bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effects of Bt Cry1Ie toxin on bacterial diversity in the midgut of Apis mellifera ligustica (Hymenoptera: Apidae)
Authors: Jia Hui-Ru , Geng Li-Li , Li Yun-He , Wang Qiang , Diao Qing-Yun , Zhou Ting , Dai Ping-Li 
Published: April 2016

AbstractThe honey bee has been regarded as a key species in the environmental risk assessment of biotech crops. Here, the potential adverse effects of Cry1Ie toxin on the midgut bacteria of the worker bees (Apis mellifera ligustica) were investigated under laboratory conditions. Newly emerged bees were fed with different concentrations of Cry1Ie toxin syrups (20 ng/mL, 200 ng/mL and 20 μg/mL), pure sugar syrup and 48 ppb of imidacloprid syrups, then sampled after 15 and 30 d. We characterized the dominant midgut bacteria and compared the composition and structure of the midgut bacterial community in all samples using the Illumina MiSeq platform targeting the V3–V4 regions of 16S rDNA. No significant differences in the diversity of the midgut bacteria were observed between the five treatments. This work was the first to show the effects of Cry1Ie toxin on honey bees and our study provided a theoretical basis for the biosafety assessment of transgenic Cry1Ie maize.
Perceptual learning shapes multisensory causal inference via two distinct mechanisms
Authors: McGovern David P. , Roudaia Eugenie , Newell Fiona N. , Roach Neil W. 
Published: April 2016

AbstractTo accurately represent the environment, our brains must integrate sensory signals from a common source while segregating those from independent sources. A reasonable strategy for performing this task is to restrict integration to cues that coincide in space and time. However, because multisensory signals are subject to differential transmission and processing delays, the brain must retain a degree of tolerance for temporal discrepancies. Recent research suggests that the width of this ‘temporal binding window’ can be reduced through perceptual learning, however, little is known about the mechanisms underlying these experience-dependent effects. Here, in separate experiments, we measure the temporal and spatial binding windows of human participants before and after training on an audiovisual temporal discrimination task. We show that training leads to two distinct effects on multisensory integration in the form of (i) a specific narrowing of the temporal binding window that does not transfer to spatial binding and (ii) a general reduction in the magnitude of crossmodal interactions across all spatiotemporal disparities. These effects arise naturally from a Bayesian model of causal inference in which learning improves the precision of audiovisual timing estimation, whilst concomitantly decreasing the prior expectation that stimuli emanate from a common source.
ATM mediates spermidine-induced mitophagy via PINK1 and Parkin regulation in human fibroblasts
Authors: Qi Yongmei , Qiu Qian , Gu Xueyan , Tian Yihong , Zhang Yingmei 
Published: April 2016

AbstractThe ATM (ataxia telangiectasia mutated) protein has recently been proposed to play critical roles in the response to mitochondrial dysfunction by initiating mitophagy. Here, we have used ATM-proficient GM00637 cells and ATM-deficient GM05849 cells to investigate the mitophagic effect of spermidine and to elucidate the role of ATM in spermdine-induced mitophagy. Our results indicate that spermidine induces mitophagy by eliciting mitochondrial depolarization, which triggers the formation of mitophagosomes and mitolysosomes, thereby promoting the accumulation of PINK1 and translocation of Parkin to damaged mitochondria, finally leading to the decreased mitochondrial mass in GM00637 cells. However, in GM05849 cells or GM00637 cells pretreated with the ATM kinase inhibitor KU55933, the expression of full-length PINK1 and the translocation of Parkin are blocked and the colocalization of Parkin with either LC3 or PINK1 is disrupted. These results suggest that ATM drives the initiation of the mitophagic cascade. Our study demonstrates that spermidine induces mitophagy through ATM-dependent activation of the PINK1/Parkin pathway. These findings underscore the importance of a mitophagy regulatory network of ATM and PINK1/Parkin and elucidate a novel mechanism by which ATM influences spermidine-induced mitophagy.
Reversal of evoked gamma oscillation deficits is predictive of antipsychotic activity with a unique profile for clozapine
Authors: Hudson M R , Rind G , O'Brien T J , Jones N C 
Published: April 2016

AbstractRecent heuristic models of schizophrenia propose that abnormalities in the gamma frequency cerebral oscillations may be closely tied to the pathophysiology of the disorder, with hypofunction of N-methyl-d-aspartate receptors (NMDAr) implicated as having a crucial role. Prepulse inhibition (PPI) is a behavioural measure of sensorimotor gating that is disrupted in schizophrenia. We tested the ability for antipsychotic drugs with diverse pharmacological actions to (1) ameliorate NMDAr antagonist-induced disruptions to gamma oscillations and (2) attenuate NMDAr antagonist-induced disruptions to PPI. We hypothesized that antipsychotic-mediated improvement of PPI deficits would be accompanied by a normalization of gamma oscillatory activity. Wistar rats were implanted with extradural electrodes to facilitate recording of electroencephalogram during PPI behavioural testing. In each session, the rats were administered haloperidol (0.25 mg kg−1), clozapine (5 mg kg−1), olanzapine (5 mg kg−1), LY379268 (3 mg kg−1), NFPS (sarcosine, 1 mg kg−1), d-serine (1800 mg kg−1) or vehicle, followed by the NMDAr antagonists MK-801(0.16 mg kg−1), ketamine (5 mg kg−1) or vehicle. Outcome measures were auditory-evoked, as well as ongoing, gamma oscillations and PPI. Although treatment with all the clinically validated antipsychotic drugs reduced ongoing gamma oscillations, clozapine was the only compound that prevented the sensory-evoked gamma deficit produced by ketamine and MK-801. In addition, clozapine was also the only antipsychotic that attenuated the disruption to PPI produced by the NMDAr antagonists. We conclude that disruptions to evoked, but not ongoing, gamma oscillations caused by NMDAr antagonists are functionally relevant, and suggest that compounds, which restore sensory-evoked gamma oscillations may improve sensory processing in patients with schizophrenia.
Fine processes of Nestin-GFP–positive radial glia-like stem cells in the adult dentate gyrus ensheathe local synapses and vasculature
Authors: Moss Jonathan , Gebara Elias , Bushong Eric A. , Sánchez-Pascual Irene , O’Laoi Ruadhan , El M’Ghari Imane , Kocher-Braissant Jacqueline , Ellisman Mark H. , Toni Nicolas 
Published: April 2016

Significance
A population of adult neural stem cells supplies the dentate gyrus with new neurons that play a role in mechanisms of learning and memory. Radial glia-like stem cells have a unique morphology, including a dense arbor of fine processes that infiltrate the neurogenic niche. Here, we provide what is, to our knowledge, the first detailed ultrastructural description of these processes, and we reveal that these cells establish a variety of contacts with local blood vessels, synapses, and astrocytes. Given that signals derived from neurons, astrocytes, and blood vessels regulate the process of adult neurogenesis, the identification of these contacts provides a structural framework for elucidating the mechanisms by which this regulation occurs. These results contribute to a greater understanding of the adult hippocampal neurogenic niche.
Structural characterization of the interaction of α-synuclein nascent chains with the ribosomal surface and trigger factor
Authors: Deckert Annika , Waudby Christopher A. , Wlodarski Tomasz , Wentink Anne S. , Wang Xiaolin , Kirkpatrick John P. , Paton Jack F. S. , Camilloni Carlo , Kukic Predrag , Dobson Christopher M. , Vendruscolo Michele , Cabrita Lisa D. , Christodoulou John 
Published: April 2016

Significance
Protein biosynthesis is carried out by ribosomes, the macromolecular machines present in all kingdoms of life. Aided by molecular chaperones, nascent proteins can begin to fold while emerging from the ribosome. Achieving their native fold, and avoiding misfolding, is thereby crucial for the fate of all newly synthesized proteins. The molecular details of this fundamental process, however, are poorly understood. In this work we develop a combined NMR and molecular simulation approach to characterize the behavior during biosynthesis of α-synuclein (αSyn), an intrinsically disordered protein associated with Parkinson’s disease. The detailed interactions of αSyn with the ribosome surface and with trigger factor, a ribosome-associated chaperone, reveal the first steps of how a nascent chain emerges from the ribosome.
Dinosaurs in decline tens of millions of years before their final extinction
Authors: Sakamoto Manabu , Benton Michael J. , Venditti Chris 
Published: April 2016

SignificanceWhether dinosaurs were in decline before their final extinction 66 Mya has been debated for decades with no clear resolution. This dispute has not been resolved because of inappropriate data and methods. Here, for the first time to our knowledge, we apply a statistical approach that models changes in speciation and extinction through time. We find overwhelming support for a long-term decline across all dinosaurs and within all three major dinosaur groups. Our results highlight that dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event 66 Mya.
Part mutual information for quantifying direct associations in networks
Authors: Zhao Juan , Zhou Yiwei , Zhang Xiujun , Chen Luonan 
Published: April 2016

Significance
Measuring direct associations between variables is of great importance in various areas of science, especially in the era of big data. Although mutual information and conditional mutual information are widely used in quantifying both linear and nonlinear associations, they suffer from the serious problems of overestimation and underestimation. To overcome these problems, in contrast to conditional independence, we propose a novel concept of “partial independence” with a new measure, “part mutual information,” based on information theory that can accurately quantify the nonlinearly direct associations between the measured variables.
Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex
Authors: Raveh Barak , Karp Jerome M. , Sparks Samuel , Dutta Kaushik , Rout Michael P. , Sali Andrej , Cowburn David 
Published: April 2016

Significance
The nuclear pore complex (NPC) mediates the trafficking of macromolecules in and out of the nucleus of eukaryotic cells. Here, we characterize how transport factors diffuse rapidly through multiple layers of disordered phenylalanine-glycine (FG) repeat domains lining the NPC. Transport factors interact with FG repeats through a dynamic sliding motion, enabling faster translocation through the NPC than that attainable by a two-state binding mechanism as well as effectively blocking the passage of large macromolecules that do not bind to transport factors. Thus, the NPC exemplifies a dynamic system in living cells, the function of which depends on protein–protein interactions that are transient on the one hand, and highly specific on the other.
Comparative systems pharmacology of HIF stabilization in the prevention of retinopathy of prematurity
Authors: Hoppe George , Yoon Suzy , Gopalan Banu , Savage Alexandria R. , Brown Rebecca , Case Kelsey , Vasanji Amit , Chan E. Ricky , Silver Randi B. , Sears Jonathan E. 
Published: April 2016

Significance
In all premature births, oxygen supplementation is a necessary life-sustaining measure, but unfortunately for these high-risk babies, oxygen toxicity may adversely and permanently affect the retina. Pharmacological activation of the hypoxia-inducible factor (HIF) pathway can prevent experimental oxygen-induced retinopathy and thus has the potential to prevent blindness in 100,000 children annually. Comprehensive analysis of liver and retinal transcriptomes after HIF stabilization demonstrates that select small molecules, given systemically, protect the retina by two pathways: stimulating the liver to secrete angiogenic hepatokines or locally stimulating retinal protection. These findings support a low dose, intermittent, systemic approach for preventing oxygen induced injury to premature infants.
Primary motor and sensory cortical areas communicate via spatiotemporally coordinated networks at multiple frequencies
Authors: Arce-McShane Fritzie I. , Ross Callum F. , Takahashi Kazutaka , Sessle Barry J. , Hatsopoulos Nicholas G. 
Published: April 2016

SignificanceSensorimotor integration is important for the acquisition and performance of motor skills. Here, we show the emergence of neuroplastic changes in the interactions between the motor and somatosensory areas of the primate cortex during learning. Interareal coherence is frequency- and network-specific and exhibits a spatiotemporal organization. Time-sensitive sensorimotor integration and plasticity may rely on coherence of local and large-scale sensorimotor networks in order for cortical processes to operate at multiple temporal and spatial scales. Understanding cortico-cortical interactions may be important for developing therapies for sensorimotor disorders, such as those affecting feeding and speech that are commonly found in stroke and Parkinson’s disease.
Energy landscapes of a mechanical prion and their implications for the molecular mechanism of long-term memory
Authors: Chen Mingchen , Zheng Weihua , Wolynes Peter G. 
Published: April 2016

Significance
The physical basis for the long timescale of memory has been mysterious. The formation of a functional prion-like fiber in the neuronal system may resolve the question. This work shows that the energy landscapes of a candidate prion, cytoplasmic polyadenylation element binding (CPEB) protein, allow external mechanical forces to facilitate the structural transition to a fiber form. The mechanical coupling thus allows a positive feedback loop between CPEB prion transitions and cytoskeletal actions to mark synapses.
Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets
Authors: Vinayagam Arunachalam , Gibson Travis E. , Lee Ho-Joon , Yilmazel Bahar , Roesel Charles , Hu Yanhui , Kwon Young , Sharma Amitabh , Liu Yang-Yu , Perrimon Norbert , Barabási Albert-László 
Published: April 2016

Significance
Large-scale biological network analyses often use concepts used in social networks analysis (e.g. finding “communities,” “hubs,” etc.). However, mathematically advanced engineering concepts have only been applied to analyze small and well-characterized networks so far in biology. Here, we applied a sophisticated engineering tool, from control theory, to analyze a large-scale directed human protein–protein interaction network. Our analysis revealed that the proteins that are indispensable, from a network controllability perspective, are also commonly targeted by disease-causing mutations and human viruses or have been identified as drug targets. Furthermore, we used the controllability analysis to prioritize novel cancer genes from cancer genomic datasets. Altogether, we demonstrated an application of network controllability analysis to identify new disease genes and drug targets.
Tissue-specific DNA demethylation is required for proper B-cell differentiation and function
Authors: Orlanski Shari , Labi Verena , Reizel Yitzhak , Spiro Adam , Lichtenstein Michal , Levin-Klein Rena , Koralov Sergei B. , Skversky Yael , Rajewsky Klaus , Cedar Howard , Bergman Yehudit 
Published: April 2016

Significance
Even though DNA methylation is known to be correlated with gene repression, it has never been demonstrated that this modification must indeed be removed from a gene in order for it to become activated during cell differentiation in vivo. In this paper, we inactivated the enzymes responsible for the demethylation reaction in the B-cell lineage and in this manner have shown that this epigenetic mark plays a critical role in development, independently of the many specific transcription factors that direct the selection of genes involved in cell differentiation. Our study is the first to our knowledge to causally connect all of the molecular components necessary to prove the link between the Tet enzymes, CpG demethylation, expression, and phenotype.
Density and Survival of Walleye Eggs and Larvae in a Great Lakes Tributary
Authors: Rutherford E. S. , Allison J. , Ruetz C. R. , Elliott J. R. , Nohner J. K. , DuFour M. R. , O'Neal R. P. , Jude D. J. , Hensler S. R. 
Published: April 2016

AbstractThe Walleye Sander vitreus is an important sport fish that has experienced low reproductive success in some Great Lakes tributaries since severe population declines began in the late 1940s. In the Muskegon River, a Lake Michigan tributary, natural reproduction of Walleyes remains low and is largely supplemented by stocking. We evaluated the influence of abiotic factors on Walleye reproductive success in the Muskegon River during April and May 2009 and 2010 by (1) estimating Walleye egg density and survival; (2) estimating the size, density, abundance, and survival of Walleye larvae; and (3) relating our estimates to physical habitat conditions. Egg densities were 70‐fold higher in 2009 than in 2010, but eggs experienced colder water temperatures, higher river discharge rates, and lower survival in 2009 relative to 2010. Egg survival in incubators was positively related to temperature and negatively related to flow at most sites. In both years, Walleye larvae that hatched during periods of cooler temperature were smaller than larvae that hatched later during periods of warmer temperature. Walleye larval densities were highest near spawning grounds and decreased downstream. Bayesian estimates of variability in larval densities indicated that temporal variability was twice as high as spatial variability in the Muskegon River. Larval survival was much lower in 2009 than in 2010, resulting in an approximately sevenfold higher production of larvae in 2010 than in 2009. Survival was highest for smaller larvae that hatched early in April 2010, when temperatures were warm and discharges were low and stable; in contrast, survival was much lower for larger larvae hatching later in 2010 or for large and small larvae in 2009, when water temperatures were colder and discharges were higher and more variable. Our results suggest that abiotic factors, primarily temperature and river flow, likely control the early survival of Walleyes in the Muskegon River.Received February 9, 2015; accepted January 11, 2016 Published online April 19, 2016
Use of Psychotropic Drug Urine Test Strips in Opiate Maintenance Therapy: A Clinical Assessment of its Advantages
Authors: Victorri-Vigneau Caroline , Rousselet Morgane , Grall-Bronnec Marie , Bouquié Regis , Belliot Emeric , Guerlais Marylène , Guillet Jean-Yves , Jolliet Pascale 
Published: April 2016

Background: Methadone and buprenorphine are the 2 opiate maintenance treatments (OMTs) available in France. According to good clinical practices, a full clinical and biological assessment is required before deciding to initiate or renew an OMT. For methadone, this assessment includes psychoactive drug consumption investigation through an initial interview completed by a systematic urine test mandatory before starting methadone treatment. In case of buprenorphine prescription, the situation is less clear and the urine test was not systematically performed. This work aims at evaluating changes in the therapeutic strategy brought by the systematic use of urine strips for detecting drug consumptions. Methods: During 1 month, for each case of OMT renewal, physicians belonging to the 3 types of prescribing structures in France (general medicine, specialized centers for drug addict patients, and specialized centers for drug addict patients in prison) had to complete a specific questionnaire about prescription renewal. This questionnaire contained 2 parts. The first part was completed by the physicians before the urine test strip realization. The second part was completed by the same physicians at the end of the consultation, after obtaining the results from the urine test strip. A change between parts 1 and 2 of the questionnaire concerning OMT prescription, dialogue with the patient, associated psychotropic drug prescription, and orientation were considered as a change in therapeutic strategy. Results: A total of 429 questionnaires have been collected. Among them, 315 showed at least 1 change in therapeutic strategy (73.4%). Conclusions: This study highlighted the important benefits brought by the urine test strip in managing patients under opiate maintenance treatment. Urine test strips provided an immediate answer that allowed physicians to optimize their therapeutic strategy. However, regulatory evolutions would be necessary to ease their implantation.
Fruit and Vegetable Intake as a Moderator of the Association between Depressive Symptoms and Cigarette Smoking
Authors: Haibach Jeffrey P. , Homish Gregory G. , Collins R. Lorraine , Ambrosone Christine B. , Giovino Gary A. 
Published: April 2016

Background: Studies have consistently reported associations among depression, cigarette smoking, and fruit and vegetable intake (FVI). This study evaluated FVI as a moderator of the association between depressive symptoms and smoking. Methods: The authors analyzed data from the National Longitudinal Survey of Youth 1979: Child and Young Adult. The study sample was adults aged 19–33 years at baseline in the year 2004 from the Young Adult Survey portion. Moderation analyses were performed using the Johnson-Neyman technique to assess whether baseline FVI moderated the association between depressive symptoms and smoking status cross-sectionally and as a predictor of smoking cessation longitudinally at 4-year follow-up. Results: Cross-sectionally, at lower levels of FVI (<4.9 times/day), there was a significant association between smoking and depressive symptoms ( P < .05), but not at higher levels of FVI (≥4.9 times/day; P > .05). Longitudinally, there was an inverse association between depressive symptoms and quitting smoking at FVI <1.2 times/day ( P < .05), but there was not a significant association at FVI ≥1.2 times/day ( P ≥ .05). Conclusions: FVI moderated the association between depressive symptoms and cigarette smoking cross-sectionally and longitudinally. The cross-sectional findings might be partially explained by the longitudinal findings paired with prior research; there might be fewer smokers with high FVI because depressive symptoms are removed as an impediment to cessation. Further experimental research is warranted to test the efficacy of increased FVI as an adjunct to smoking cessation, with a possible mechanism of action being reduced depressive symptoms during quit attempts.