bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunological tolerance, pregnancy and pre-eclampsia: the roles of semen microbes and the father1
Authors: Kenny Louise C. , Kell Douglas B. 
Published: October 2017

AbstractAlthough it is widely recognised as involving two stages (poor placentation followed by oxidative stress/inflammation), the precise originating causes of pre-eclampsia (PE) remain elusive. We have previously brought together some of the considerable evidence that a (dormant) microbial component is commonly a significant part of its aetiology. However, apart from recognising, consistent with this view, that the many inflammatory markers of PE are also increased in infection, we had little to say about immunity, whether innate or adaptive. In addition, we focussed on the gut, oral and female urinary tract microbiomes as the main sources of the infection. We here marshall further evidence for an infectious component in PE, focussing on the immunological tolerance characteristic of pregnancy, and the well-established fact that increased exposure to the father’s semen assists this immunological tolerance. As well as these benefits, however, semen is not sterile, microbial tolerance mechanisms may exist, and we also review the evidence that semen may be responsible for inoculating the developing conceptus with microbes, not all of which are benign. It is suggested that when they are not, this may be a significant cause of preeclampsia. A variety of epidemiological and other evidence is entirely consistent with this, not least correlations between semen infection, infertility and PE. Our view also leads to a series of other, testable predictions. Overall, we argue for a significant paternal role in the development of PE through microbial infection of the mother via insemination.“In one of the last articles which he wrote, the late Professor F J Browne (1958) expressed the opinion that all the essential facts about pregnancy toxaemia are now available and that all that is required to solve the problem is to fit them together in the right order, like the pieces of a jigsaw puzzle” [1]“It appears astonishing how little attention has been given in reproductive medicine to the maternal immune system over the last few decades.” [2]
Epidemiology of the Zika virus outbreak in the Cabo Verde Islands, West Africa
Authors: Lourenço José , de Lourdes Monteiro Maria , Valdez Tomás , Rodrigues Júlio Monteiro , Pybus Oliver G. , Faria Nuno Rodrigues 
Published: October 2017

AbstractIntroductionThe Zika virus (ZIKV) outbreak in the island nation of Cabo Verde was of unprecedented magnitude in Africa and the first to be associated with microcephaly in the continent.MethodsUsing a simple mathematical framework we present a first epidemiological assessment of attack and observation rates from 7,580 ZIKV notified cases and 18 microcephaly reports between July 2015 and May 2016.ResultsIn line with observations from the Americas and elsewhere, the single-wave Cabo Verdean ZIKV epidemic was characterized by a basic reproductive number of 1.85 (95% CI, 1.5 −2.2), with overall the attack rate of 51.1% (range 42.1 - 61.1) and observation rate of 2.7% (range 2.29 - 3.33).ConclusionCurrent herd-immunity may not be sufficient to prevent future small-to-medium epidemics in Cabo Verde. Together with a small observation rate, these results highlight the need for rapid and integrated epidemiological, molecular and genomic surveillance to tackle forthcoming outbreaks of ZIKV and other arboviruses.
Attending to what and where: Background connectivity integrates categorical and spatial attention
Authors: Tompary Alexa , Al-Aidroos Naseem , Turk-Browne Nicholas B. 
Published: October 2017

AbstractTop-down attention prioritizes the processing of goal-relevant information throughout visual cortex, based on where that information is found in space and what it looks like. Whereas attentional goals often have both spatial and featural components, most research on the neural basis of attention has examined these components separately. This may reflect the fact that attention is typically studied in individual visual areas that preferentially code for either spatial locations or particular features. Here we investigated how these attentional components are integrated by examining the attentional modulation of functional connectivity between visual areas with different selectivity. Specifically, we used fMRI to measure temporal correlations between spatially-selective regions of early visual cortex and category-selective regions in ventral temporal cortex while participants performed a task that benefitted from both spatial and categorical attention. We found that categorical attention modulated the connectivity of category-selective areas, but only with retinotopic areas that coded for the spatially attended location. The reverse was not true, however, with spatial attention modulating the connectivity of retinotopic areas with category-selective areas coding for both attended and unattended features. This pattern of results suggests that attentional modulation of connectivity is dominated by spatial selection, which in turn gates featural biases. Combined with exploratory analyses of frontoparietal areas that track these changes in connectivity among visual areas, this study begins to shed light on how different components of attention are integrated in support of more complex behavioral goals.
Demonstration of the potential of environmental DNA as a tool for the detection of avian species
Authors: Ushio Masayuki , Murata Koichi , Sado Tetsuya , Nishiumi Isao , Takeshita Masamichi , Iwasaki Wataru , Miya Masaki 
Published: October 2017

AbstractBirds play unique functional roles in the maintenance of ecosystems, such as pollina-tion and seed dispersal, and thus monitoring bird communities (e.g., monitoring bird species diversity) is a first step towards avoiding undesirable consequences of anthro-pogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performingin silicoanalyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with the Il-lumina MiSeq platform could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual detection and identification of bird species is difficult.
A low-level perceptual correlate of behavioral and clinical deficits in ADHD
Authors: Mihali Andra , Young Allison G , Adler Lenard A. , Halassa Michael M. , Ma Wei Ji 
Published: October 2017

AbstractIn many studies of attention-deficit hyperactivity disorder (ADHD), stimulus encoding and processing (per-ceptual function) and response selection (executive function) have been intertwined. To dissociate deficits in these functions, we introduced a task that parametrically varied low-level stimulus features (orientation and color) for fine-grained analysis of perceptual function. It also required participants to switch their attention between feature dimensions on a trial-by-trial basis, thus taxing executive processes. Furthermore, we used a response paradigm that captured task-irrelevant motor output (TIMO), reflecting failures to use the correct stimulus-response rule. ADHD participants had substantially higher perceptual variability than Controls, especially for orientation, as well as higher TIMO. In both ADHD and Controls, TIMO was strongly affected by the switch manipulation. Across participants, the perceptual variability parameter was correlated with TIMO, suggesting that perceptual deficits are associated with executive function deficits. Based on perceptual variability alone, we were able to classify participants into ADHD and Controls with a mean accuracy of about 77%. Participants’ self-reported General Executive Composite score correlated not only with TIMO but also with the perceptual variability parameter. Our results highlight the role of perceptual deficits in ADHD and the usefulness of computational modeling of behavior in dissociating perceptual from executive processes.
De novoassemblies of high-quality reference transcriptomes identifies Rosaceae-common andRosa-specific encoding genes
Authors: Li Shubin , Zhong Micai , Dong Xue , Jiang Xiaodong , Sun Yibo , Dezhu Li , Tang Kaixue , Hu Jin-Yong 
Published: October 2017

AbstractRoses are important plants for human beings with important economical and biological traits like continuous flowering, flower architecture, color and scent, that current model plants do not feature, thus are becoming ideal models for studying these traits. Due to high heterozygosity of rose genomes likely caused by frequent inter-species hybridization, a high-quality and well-annotated genome forRosaplants is not available yet. Developing genetic and genomic tools with high quality has become necessary for further roses breeding and for disentangling the molecular genetic mechanisms underlying roses domestication. We here generated the high quality and comprehensive reference transcriptomes forRosa chinensis‘Old Blush’ (OB) andR. wichuriana‘Basyes’ Thornless’ (BT), two roses contrasting at several important traits. These reference transcriptomes showed transcripts N50 above 2000bp. The two species shared about 23310 transcripts (N50 = 2364bp), among which about 8975 orthologs were conserved within genera ofRosa.Rosaplants shared about 5049 transcripts (Rosaceae-common) with these fromMalus, Prunus, Rubus, andFragaria. Finally, a pool of 417 transcripts unique toRosaplants (Rosa-specific) was identified. These Rosaceae-common andRosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants and investigation ofRosa-specific traits. The data reported here should provide the fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses.
Top-down expectation effects of food labels on motivation
Authors: Wegman Joost , Loon Ilke van , Smeets Paul A.M. , Cools Roshan , Aarts Esther 
Published: October 2017

AbstractWhen we buy our food, the information on the package informs us about the properties of the product, such as its taste and healthiness. These beliefs can influence the processing of food rewards and impact decision making beyond objective sensory properties. However, no studies, within or beyond the food domain, have assessed how written information, such as food labels, affect implicit motivation to obtain rewards, even though choices in daily life might be strongly driven by implicit motivational biases. We investigated how written information affects implicit motivation to obtain food rewards. We used food labels (high- and low-calorie), associated with an identical lemonade, to study motivation for food rewards during fMRI. In a joystick task, hungry participants (N=31) were instructed to make fast approach or avoid movements to earn the cued drinks. Behaviorally, we found a general approach bias, which was stronger for the drink that was most preferred during a subsequent choice test, i.e. the one labeled as low-calorie. This behavioral effect was accompanied by increased BOLD signal in the sensorimotor cortex during the response phase of the task for the preferred, low-calorie drink compared with the non-preferred, high-calorie drink. During the anticipation phase, the non-preferred, high-calorie drink label elicited stronger fMRI signal in the right ventral anterior insula, a region associated with aversion and taste intensity, than the preferred, low-calorie label. Together, these data suggest that high-calorie labeling can increase avoidance of drinks and reduce neural activity in brain regions associated with motor control. In conclusion, we show effects of food labeling on fMRI responses during anticipation and subsequent motivated action and on behavior, in the absence of objective taste differences, demonstrating the influence of written information on implicit biases. These findings contribute to our understanding of implicit biases in real-life eating behavior.
Exploiting modal demultiplexing properties of tapered optical fibers for tailored optogenetic stimulation
Authors: Pisanello Marco , Pisano Filippo , Sileo Leonardo , Maglie Emanuela , Bellistri Elisa , Spagnolo Barbara , Mandelbaum Gil , Sabatini Bernardo L. , De Vittorio Massimo , Pisanello Ferruccio 
Published: October 2017

AbstractOptogenetic control of neural activity in deep brain regions requires precise and flexible light delivery with non-invasive devices. To this end, Tapered Optical Fibers (TFs) represent a minimally-invasive tool that can deliver light over either large brain volumes or spatially confined subregions. This work links the emission properties of TFs with the modal content injected into the fiber, finding that the maximum transversal propagation constant (kt) and the total number of guided modes sustained by the waveguide are key parameters for engineering the mode demultiplexing properties of TFs. Intrinsic features of the optical fiber (numerical aperture and core/cladding diameter) define the optically active segment of the taper (up to ∼3mm), along which a linear relation between the propagating set of ktvalues and the emission position exists. These site-selective light-delivery properties are preserved at multiple wavelengths, further extending the range of applications expected for tapered fibers for optical control of neural activity.
Cross-task contributions of fronto-basal ganglia circuitry in response inhibition and conflict-induced slowing
Authors: Jahfari Sara , Ridderinkhof K Richard , Collins Anne GE , Knapen Tomas , Waldorp Lourens J , Frank Michael J 
Published: October 2017

ABSTRACTWhy are we so slow in choosing the lesser of two evils? We considered whether such slowing relates to uncertainty about the value of these options, which arises from the tendency to avoid them during learning, and whether such slowing relates to fronto-subthalamic inhibitory control mechanisms. 49 participants performed a reinforcement-learning task and a stop-signal task while fMRI was recorded. A reinforcement-learning model was used to quantify learning strategies. Individual differences in lose-lose slowing related to information uncertainty due to sampling, and independently, to less efficient response inhibition in the stop-signal task. Neuroimaging analysis revealed an analogous dissociation: subthalamic nucleus (STN) BOLD activity related to variability in stopping latencies, whereas weaker fronto-subthalamic connectivity related to slowing and information sampling. Across tasks, fast inhibitors increased STN activity for successfully cancelled responses in the stop task, but decreased activity for lose-lose choices. These data support the notion that fronto-STN communication implements a rapid but transient brake on response execution, and that slowing due to decision uncertainty could result from an inefficient release of this “hold your horses” mechanism.
Pausing controls branching between productive and non-productive pathways during initial transcription
Authors: Dulin David , Bauer David L. V. , Malinen Anssi M. , Bakermans Jacob J. W. , Kaller Martin , Morichaud Zakia , Petushkov Ivan , Depken Martin , Brodolin Konstantin , Kulbachinskiy Andrey , Kapanidis Achillefs N. 
Published: October 2017

AbstractTranscription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. Recently, initial RNA synthesis by the bacterial RNA polymerase (RNAP) has been shown to be interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Here, we employed single-molecule FRET and biochemical analysis to disentangle the pausing-related pathways of bacterial initial transcription. We present further evidence that region σ3.2constitutes a barrier after the initial transcribing complex synthesizes a 6-nt RNA (ITC6), halting transcription. We also show that the paused ITC6 state acts as a checkpoint that directs RNAP, in an NTP-dependent manner, to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway that blocks transcription initiation. Our results show that abortive RNA release and DNA unscrunching are not as tightly coupled as previously thought.
VASC: dimension reduction and visualization of single cell RNA sequencing data by deep variational autoencoder
Authors: Wang Dongfang , Gu Jin 
Published: October 2017

AbstractSingle cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities in single cell level. It is an important step for studying cell sub-populations and lineages based on scRNA-seq data by finding an effective low-dimensional representation and visualization of the original data. The scRNA-seq data are much noiser than traditional bulk RNA-Seq: in the single cell level, the transcriptional fluctuations are much larger than the average of a cell population and the low amount of RNA transcripts will increase the rate of technical dropout events. In this study, we proposed VASC (deep Variational Autoencoder for scRNA-seq data), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. It can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on twenty datasets, VASC shows superior performances in most cases and broader dataset compatibility compared with four state-of-the-art dimension reduction methods. Then, for a case study of pre-implantation embryos, VASC successfully re-establishes the cell dynamics and identifies several candidate marker genes associated with the early embryo development.
The common origin of symmetry and structure in genetic sequences
Authors: Cristadoro G. , Degli Esposti M. , Altmann E.G. 
Published: October 2017

AbstractWhen exploring statistical properties of genetic sequences two main features stand out: the existence of non-random structures at various scales (e.g., long-range correlations) and the presence of symmetries (e.g., Chargaff parity rules). In the last decades, numerous studies investigated the origin and significance of each of these features separately. Here we show that both symmetry and structure have to be considered as the outcome of the same biological processes, whose cumulative effect can be quantitatively measured on extant genomes. We present a novel analysis (based on a minimal model) that not only explains and reproduces previous observations but also predicts the existence of a nested hierarchy of symmetries emerging at different structural scales. Our genome-wide analysis of H. Sapiens confirms the theoretical predictions.
A novel zebrafish intestinal tumor model reveals a role forcyp7a1-dependent tumor-liver crosstalk in tumor's adverse effects on host
Authors: Enya Sora , Kawakami Koichi , Suzuki Yutaka , Kawaoka Shinpei 
Published: October 2017

AbstractThe nature of host organs and genes that underlie tumor-induced physiological disruption on host remains ill-defined. Here, we establish a novel zebrafish intestinal tumor model that is optimized for addressing this issue, and find that hepaticcyp7a1, the rate-limiting factor for synthesizing bile acids (BAs), is such a host gene. InducingkrasG12DbyGal4specifically expressed in the posterior intestine resulted in formation of an intestinal tumor classified as dysplasia. The local intestinal tumor caused systemic detrimental effects on host including liver inflammation, hepatomegaly, growth defects, and organismal death. Whole-organismal level gene expression analysis and metabolite measurements revealed that the intestinal tumor reduced total BAs levels via down-regulation of hepaticcyp7a1. Genetically rescuingcyp7a1expression in the liver restored the BAs synthesis and ameliorated tumor-induced liver inflammation, but not other tumor-dependent phenotypes. Thus, we found a previously unknown role ofcyp7a1as the host gene that links the intestinal tumor, hepatic cholesterol-BAs metabolism, and liver inflammation in tumor-bearing fish. Our model provides an important basis to discover host genes responsible for tumor-induced phenotypes and to uncover mechanisms underlying how tumors adversely affect host organisms.
Spatially segregated responses to visuo-tactile stimuli in mouse neocortex during active sensation
Authors: Couto J , Kandler S , Mao D , McNaughton BL , Arckens L , Bonin V 
Published: October 2017

ABSTRACTMultisensory integration is key for perception and animal survival yet how information from separate senses is integrated has been debated for decades. In the cortex, information from each sense is first processed in primary sensory areas and then combined in association areas. An alternative hypothesis to this hierarchical model is that primary sensory cortices partake in multisensory encoding. We probed tactile and visual responses in primary somatosensory and visual cortices in awake behaving animals using two-photon calcium imaging from layer 2/3 excitatory neurons. In support of an hierarchical model we found segregation of visual and tactile responses. Tactile stimuli evoked responses in S1 neurons. In striking contrast, V1 neurons failed to respond to tactile stimuli. This was true for passive whisker stimulation and for stimulation during active whisking. Furthermore, responses of V1 neurons to congruent visuo-tactile cues during active exploration, a condition where vision precedes touch, were completely abolished in darkness. The rostro-lateral area of the visual cortex responded to both visual and tactile aspects of the stimuli and may form a substrate for encoding multisensory signals during active exploration. Our results indicate that primary sensory areas mainly encode their primary sense and that the impact of other modalities may be restricted to modulatory effects.
The circadian hippocampus and its reprogramming in epilepsy: impact for chronotherapeutics
Authors: Debski K. J. , Ceglia N. , Ghestem A. , Ivanov A. I. , Brancati G. E. , Bröer S. , Bot A. M. , Müller J. A. , Schoch S. , Becker A. , Löscher W. , Guye M. , Sassone-Corsi P. , Lukasiuk K. , Baldi P. , Bernard C. 
Published: October 2017

AbstractGene and protein expression displays circadian oscillations in numerous body organs. These oscillations can be disrupted in diseases, thus contributing to the disease pathology. Whether the molecular architecture of cortical brain regions oscillates daily and whether these oscillations are modified in brain disorders is less understood. We identified 1200 daily oscillating transcripts in the hippocampus of control mice. More transcripts (1600) were oscillating in experimental epilepsy, with only one fourth oscillating in both conditions. Proteomics confirmed these results. Metabolic activity and targets of antiepileptic drugs displayed different circadian regulation in control and epilepsy. Hence, the hippocampus, and perhaps other cortical regions, shows a daily remapping of its molecular landscape, which would enable different functioning modes during the night/day cycle. The impact of this remapping in brain pathologies needs to be taken into account not only to study their mechanisms, but also to design drug treatments and time their delivery.