bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causes of Horner Syndrome: A Study of 318 Patients
Authors: Sabbagh Mohammad Amr , De Lott Lindsey B. , Trobe Jonathan D. 
Published: October 2019

Background:
Some reports have indicated that when a cause for Horner syndrome can be determined, it is most often chest and neck tumors and stroke. Others have suggested that Horner syndrome is more frequently caused by surgical procedures in the neck and chest. These differences may be explained by disparate accrual methods. Therefore, we decided to compare the cause of Horner syndrome in cases where the diagnosis was confirmed by apraclonidine testing conducted by ophthalmologists to cases in which the diagnosis was made entirely on clinical grounds mostly by nonophthalmologists.

Methods:
We applied a new search engine to the inpatient and outpatient electronic medical records text at the University of Michigan Medical Center from 1996 to 2018 for Horner syndrome with and without pharmacologic confirmation through ocular instillation of apraclonidine 0.5%. Among apraclonidine-confirmed cases, 159 met inclusion criteria. Among apraclonidine-unconfirmed cases, more than 2,000 cases were identified, so that we included only the first 159 cases that met inclusion criteria. In these 318 cases, we documented patient demographics, ophthalmologic features, imaging, underlying cause, and whether the cause was discovered before or after the diagnosis of Horner syndrome.

Results:
In the cohort of 159 apraclonidine-confirmed cases of Horner syndrome, a cause was identified in 97 (61%). Procedures in the neck, chest, skull base, and paraspinal region accounted for most of the identified causes, with cervical carotid dissection the next most common cause. In a cohort of 159 cases of Horner syndrome not tested with apraclonidine because the clinical diagnosis appeared firm, procedures again accounted for the largest percentage, but tumor was the next most common cause. In both groups, when a cause for Horner syndrome could be identified, that cause was nearly always known before Horner syndrome was identified. However, in an important minority of cases, mostly involving carotid dissection or tumor, the identification of Horner syndrome was critical to the discovery of those conditions.

Conclusions:
The prevalence of causes of Horner syndrome depends on the accrual method. Among pharmacologically-confirmed cases, the cause was often undetermined or due to a preceding neck or chest procedure. Among pharmacologically-unconfirmed cases, a substantial proportion had also been caused by neck and chest procedures, but tumors in that region were also common. When a cause of Horner syndrome was found in both cohorts, it was usually known before Horner syndrome was discovered, making Horner syndrome an afterthought. However, in an important minority of cases where the cause was not yet known, the identification of Horner syndrome was valuable in leading to important diagnoses such as carotid dissection and tumor.
Analysis of fan-stage gap-flow data to inform simulation of fan broadband noise
Authors: Grace Sheryl , Gonzalez-Martino Ignacio , Casalino Damiano 
Published: October 2019

Time-resolved simulations present a new opportunity for studying the disturbances responsible for the broadband interaction noise created by the fan stage. In this paper, two vane configurations from the source diagnostic test at the approach rotor speed were computed with PowerFLOW's very large-eddy simulation (VLES) method using two solution strategies: a coarser mesh near the rotor and a trip to trigger turbulent transition on the rotor; and a much finer mesh near the rotor with no trip. The simulated data allow for an investigation of the potential effect from the vane configuration and an in-depth study of the mean and turbulent flow in the interstage gap. A challenge related to post-processing of high-resolution simulations is discussed. Comparison of the flow quantities with previously obtained Reynolds Averaged Navier–Stokes simulation results indicates that little advantage is gained by running a lattice Boltmann method (LBM)/VLES to simply recover the gap flow parameters for use with a lower-order fan broadband interaction noise calculation method. The true benefit of the LBM/VLES is that the noise calculation can be directly and simultaneously completed with the flow simulation.This article is part of the theme issue ‘Frontiers of aeroacoustics research: theory, computation and experiment’.
Effect of fluid injection on turbulence and noise reduction of a supersonic jet
Authors: Prasad Chitrarth , Morris Philip 
Published: October 2019

Supersonic jets, such as the ones used in high-performance military aircraft, have both downstream and upstream noise components due to the large-scale turbulent structures and the presence of shock cells in the jet plume. The fluid insert technology is a noise reduction method that has been shown to effectively reduce both these noise components. This paper analyses the unsteady flow changes associated with different fluid insert configurations with a goal of helping to understand the detailed noise reduction mechanisms. Using direct cross-correlations of the near-field data with the far-field microphone signals, it is found that even the use of a single injector as a fluid insert helps break up the large-scale structures of the flow. However, a more azimuthally distributed blowing is required to reduce the upstream broadband shock-associated noise (BBSAN). Addition of upstream injectors at each azimuthal location further enhances the BBSAN reduction. Decomposition of the jet flow-field into hydrodynamic and acoustic modes shows that fluid insert nozzles reduce the amplitude and convection speed of the coherent acoustic mode in the plane of highest noise reduction.
This article is part of the theme issue ‘Frontiers of aeroacoustics research: theory, computation and experiment’.
Novel insights into expansion and functional diversification of MIR169 family in tomato
Authors: Rao Sombir , Balyan Sonia , Jha Sarita , Mathur Saloni 
Published: October 2019

AbstractMIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report eighteen miR169 precursors, annotating new loci for MIR169a, b and d, as well as four novel mature isoforms (MIR169f/g/h/i). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair ‘MIR169b/b-1 and MIR169b-2/h’ is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding-protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoterMIR169:GUS-reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.HighlightExpansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increases the functional diversification of MIR169 in tomato. (29/30)
Channel Capacity Computations for Unregulated and Autoregulated Gene Expression
Authors: Vahdat Zahra , Nienałtowski Karol , Farooq Zia , Komorowski Michał , Singh Abhyudai 
Published: October 2019

AbstractHow living cells can reliably process biochemical cues in the presence of molecular noise is not fully understood. Here we investigate the fidelity of information transfer in the expression of a single gene. We use the established model of gene expression to examine how precisely the protein levels can be controlled by two distinct mechanisms: (i) the transcription rate of the gene, or (ii) the translation rate for the corresponding mRNA. The fidelity of gene expression is quantified with the information-theoretic notion of information capacity. Derived information capacity formulae reveal that transcriptional control generally provides a tangibly higher capacity as compared to the translational control. We next introduce negative feedback regulation in gene expression, where the protein directly inhibits its own transcription. While negative feedback reduces noise in the level of the protein for a given input signal, it also decreases the input-to-output sensitivity. Our results show that the combined effect of these two opposing forces is a reduced capacity in the presence of feedback. In summary, our analysis presents the first analytical quantification of information transfer in simple gene expression models, which provides insight into the fidelity of basic gene expression control mechanisms.
Decisions bias future choices by modifying hippocampal associative memories
Authors: Luettgau Lennart , Tempelmann Claus , Kaiser Luca Franziska , Jocham Gerhard 
Published: October 2019

AbstractDecision making is guided by memories of option values. However, retrieving items from memory renders them malleable. Here, we show that merely retrieving values from memory and making a choice between options is sufficient both to induce changes to stimulus-reward associations in the hippocampus and to bias future decision making. After allowing participants to make repeated choices between reward-conditioned stimuli, in the absence of any outcome, we observed that participants preferred stimuli they had previously chosen, and neglected previously unchosen stimuli, over otherwise identical-valued options. Using functional brain imaging, we show that decisions induced changes to hippocampal representations of stimulus-outcome associations. These changes were correlated with future decision biases. Our results indicate that choice-induced preference changes are partially driven by choice-induced modification of memory representations and suggest that merely making a choice - even without experiencing any outcomes - induces associative plasticity.
Amphetamine disrupts haemodynamic correlates of prediction errors in nucleus accumbens and orbitofrontal cortex
Authors: Werlen Emilie , Shin Soon-Lim , Gastambide Francois , Francois Jennifer , Tricklebank Mark D , Marston Hugh M , Huxter John R , Gilmour Gary , Walton Mark E 
Published: October 2019

AbstractIn an uncertain world, the ability to predict and update the relationships between environmental cues and outcomes is a fundamental element of adaptive behaviour. This type of learning is typically thought to depend on prediction error, the difference between expected and experienced events, and in the reward domain this has been closely linked to mesolimbic dopamine. There is also increasing behavioural and neuroimaging evidence that disruption to this process may be a cross-diagnostic feature of several neuropsychiatric and neurological disorders in which dopamine is dysregulated. However, the precise relationship between haemodynamic measures, dopamine and reward-guided learning remains unclear. To help address this issue, we used a translational technique, oxygen amperometry, to record haemodynamic signals in the nucleus accumbens (NAc) and orbitofrontal cortex (OFC) while freely-moving rats performed a probabilistic Pavlovian learning task. Using a model-based analysis approach to account for individual variations in learning, we found that the oxygen signal in the NAc correlated with a reward prediction error, whereas in the OFC it correlated with an unsigned prediction error or salience signal. Furthermore, an acute dose of amphetamine, creating a hyperdopaminergic state, disrupted rats’ ability to discriminate between cues associated with either a high or a low probability of reward and concomitantly corrupted prediction error signalling. These results demonstrate parallel but distinct prediction error signals in NAc and OFC during learning, both of which are affected by psychostimulant administration. Furthermore, they establish the viability of tracking and manipulating haemodynamic signatures of reward-guided learning observed in human fMRI studies using a proxy signal for BOLD in a freely behaving rodent.
Under-ice mesocosms reveal the primacy of light but the importance of zooplankton in winter phytoplankton dynamics
Authors: Hrycik Allison R. , Stockwell Jason D. 
Published: October 2019

AbstractFactors that regulate planktonic communities under lake ice may be vastly different than the open-water season. However, under-ice food webs in temperate lakes are poorly understood, despite expected changes in light availability, ice cover, and snowfall associated with climate change. We hypothesized that light limitation (bottom-up control) outweighs zooplankton grazing (top-down control) on phytoplankton biovolume and community structure under ice in a north temperate lake. Using in situ under-ice mesocosms, we found that light had stronger effects on phytoplankton abundance than zooplankton, as expected. Specifically, low light limited growth of diatoms, cryptophytes, chrysophytes, and chlorophytes. Zooplankton, however, also significantly affected phytoplankton by decreasing diatoms and cryptophytes, in contrast to the common assumption that zooplankton grazing has negligible effects under ice. Ammonia and soluble reactive phosphorus decreased in high light treatments presumably through uptake by phytoplankton, whereas ammonia and soluble reactive phosphorus increased in high zooplankton treatments, likely through excretion. In situ experimental studies are commonly applied to understand food web dynamics in open-water conditions, but are extremely rare under ice. Our results suggest that changes in the light environment under ice have significant, rapid effects on phytoplankton growth and community structure and that zooplankton may play a more active role in winter food webs than previously thought. Changes in snow and ice dynamics associated with climate change may alter the light environment in ice-covered systems and significantly influence community structure.
Active zone compaction in presynaptic homeostatic potentiation
Authors: Mrestani Achmed , Kollmannsberger Philip , Pauli Martin , Repp Felix , Kittel Robert J. , Eilers Jens , Doose Sören , Sauer Markus , Sirén Anna-Leena , Heckmann Manfred , Paul Mila M. 
Published: October 2019

ABSTRACTBrain function relies on neurotransmission which is stabilized by presynaptic homeostatic potentiation (PHP). PHP operates on time scales ranging from minute- to life-long adaptations and likely involves reorganization of presynaptic active zones (AZs). At Drosophila melanogaster neuromuscular junctions, earlier work ascribed AZ enlargement by incorporating more Bruchpilot (Brp) scaffold protein a central mechanistic role in PHP.We used localization microscopy (direct stochastic optical reconstruction microscopy, dSTORM) and hierarchical density-based spatial clustering of applications with noise (HDBSCAN) to study AZ plasticity during PHP. We found that both acute, philanthotoxin (PhTx)-induced and chronic, genetically-induced PHP lead to compaction of individual AZs without altering Brp copy numbers per AZ. This compaction even occurs within Brp subclusters of the AZ scaffold which also move towards AZ centers. Furthermore, lowering imaging resolution revealed how AZ compaction in PHP translates into apparent increases in AZ area and Brp protein content as implied earlier. Our results suggest AZ compaction in PHP as an effective mechanism to raise presynaptic protein density and transmitter release.SIGNIFICANCE STATEMENTHomeostatic plasticity stabilizes chemical synaptic transmission in multiple organisms ranging from insects to humans. Changes in active zones (AZs), membrane specializations of the presynapse where synaptic vesicles are discharged, are thought to be crucial in homeostatic adaptations. AZ growth by protein incorporation was proposed as a core mechanism in presynaptic homeostatic potentiation (PHP). Localization microscopy of an abundant AZ scaffold protein uncovered that instead of growing, AZs are compacted in acute and chronic PHP. At lower imaging resolution, however, AZs appear larger and brighter although protein numbers are not increased. In summary, our findings suggest AZ compaction as new and effective mechanism to raise presynaptic protein density and transmitter release in PHP.
High Affinity binding of Yeast Nucleolin Nsr1 to Co-transcriptionally Formed G4 DNA Obstructs Replication and Elevates Genome Instability
Authors: Singh Shivani , Berroyer Alexandra , Kim Minseon , Kim Nayun 
Published: October 2019

ABSTRACTA significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNAin vivohas been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin NCL is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. The consequence of thein vivointeraction between G4 DNA and nucleolin in respect to the genome instability has not been previously investigated. We show here that G4 DNA-binding is a conserved function in the yeast nucleolin Nsr1. Furthermore, we demonstrate that the Nsr1-G4 DNA complex formation results in replication obstruction and is a major factor in inducing the genome instability associated with the co-transcriptionally formed G4 DNA in the yeast genome. The G4-associated genome instability and the G4 DNA-bindingin vivorequires the arginine-glycine-glycine (RGG) repeats located at the C-terminus of the Nsr1 protein. Nsr1 with the deletion of RGG domain supports normal cell growth and is sufficient for its pre-rRNA processing function. However, the truncation of RGG domain of Nsr1 significantly weakens its interaction with G4 DNAin vitroandin vivoand restores unhindered replication, overall resulting in a sharp reduction in the G4-associated genome instability. Our data suggest that the interaction between Nsr1 with the intact RGG repeats and G4 DNA impairs genome stability by precluding the access of G4-resolving proteins and obstructing replication.AUTHOR SUMMARYGenome instability is uniquely elevated at sequences containing multiple runs of guanines, which can fold into the unusual, four-stranded G-quadruplex (G4) DNA. In this study, we report a novel finding that a highly conserved G4 DNA binding protein Nsr1 can elevate the rate of recombination and chromosomal rearrangement occurring at a G4 DNA-forming sequence in the genome ofSaccharomyces cerevisiae. The elevated genome instability requires the C-terminally located RGG domain of Nsr1, which supports the high-affinity interaction between the protein and G4 DNA. The connection between G4-specific genome instability and the function of Nsr1 to form stable complex with G4 DNA led to the hypothesis that the high-affinity Nsr1-G4 DNA complexes can become a barrier to replication. We demonstrate here that the presence of Nsr1 in fact slows the replication past a G4 DNA-containing genomic site and that the RGG domain is required to facilitate such replication block.
A dual functioning small RNA/Riboswitch controls the expression of the methionine biosynthesis regulator SahR inDesulfovibrio vulgarisHildenborough
Authors: Kempher M. L. , Burns A. S. , Novichkov P. S. , Bender K. S. 
Published: October 2019

ABSTRACTRiboswitches arecis-acting RNA regulatory elements that control expression of a downstream gene(s) by directly binding to a specific metabolite. Here we report aS-adenosylmethionine (SAM)-I riboswitch in the sulfate-reducing bacteriumDesulfovibrio vulgarisHildenborough (DvH) that plays an additional regulatory role as atranssmall noncoding RNA (sRNA) targeting the methionine biosynthesis cycle transcriptional regulator SahR. Sequence and expression analyses indicated that DseA (Desulfovibrio SAMelementA) is located upstream of a small hypothetical protein DVU1170 and that the two are co-transcribed. Multiple techniques were used to verify the riboswitch activity of DseA and its activity as a transcriptional terminator in response to SAM. While determining a potential role for DseA in the methionine biosynthesis pathway, a mRNA target encoding SahR was identified. Subsequent electrophoretic mobility shift assays confirmed the ability of DseA to bind thesahRtranscript and qRT-PCR analysis of a DseA deletion strain suggested a negative regulatory role. This study presents the first regulatory role for a newly discovered sRNA inDesulfovibrio. Additionally, this study suggests that DseA acts not only as a riboswitch, but also as atransregulatory molecule.IMPORTANCESulfate-reducing bacteria (SRB) are important contributors to global geochemical cycles while also causing major issues for the petroleum and oil industry due to biocorrosion and souring of oil wells. Despite their significance, gene regulatory networks and pathways remain poorly understood in SRB. Here, we report atransacting small noncoding RNA that plays a dual role as a SAM sensing riboswitch that controls the expression of a small hypothetical protein. Our findings provide important insights into the regulatory repertoire of sulfate-reducing bacteria.
CCmed: cross-condition mediation analysis for identifying robust trans-eQTLs and assessing their effects on human traits
Authors: Yang Fan , Gleason Kevin J. , Wang Jiebiao ,   The GTEx consortium, Duan Jubao , He Xin , Pierce Brandon L , Chen Lin S 
Published: October 2019

AbstractTrans-eQTLs collectively explain a substantial proportion of expression variation, yet are challenging to detect and replicate since their effects are individually weak. Many trans-effects are mediated by cis-gene expression and some of those effects are shared across tissue types/conditions. To detect robust cis-mediated trans-associations at the gene-level and for specific single nucleotide polymorphisms (SNPs), we proposed two Cross-Condition Mediation methods – CCmedgene and CCmedGWAS, respectively. We analyzed data from 13 brain tissue types from the Genotype-Tissue Expression (GTEx) project, and identified trios with cis-eQTLs of a cis-gene having associations with a trans-gene, many of which show evidence of replication in other datasets. By applying CCmedGWAS, we identified trans-genes associated with known schizophrenia susceptibility loci. We further conducted validation analyses assessing the schizophrenia-risk-associations of the identified trans-genes, by harnessing GWAS summary statistics from the Psychiatric Genomics Consortium and multitissue eQTL statistics from GTEx.