin for targeting to proteasomal degradation. Conversely, knockdown of Nrf1 by its short-hairpin RNA (shNrf1) caused accumulation of β-catenin so as to translocate the nucleus, allowing activation of a subset of Wnt–β-catenin signaling responsive genes, which leads to the epithelial-mesenchymal transition (EMT) and related cellular processes. Such silencing of Nrf1 resulted in malgrowth of human hepatocellular carcinoma, along with malignant invasion and metastasis to the lung and liver in xenograft model mice. Further transcriptomic sequencing unraveled significant differences in the expression of both Wnt/β-catenin-dependent and -independent responsive genes implicated in the cell process, shape and behavior of the shNrf1-expressing tumor. Notably, we identified that β-catenin is not a target gene of Nrf1, but this CNC-bZIP factor contributes to differential or opposing expression of other critical genes, such asCDH1, Wnt5A, Wnt11A, FZD10, LEF, TCF4, SMAD4, MMP9, PTEN, PI3K, JUN and p53, each of which depends on the positioning of distinctcis-regulatory sequences (e.g., ARE and/or AP-1 binding sites) in the gene promoter contexts. In addition, altered expression profiles of some Wnt–β-catenin signaling proteins were context-dependent, as accompanied by decreased abundances of Nrf1 in the clinic human hepatomas with distinct differentiation. Together, these results corroborate the rationale that Nrf1 acts as abona fidedominant tumor-repressor, by its intrinsic inhibition of Wnt–β-catenin signaling and relevant independent networks in cancer development and malignant progression.
Taste quality representation in the human brain
Authors: Avery Jason A. , Liu Alexander G. , Ingeholm John E. , Riddell Cameron D. , Gotts Stephen J. , Martin Alex 
Published: August 2019

SUMMARYIn the mammalian brain, the insula is the primary cortical substrate involved in the perception of taste. Recent imaging studies in rodents have identified a gustotopic organization in the insula, whereby distinct insula regions are selectively responsive to one of the five basic tastes. However, numerous studies in monkeys have reported that gustatory cortical neurons are broadly-tuned to multiple tastes, and tastes are not represented in discrete spatial locations. Neuroimaging studies in humans have thus far been unable to discern between these two models, though this may be due to the relatively low spatial resolution employed in taste studies to date. In the present study, we examined the spatial representation of taste within the human brain using ultra-high resolution functional magnetic resonance imaging (MRI) at high magnetic field strength (7-Tesla). During scanning, participants tasted sweet, salty, sour and tasteless liquids, delivered via a custom-built MRI-compatible tastant-delivery system. Our univariate analyses revealed that all tastes (vs. tasteless) activated primary taste cortex within the bilateral dorsal mid-insula, but no brain region exhibited a consistent preference for any individual taste. However, our multivariate searchlight analyses were able to reliably decode the identity of distinct tastes within those mid-insula regions, as well as brain regions involved in affect and reward, such as the striatum, orbitofrontal cortex, and amygdala. These results suggest that taste quality is not represented topographically, but by a combinatorial spatial code, both within primary taste cortex as well as regions involved in processing the hedonic and aversive properties of taste.
Periaxonal and nodal plasticity modulate action potential conduction in the adult mouse brain
Authors: Cullen Carlie L , Pepper Renee E , Clutterbuck Mackenzie T , Pitman Kimberley A , Oorschot Viola , Auderset Loic , Tang Alexander D , Ramm Georg , Emery Ben , Rodger Jennifer , Jolivet Renaud B , Young Kaylene M 
Published: August 2019

SummaryCentral nervous system myelination increases action potential conduction velocity, however, it is unclear how myelination is coordinated to ensure the temporally precise arrival of action potentials, and facilitate information processing within cortical and associative circuits. Here, we show that mature myelin remains plastic in the adult mouse brain and can undergo subtle structural modifications to influence action potential arrival times. Repetitive transcranial magnetic stimulation and spatial learning, two stimuli that modify neuronal activity, alter the length of the nodes of Ranvier and the size of the periaxonal space within active brain regions. This change in the axon-glial configuration is independent of oligodendrogenesis and tunes conduction velocity to increase the synchronicity of action potential transit.
The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates
Authors: Thomelin Pauline , Bonneau Julien , Brien Chris , Suchecki Radoslaw , Baumann Ute , Kalambettu Priyanka , Langridge Peter , Tricker Penny , Fleury Delphine 
Published: August 2019

AbstractWheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits with high temperature and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We completed the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene - seven in absentia, TaSINA. This was associated with the QTL’s effects on early vigour, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.Significance statementWheat is the world’s most widely grown crop and a staple of human diet. Even brief episodes of high temperature in the growing season cause severe yield reductions. Finding and deploying genes for heat stress tolerance in new varieties is a priority for food security with climate change. We narrowed a genetic locus to a small genomic region where genetic variation was present only in one gene that showed clear differences of expression and improved yield and physiology under stress in the populations. Using diagnostic markers to track the positive haplotype in nearly 750 accessions, we found many regions where the allele could be used in breeding programmes to increase wheat’s heat tolerance.
Structural basis for transcription activation by Crl through tethering of σS and RNA polymerase
Authors: Cartagena Alexis Jaramillo , Banta Amy B. , Sathyan Nikhil , Ross Wilma , Gourse Richard L. , Campbell Elizabeth A. , Darst Seth A. 
Published: August 2019

AbstractIn bacteria, a primary σ factor associates with the core RNA polymerase (RNAP) to control most transcription initiation, while alternative σ factors are used to coordinate expression of additional regulons in response to environmental conditions. Many alternative σ factors are negatively regulated by anti-σ factors. In Escherichia coli, Salmonella enterica, and many other γ-proteobacteria, the transcription factor Crl positively regulates the alternative σS regulon by promoting the association of σS with RNAP without interacting with promoter DNA. The molecular mechanism for Crl activity is unknown. Here, we determined a single-particle cryo-electron microscopy structure of Crl-σS-RNAP in an open promoter complex with a σS regulon promoter. In addition to previously predicted interactions between Crl and domain 2 of σS (σS), the structure, along with p-benzoylphenylalanine crosslinking, reveals that Crl interacts with a structural element of the RNAP β’ subunit we call the β’-clamp-toe (β’CT). Deletion of the β’CT decreases activation by Crl without affecting basal transcription, highlighting the functional importance of the Crl-β’CT interaction. We conclude that Crl activates σS-dependent transcription in part through stabilizing σS-RNAP by tethering σS and the β’CT. We propose that Crl, and other transcription activators that may use similar mechanisms, be designated σ-activators.Significance StatementIn bacteria, multiple σ factors can bind to a common core RNA polymerase (RNAP) to alter global transcriptional programs in response to environmental stresses. Many γ-proteobacteria, including the pathogens Yersinia pestis, Vibrio cholera, Escherichia coli, and Salmonella typhimurium, encode Crl, a transcription factor that activates σS-dependent genes. Many of these genes are involved in processes important for infection, such as biofilm formation. We determined a high-resolution cryo-electron microscopy structure of a Crl-σS-RNAP transcription initiation complex. The structure, combined with biochemical experiments, shows that Crl stabilizes σS-RNAP by tethering σS directly to the RNAP.
Megaloneurite, a giant neurite of vasoactive intestinal peptide and nitric oxide synthase in the aged dog and identification by human sacral spinal cord
Authors: Li Yinhua , Hou Wei , Jia Yunge , Rao Chenxu , Wei Zichun , Xu Ximeng , Li Hang , Li Fuhong , Wang Xinghang , Zhang Tianyi , Sun Jingjing , Tan Huibing 
Published: August 2019

AbstractMegaloneurite of NADPH diaphorase (NADPH-d) positivity is a new kind of aging-related neurodegeneration and also co-localized with vasoactive intestinal peptide (VIP) in the sacral spinal cord of aged dog and monkey. However, no immunocytochemistry of VIP was exclusively tested in the aged dog and no evidence has been reported in the aged human spinal cord. Aged dogs were used to examine the distribution of VIP immunopositivity in the sacral spinal cord. Immunocytochemistry of VIP and alpha-synuclein were also examined in the aged human spinal cord. The VIP immunopositivity in aged dog was reconfirmed our previous finding illustrated by immunofluorescent study. Megalogneurite was also identified by nitric oxide synthase (NOS) immunoreaction in aged dog. The VIP positive megaloneurites both in age dog and human were detected in dorsal root entry zoon, Lissauer’s tract, dorsal commissural nucleus and anterior commissural gray as well as in the lateral funiculus of the sacral spinal cord exclusive of other segments of spinal cord. Alpha-synuclein positivity was present mini-aggregation and Lewy body in the sacral spinal cord of aged human, that also occurred in the lumber, thoracic and cervical spinal cord. It was firstly tested that VIP megaloneurites occurred in the aged human sacral spinal cord, especially in the white matter. Megaloneurites identified by NADPH-d-VIP-NOS immunoreaction could implicate for the dysfunction of pelvic organs in the aged human being.