bluuebunny/crossref_metadata_2025_split huggingface dataset:
Buildup and bistability in auditory streaming as an evidence accumulation process with saturation
Authors: Nguyen Quynh-Anh , Rinzel John , Curtu Rodica 
Published: January 2020

AbstractA repeating triplet-sequenceABA_ of non-overlapping brief tones,AandB, is a valued paradigm for studying auditory stream formation and the cocktail party problem. The stimulus is “heard” either as a galloping pattern (integration) or as two interleaved streams (segregation); the initial percept is typically integration then followed by spontaneous alternations between segregation and integration, each being dominant for a few seconds. The probability of segregation grows over seconds, from near-zero to a steady value, defining the buildup function, BUF. Its stationary level increases with the difference in tone frequencies,DF, and the BUF rises faster. Percept durations haveDF-dependent means and are gamma-like distributed. Behavioral and computational studies usually characterize triplet streaming either during alternations or during buildup. Here, our experimental design and modeling encompass both. We propose a pseudo-neuromechanistic model that incorporates spiking activity in primary auditory cortex, A1, as input and resolves perception along two network-layers downstream of A1. Our model is straightforward and intuitive. It describes the noisy accumulation of evidence against the current percept which generates switches when reaching a threshold. Accumulation can saturate either above or below threshold; if below, the switching dynamics resemble noise-induced transitions from an attractor state. Our model accounts quantitatively for three key features of data: the BUFs, mean durations, and normalized dominance duration distributions, at variousDFvalues. It describes perceptual alternations without competition per se, and underscores that treating triplets in the sequence independently and averaging across trials, as implemented in earlier widely cited studies, is inadequate.Author summarySegregation of auditory objects (auditory streaming) is widely studied using ambiguous stimuli. A sequence of repeating tripletsABA_ of non-overlapping brief pure tones,AandB, frequency-separated, is a valued stimulus. Studies typically focus on one of two behavioral phases: the early (say, ten seconds) buildup of segregation from the default integration or later spontaneous alternations (bistability) between seconds-long integration and segregation percepts. Our experiments and modeling encompass both. Our novel, data-driven, evidence-accumulation model accounts for key features of the observations, taking as input recorded spiking activity from primary auditory cortex (as opposed to most existing, more abstract, models). Our results underscore that assessing individual triplets independently and averaging across trials, as in some earlier studies, is inadequate (lacking neuronal-accountability for percept duration statistics, the underlying basis of buildup). Further, we identify fresh parallels between evidence accumulation and competition as potential dynamic processes for choice in the brain.
Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response
Authors: Picart-Picolo Ariadna , Grob Stefan , Picault Nathalie , Franek Michal , halter Thierry , Maier Tom R. , Llauro Christel , Jobet Edouard , Zhang Panpan , Vijayapalani Paramasivan , Baum Thomas J. , Navarro Lionel , Dvorackova Martina , Mirouze Marie , Pontvianne Frederic 
Published: January 2020

ABSTRACTAmong the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process. The role of these extra-copies remains elusive, but previous studies suggested their importance in genome stability and global gene expression. Because the nucleolus is also a platform for nuclear organization, we tested the impact of a decreased amount of rRNA gene copies on theArabidopsis thaliana3D genome organization and stability, using anA. thalianaline only containing 20% of rRNA gene copies (20rDNA line). Compared to the wild-type Col-0, the 20rDNA line shows several signs of genomic instability, such as variations in 3D genome organization, spontaneous double-strand breaks accumulation, transcriptomic changes, and higher DNA methylation level. Strikingly, using genomic and microscopic approaches, we identified seven large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. As a consequence, more than 600 genes were duplicated, often associated with an increase in their expression level. Among them, we found several upregulated genes involved in plant-pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and we discuss their potential implications on plant genome evolution.
Can Intestinal Absorption of Dietary Protein Be Improved Through Early Exposure to Plant-Based Diet?
Authors: Molinari Giovanni S. , McCracken Vance J. , Wojno Michal , Rimoldi Simona , Terova Genciana , Kwasek Karolina 
Published: January 2020

AbstractNutritional Programming (NP) has been studied as a means of mitigating the negative effects of dietary plant protein (PP), but the optimal timing and mechanism behind NP are still unknown. The objectives of this study were: 1) To determine whether zebrafish (Danio rerio) can be programmed to soybean meal (SBM) through early feeding and broodstock exposure to improve SBM utilization; 2) To determine if NP in zebrafish affects expression of genes associated with intestinal nutrient uptake; 3) To determine if early stage NP and/or broodstock affects gene expression associated with intestinal inflammation or any morphological changes in the intestinal tract that might improve dietary SBM utilization. Two broodstocks were used to form the six experimental groups. One broodstock group received fishmeal (FM) diet (FMBS), while the other was fed (“programmed with”) SBM diet (PPBS). The first ((+) Control) and the second group ((-) Control) received FM and SBM diet for the entire study, respectively, and were progeny of FMBS. The last four groups consisted of a non-programmed(FMBS-X-PPandPPBS-X-PP)and a programmed group(FMBS-NP-PPandPPBS-NP-PP)from each of the broodstocks. The programming occurred through feeding with SBM diet during 13-23 dph. The non-control groups underwent a PP-Challenge, receiving SBM diet during 36-60 dph. During the PP-Challenge, both PPBS groups experienced significantly lower weight gains than the (+) Control group. NP in early life stages significantly increased the expression of PepT1 in PPBS-NP-PP, compared to PPBS-X-PP. NP also tended to increase the expression offabp2in the programmed vs. non-programmed groups of both broodstocks. The highest distal villus length-to-width ratio was observed in the dual-programmed group, suggesting an increase in surface area for nutrient absorption within the intestine. The results of this study suggest that NP during early life stages may increase intestinal absorption of nutrients from PP-based feeds.
A systematic review of scientific research focused on farmers in agricultural adaptation to climate change (2008-2017)
Authors: Yang Yao , Seyler Barnabas C. , Feng Miao , Tang Ya 
Published: January 2020

AbstractDue to the severe consequences of climate change, associated risks to global food security, and the contribution of agriculture to greenhouse gas emissions, agriculture must necessarily adapt to meet these challenges. Many studies have therefore sought to investigate agricultural adaptation to climate change, and as key stakeholders in agriculture, farmers play a vital role in this process. There is a rapidly increasing corpus of scholarship on agricultural adaptation to climate change, with many studies beginning to incorporate survey methods to examine farmer perceptions and adaptation responses. Nevertheless, in-depth understanding of farmers worldwide is inadequate due to insufficiently robust methodologies, socio-economic disparities, and unequal geographic distribution. In this study, we searched and reviewed the existing peer-reviewed, English-language scientific articles published between 2008 and 2017 on agricultural adaptation to climate change that have incorporated farmers into their research methodologies. The main findings include the following: (1) a small but increasing number of studies focus on farmers in climate change adaptation; (2) the global geographic distribution of the reviewed studies is uneven, and many of the most vulnerable nations (e.g., lower-income/agricultural-dependent economies) have no representation at all; (3) there were diverse rationales and methods for incorporating farmers into the studies, and many of the methodological differences were due to practical and logistical limitations in lower-income/agricultural-dependent nations; and (4) studies were from multiple academic fields, indicating the need for more interdisciplinary collaboration moving forward because agricultural adaptation to climate change is too complex for a single discipline to fully explore. Although English is increasingly recognized as the “international language of science,” due to the challenge of language segmentation limiting broader understanding of global scholarship whenever possible, future reviews should be jointly conducted in both English and non-English languages.
Isolation and characterization of bovine herpes virus 5 (BHV5) from cattle in India
Authors: Kumar Naveen , Chander Yogesh , Riyesh Thachamvally , Khandelwal Nitin , Kumar Ram , Kumar Harish , Tripathi Bhupendra N. , Barua Sanjay 
Published: January 2020

AbstractBovine herpesvirus 1 (BHV1) and 5 (BHV5) are genetically and antigenically related alphaherpesviruses. Infection with one virus induces protective immunity against the other. However, disease associated with BHV1 and BHV5 varies significantly; whereas BHV1 infection is usually associated with rhinotracheitis and abortion, BHV5 causes encephalitis in cattle. BHV5 outbreaks are sporadic and mainly restricted to the South American countries. We report BHV5 infection for the first time from aborted cattle in India. Based on the characteristic cytopathic effects in MDBK cells, amplification of the viral genome in PCR, differential PCR for BHV1/BHV5, nucleotide sequencing and restriction endonuclease patterns, identity of the virus was confirmed as BHV5 subtype A. Serum samples from the aborted cattle strongly neutralized both BHV1 and BHV5 suggesting an active viral infection in the herd. UponUL27, UL44andUL54gene-based sequence and phylogenetic analysis, the isolated virus clustered with BHV5 strains and showed highest similarity with the Brazilian BHV5 strains.Author SummaryBHV5 causes fatal meningoencephalitis that may result in a mortality rate of up to 100% in cattle. BHV5 is rarely associated with abortion and its distribution is restricted to South American countries. Only a few cases of this disease have been reported from other countries. For the first time, we provide a strong evidence of BHV5 infection from aborted cattle in India. The finding may necessitate inclusion of BHV5 test protocol in testing of semen for sexually transmitted diseases. Also, the isolated virus would be useful for developing diagnostic, prophylactic and therapeutic agents to combat BHV5 disease in the country.
Regulation of olfactory-based sex behaviors in the silkworm by genes in the sex-determination cascade
Authors: Xu Jun , Liu Wei , Yang Dehong , Chen Shuqing , Chen Kai , Liu Zulian , Yang Xu , Meng Jing , Zhu Guanheng , Dong Shuanglin , Zhang Yong , Zhan Shuai , Wang Guirong , Huang Yongping 
Published: January 2020

AbstractInsect courtship and mating depend on integration of olfactory, visual, and tactile cues. Compared to other insects,Bombyx mori, the domesticated silkworm, has relatively simple sexual behaviors as it cannot fly. Here by using CRISPR/Cas and electrophysiological techniques we found that courtship and mating behaviors are regulated in male silk moths by mutating genes in the sex determination cascade belonging to two conserved pathways. Loss ofBmdsxgene expression significantly reduced the peripheral perception of the major pheromone component bombykol by reducing expression of the product of theBmOR1gene which completely blocked courtship in adult males. Interestingly, we found that mating behavior was regulated independently by another sexual differentiation gene,Bmfru.Loss ofBmfrucompletely blocked mating, but males displayed normal courtship behavior. Lack ofBmfruexpression significantly reduced the perception of the minor pheromone component bombykal due to the down regulation ofBmOR3expression; further, functional analysis revealed that loss of the product ofBmOR3played a key role in terminating male mating behavior. Our results suggest thatBmdsxandBmfruare at the base of the two primary pathways that regulate olfactory-based sexual behavior.Author SummaryThe fundamental insect sexual behaviors, courtship and mating, result from successful integration of olfactory, vision, tactile and other complex innate behaviors. In the widely used insect model,Drosophila melanogaster, the sex determination cascade genesfruitlessanddoublesexare involved in the regulation of courtship and mating behaviors; however, little is known about the function of these sexual differentiation genes in regulating sex behaviors of Lepidoptera. Here we combine genetics and electrophysiology to investigate regulation pathway of sexual behaviors in the model lepidopteran insect, the domesticated silk moth,Bombyx mori. Our results support the presence of two genetic pathways inB. mori, namedBmdsx-BmOR1-bombykol andBmfru-BmOR3-bombykal, which control distinct aspects of male sexual behavior that are modulated by olfaction. This is the first comprehensive report about the role of sex differentiation genes in the male sexual behavior in the silk moth.
Pesticides and transgenerational inheritance of pathologies: Designing, analysing and reporting rodent studies
Authors: Plewis Ian 
Published: January 2020

AbstractThe evidence for transgenerational transmission of pathologies in rodents exposed to pesticides is largely based on studies with weaknesses in design and analysis and a lack of transparency in reporting the results. This paper examines these methodological and statistical issues in detail. Its particular focus is on the estimation of ‘litter effects’: the tendency for rodents within a litter to be more alike than rodents in different litters. Appropriate statistical models were fitted to published data from a series of widely reported studies carried out at Washington State University. These studies were amalgamated into a single dataset in order to estimate these litter effects and the associated treatment effects. Litter effects varied by outcome and were often substantial. Consequently, the effective sample size was often substantially less than the number of observations with implications for the power of the studies. Moreover, the reported precision of the estimates of treatment effects was too low. These problems are exacerbated by unexplained missing data across generations. Researchers in the life sciences could be more cognisant of the guidelines established in medicine for reporting randomised controlled trials, particularly cluster randomised trials. More attention should be paid to the design and analysis of multi-generational rodent studies; their imperfections have important implications for assessments of the evidence relating to the risks of pesticides for public health.
Ameliorative effect of a quinazoline-based bromodomain inhibitor, CN210, on experimentally-induced Crohn’s disease-like murine ileitis via inhibition of inflammatory cytokine expression
Authors: Noguchi Takehisa , Hidaka Kyosuke , Kobayashi Satsuki , Matsumoto Kenjiro , Yoshioka Makoto , Yang Shyh-Ming , Maloney David J. , Kato Shinichi 
Published: January 2020

AbstractInhibitors of bromodomain and extra-terminal motif proteins (“BET inhibitors”) are emerging epigenetic therapeutics that exert their effects by suppressing the expression of genes that drive cancer and inflammation. The present study examined the anti-inflammatory effects of a quinazoline-based BET inhibitor, CN210, which also inhibits bromodomains of two paralogous histone acetyltransferases (HATs), such as cAMP-responsive element binding protein-binding protein (CBP) and p300. To assess its effectiveness against inflammatory bowel disease (IBD), CN210 was tested in an experimentally-induced murine Crohn’s disease (CD)-like ileitis model. Ileitis was induced in mice by subcutaneous administration of indomethacin and CN210 was given orally 30 min before and 24 h after the indomethacin administration. Whilst indomethacin produced severe ileitis accompanied by an increase in ileal mucosal myeloperoxidase (MPO) activity, administration of CN210 reduced the severity of ileitis in a dose-dependent manner and suppressed the MPO activity. Similarly, upregulation of inflammatory cytokines was observed in ileitis mucosa after indomethacin injection but this response was significantly attenuated by CN210 administration. To further characterize the effects of CN210 on inflammatory pathways, monocyte/macrophage-like cell line RAW264 treated with lipopolysaccharide (LPS) was exposed to CN210. CN210 significantly attenuated the expression of inflammatory cytokines and reversed the activation of NF-κB and MAP kinases induced by LPS. These findings suggest that CN210 ameliorates indomethacin-induced ileitis due at least in part to the inhibition of inflammatory cytokine expressionviaattenuation of NF-κB and MAP kinase pathways, thus representing a new mode of therapy for CD.
Structural and Functional NIR-II Fluorescence Bioimaging in Urinary System via Clinically Approved Dye Methylene Blue
Authors: Xue Dingwei , Wu Di , Lu Zeyi , Zebibula Abudureheman , Feng Zhe , Qian Jun , Li Gonghui 
Published: January 2020

AbstractAccurate structural and functional imaging is vital for the diagnosis and prognosis of the urinary system diseases. Near-infrared region (NIR) II fluorescence imaging has shown advantages of high sensitivity, high safety, and fast feedback compared to the conventional imaging methods but limited to its clinical applicability. Herein, we first report that in vivo NIR-II fluorescence imaging of the urinary system enabled by clinically approved and renal-clearable NIR dye methylene blue, which can not only achieve clear invasive/non-invasive urography but also noninvasively detect renal function. These results demonstrate that MB assisted NIR-II fluorescence imaging holds great promise for invasive/noninvasive structural imaging of the urinary system clinically and investigation of renal function in animal models preclinically.
Identification of microRNAs involved in NOD-dependent induction of pro-inflammatory genes in pulmonary endothelial cells
Authors: Vlacil Ann-Kathrin , Vollmeister Evelyn , Bertrams Wilhelm , Schoesser Florian , Oberoi Raghav , Schuett Jutta , Schuett Harald , Huehn Sonja , Bedenbender Katrin , Schmeck Bernd T. , Schieffer Bernhard , Grote Karsten 
Published: January 2020

AbstractThe nucleotide-binding oligomerization domain-containing proteins (NOD) 1 and 2 are mammalian cytosolic pattern recognition receptors sensing bacterial peptidoglycan fragments in order to initiate cytokine expression and pathogen host defence. Since endothelial cells are relevant cells for pathogen recognition at the blood/tissue interface, we here analysed the role of NOD1- and NOD2-dependently expressed microRNAs (miRNAs, miR) for cytokine regulation in murine pulmonary endothelial cells. The induction of inflammatory cytokines in response to NOD1 and NOD2 was confirmed by increased expression of tumour necrosis factor (Tnf)-αand interleukin (Il)-6. MiRNA expression profiling revealed NOD1- and NOD2-dependently regulated miRNA candidates, of which miR-147-3p, miR-200a-3p, and miR-298-5p were subsequently validated in pulmonary endothelial cells isolated fromNod1/2-deficient mice.In-silicoanalysis of the two down-regulated candidates miR-147-3p and miR-298-5p revealed predicted binding sites in the 3’ untranslated region (UTR) of the murineTnf-αandIl-6mRNA. Consequently, transfection of endothelial cells with miRNA mimics decreasedTnf-αandIl-6mRNA levels. Finally, a novel direct interaction of miR-298-5p with the 3’UTR of theIl-6mRNA was uncovered by luciferase reporter assays. We here identified a mechanism of miRNA-down-regulation by NOD stimulation thereby enabling the induction of inflammatory gene expression in endothelial cells.
Host-derived Circular RNAs Display Proviral Activities in Hepatitis C Virus - Infected Cells
Authors: Chen Tzu-Chun , Tallo-Parra Marc , Kadener Sebastian , Böttcher René , Pérez-Vilaró Gemma , Boonchuen Pakpoom , Somboonwiwat Kunlaya , Díez Juana , Sarnow Peter 
Published: January 2020

AbstractViruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Surprisingly, circPSD3 also inhibited the cellular nonsense-mediated decay (NMD) pathway in liver cells. Thus, enhanced abundance of circPSD3 in virus-infected cells aids in viral replication and likely contributes to the known inhibition of NMD in HCV-infected cells. Findings from the global analyses of the circular RNA landscape argue pro-, and likely, anti-viral functions are executed by circRNAs that modulate both viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis.Author SummaryUsually, cells are infected by one or a few virus particles that carry genomes with limited expression capacity. Thus, the expression of viral genomes has to compete with a sea of cellular components that aid in viral translation, replication and virion production. Depending on their lifestyle, viruses have evolved to avoid or to subvert cellular pathways, especially those that display anti-viral functions. Host-derived circular RNA molecules have recently been discovered in the cytoplasm of cells, although, as-of yet, few functions have been assigned to them. Here, we describe alterations in the circular RNA landscape in hepatitis C virus-infected liver cells. Up-regulated and down-regulated circular RNAs were identified, and three of the upregulated RNAs were shown to promote HCV infection. One of them, circPSD3, inhibited the cellular nonsense-mediated RNA decay that is a powerful antiviral response in infected cells. Because circular RNAs are more stable than linear RNAs, they may have important functions during viral infection, dictating the outcomes of innate immune responses and viral pathogenesis.