bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vascular Anomalies of Posterior Fossa and Their Implications
Authors: Singh Rajani , Kumar Raj , Kumar Arushi 
Published: September 2017

Abstract
Posterior fossa houses very vital and sensitive structures namely midbrain, pons, medulla, and cerebellum. These structures are irrigated by vertebral, posterior inferior cerebellar, anterior inferior cerebellar, and superior cerebellar arteries. Parts of brain located in posterior fossa control important parts of body so any variation pertaining to stenosis, atresia, hypoplasia, fenestration, agenesis, and duplication in the arteries supplying these parts alter the irrigation pattern culminating into various morbid and mortal neurologic disorders. Therefore, a sound understanding and thorough knowledge of posterior circulation vascular variant anatomy builds the foundation for the accurate diagnosis and appropriate management of neurovascular ischemic and hemorrhagic diseases of posterior fossa. To aid in addressing these complex neurologic disorders and neurosurgical treatment to be carried out successfully, updating and consolidating the knowledge of all the variations/insults of these arteries becomes essential. Therefore, review study has been carried out.
Literature search was carried out using databases, including Scielo, Scopmed, Medline, PubMed, and Wiley online library. Papers containing original data were selected and secondary references retrieved from bibliographies. Search terms used were posterior fossa, anomalies of vertebral, posterior inferior cerebellar, anterior inferior cerebellar, and superior cerebellar arteries.
The study will be of paramount importance to angiographers in interpreting angiographs, neurologists in diagnosis and treatment of neurologic disorders, and neurosurgeons in performing surgery in posterior fossa and craniovertebral region particularly dealing with tumors and vascular malformations.
Maxillary Hypoplasia: Differential Diagnosis of Nasal Obstruction in Infants
Authors: da Costa Amanda Lucas , Manica Denise , Manzini Michelle , Bernardi Andressa , Pérez Juliano Adams , Sekine Leo , Collares Marcus Vinicius Martins , Kuhl Gabriel , Schweiger Claudia 
Published: September 2017

Abstract
Maxillary hypoplasia (MH) is a rare cause of respiratory dysfunction in infants and may occur in association with genetic abnormalities or as an isolated condition. It is included in the differential diagnosis of congenital nasal obstruction. This paper seeks to report a case series of infants with MH, discuss methods for its diagnosis, and compare computed tomography (CT) measurements of nasal cavities of infants with MH and without craniomaxillofacial abnormalities. The therapeutic approach in each patient is also described. All infants with MH admitted to a tertiary hospital between 2012 and 2015 were included. Baseline nasal endoscopy was performed at bedside. The width of the infants’ nasal cavities was measured by a radiologist with experience in CT scanning of facial bones. Control patients were infants of matched sex and similar age who underwent head CT scanning for various reasons. Overall, 8 infants with MH and 8 controls were assessed. All nasal cavity dimensions of infants with MH were significantly smaller than those of control subjects. The authors conclude that the diagnosis of MH should be considered in infants with nasal obstruction and nasal cavity narrowing at nasal endoscopy.
Alpha oscillations control cortical gain by modulating excitatory-inhibitory background activity
Authors: Peterson Erik J. , Voytek Bradley 
Published: September 2017

SUMMARYThe first recordings of human brain activity in 1929 revealed a striking 8-12 Hz oscillation in the visual cortex. During the intervening 90 years, these alpha oscillations have been linked to numerous physiological and cognitive processes. However, because of the vast and seemingly contradictory cognitive and physiological processes to which it has been related, the physiological function of alpha remains unclear. We identify a novel neural circuit mechanism—the modulation of both excitatory and inhibitory neurons in abalancedconfiguration—by which alpha can modulate gain. We find that this model naturally unifies the prior, highly diverse reports on alpha dynamics, while making the novel prediction that alpha rhythms have two functional roles: a sustained high-power mode that suppresses scortical gain and a weak, bursting mode that enhances gain.
Cueing memory during sleep is optimal during slow-oscillatory up-states
Authors: Göldi Maurice , van Poppel Eva , Rasch Björn , Schreiner Thomas 
Published: September 2017

AbstractSlow oscillations play a major role in neural plasticity. It is assumed that slow oscillatory up-states represent crucial time windows for memory reactivation and consolidation during sleep. Here we experimentally tested this assumption by utilizing closed-loop targeted memory reactivation (closed-loop TMR): Healthy participants were re-exposed to prior learned foreign vocabulary during up- and down-states of slow oscillations, respectively, in a within-subject design. We show that presenting memory cues during slow oscillatory up-states robustly improves recall performance, whereas memory cueing during down-states did not result in a clear behavioral benefit. On a neural basis successful memory reactivation during up-states was associated with a characteristic power increase in the theta and sleep spindle band. Such increases were completely absent for down-state memory cues. Our findings provide experimental support for the assumption that slow oscillatory up-states represent privileged time windows for memory reactivation, while the interplay of slow oscillations, theta and sleep spindle activity promote successful memory consolidation during sleep.
Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments
Authors: Bacher Rhonda , Leng Ning , Chu Li-Fang , Thomson James , Kendziorski Christina , Stewart Ron 
Published: September 2017

AbstractHigh throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for profiling detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide important insights about genes, pathways, and critical time-points. We present an R package,Trendy, which utilizes segmented regression models to simultaneously characterize each gene’s expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. We demonstrate the utility of Trendy to provide biologically relevant results on both microarray and RNA-seq datasets. Trendy is a flexible R package which characterizes gene-specific expression patterns and summarizes changes of global dynamics over ordered conditions. Trendy is freely available as an R package with a full vignette athttps://github.com/rhondabacher/Trendy.
Paratope Prediction using Convolutional and Recurrent Neural Networks
Authors: Liberis Edgar , Veličković Petar , Sormanni Pietro , Vendruscolo Michele , Liò Pietro 
Published: September 2017

AbstractAntibodies play an essential role in the immune system of vertebrates and are vital tools in research and diagnostics. While hypervariable regions of antibodies, which are responsible for binding, can be readily identified from their amino acid sequence, it remains challenging to accurately pinpoint which amino acids will be in contact with the antigen (the paratope). In this work, we present a sequence-based probabilistic machine learning algorithm for paratope prediction, named Parapred. Parapred uses a deep-learning architecture to leverage features from both local residue neighbourhoods and across the entire sequence. The method outperforms the current state-of-the-art methodology, and only requires a stretch of amino acid sequence corresponding to a hypervariable region as an input, without any information about the antigen. We further show that our predictions can be used to improve both speed and accuracy of a rigid docking algorithm. The Parapred method is freely available athttps://github.com/eliberis/parapredfor download.
Impeding transcription of expanded microsatellite repeats by deactivated Cas9
Authors: Pinto Belinda S. , Saxena Tanvi , Oliveira Ruan , Méndez-Gómez Héctor R. , Cleary John D. , Denes Lance T. , McConnell Ona , Arboleda Juan , Xia Guangbin , Swanson Maurice S. , Wang Eric T. 
Published: September 2017

SummaryTranscription of expanded microsatellite repeats is associated with multiple human diseases, including myotonic dystrophy, Fuchs’ endothelial corneal dystrophy, andC9orf72-ALS/FTD. Eliminating or reducing production of RNA and proteins arising from these expanded loci holds therapeutic benefit. Here, we tested the hypothesis that a deactivated form of the Cas9 enzyme impedes transcription across expanded microsatellites. We observed a repeat length-, PAM-, and strand-dependent reduction in the abundance of repeat-containing RNAs upon targeting dCas9 directly to repeat sequences. Aberrant splicing patterns were rescued in DM1 cells, and production of RAN peptides characteristic of DM1, DM2, andC9orf72-ALS/FTD cells was drastically decreased. Systemic delivery of dCas9/gRNA by adeno-associated virus led to reductions in pathological RNA foci, rescue of chloride channel 1 protein expression, and decreased myotonia. These observations suggest that transcription of microsatellite repeat-containing RNAs is more sensitive to perturbation than transcription of other RNAs, indicating potentially viable strategies for therapeutic intervention.
Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with signatures from post mortem adult brains
Authors: Hoffman Gabriel E. , Hartley Brigham J. , Flaherty Erin , Ladran Ian , Gochman Peter , Ruderfer Doug , Stahl Eli A. , Rapoport Judith , Sklar Pamela , Brennand Kristen J. 
Published: September 2017

ABSTRACTWhereas highly penetrant variants have proven well-suited to human induced pluripotent stem cell (hiPSC)-based models, the power of hiPSC-based studies to resolve the much smaller effects of common variants within the size of cohorts that can be realistically assembled remains uncertain. In developing a large case/control schizophrenia (SZ) hiPSC-derived cohort of neural progenitor cells and neurons, we identified and accounted for a variety of technical and biological sources of variation. Reducing the stochastic effects of the differentiation process by correcting for cell type composition boosted the SZ signal in hiPSC-based models and increased the concordance with post mortem datasets. Because this concordance was strongest in hiPSC-neurons, it suggests that this cell type may better model genetic risk for SZ. We predict a growing convergence between hiPSC and post mortem studies as both approaches expand to larger cohort sizes. For studies of complex genetic disorders, to maximize the power of hiPSC cohorts currently feasible, in most cases and whenever possible, we recommend expanding the number of individuals even at the expense of the number of replicate hiPSC clones.
Cued reactivation during slow-wave sleep induces connectivity changes related to memory stabilization
Authors: Berkers Ruud M.W.J. , Ekman Matthias , van Dongen Eelco V. , Takashima Atsuko , Barth Marcus , Paller Ken A. , Fernandez Guillen 
Published: September 2017

AbstractMemory reprocessing following acquisition enhances memory consolidation. Specifically, neural activity during encoding is thought to be ‘replayed’ during subsequent slow-wave sleep (SWS). This natural tendency of memory replay can be induced by external cueing, known as “targeted memory reactivation”. Here, we analyzed data from a published study (van Dongen, Takashima, et al. 2012), where auditory cues reactivated learned visual object-location memories during SWS. Memory replay during sleep presumably involves a shift in connectivity across the brain. Therefore, we characterized the effects of memory reactivation on brain network connectivity using graph-theory. We found that cue presentation during SWS introduced increased network integration of the occipital cortex, a visual region that was also active during the object retrieval task. Importantly, enhanced network integration of the occipital cortex showed a behavioural benefit and predicted overnight memory stabilization. Furthermore, occipital cortex displayed enhanced connectivity with mnemonic regions, namely the hippocampus, parahippocampal gyrus, thalamus and medial prefrontal cortex during cue versus control sound presentation. Finally, network integration of early occipital cortex during cueing in SWS was related to increased activation of the bilateral parahippocampal gyrus, a region involved in coding for spatial associative information, at the post-sleep test. Together, these results support a neural mechanism where cue-induced replay during sleep promotes memory consolidation by increased integration of task-relevant perceptual regions with mnemonic regions.
An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
Authors: Zenil Hector , Kiani Narsis A. , Marabita Francesco , Deng Yue , Elias Szabolcs , Schmidt Angelika , Ball Gordon , Tegnér Jesper 
Published: September 2017

AbstractWe introduce a new conceptual framework and a model-based interventional calculus to steer, manipulate, and reconstruct the dynamics and generating mechanisms of non-linear dynamical systems from partial and disordered observations based on the contributions of each of the systems, by exploiting first principles from the theory of computability and algorithmic information. This calculus entails finding and applying controlled interventions to an evolving object to estimate how its algorithmic information content is affected in terms ofpositiveornegativeshifts towards and away from randomness in connection to causation. The approach is an alternative to statistical approaches for inferring causal relationships and formulating theoretical expectations from perturbation analysis. We find that the algorithmic information landscape of a system runs parallel to its dynamic attractor landscape, affording an avenue for moving systems on one plane so they can be controlled on the other plane. Based on these methods, we advance tools for reprogramming a system that do not require full knowledge or access to the system’s actual kinetic equations or to probability distributions. This new approach yields a suite of universal parameter-free algorithms of wide applicability, ranging from the discovery of causality, dimension reduction, feature selection, model generation, a maximal algorithmic-randomness principle and a system’s (re)programmability index. We apply these methods to static (e.coli Transcription Factor network) and to evolving genetic regulatory networks (differentiating naïve from Th17 cells, and the CellNet database). We highlight their ability to pinpoint key elements (genes) related to cell function and cell development, conforming to biological knowledge from experimentally validated data and the literature, and demonstrate how the method can reshape a system’s dynamics in a controlled manner through algorithmic causal mechanisms.
Estimating the Mutational Fitness Effects Distribution during early HIV infection
Authors: Bons Eva , Bertels Frederic , Regoes Roland R 
Published: September 2017

AbstractThe evolution of HIV during acute infection is often considered a neutral process. Recent analysis of sequencing data from this stage of infection, however, showed high levels of shared mutations between independent viral populations. This suggests that selection might play a role in the early stages of HIV infection. We adapted an existing model for random evolution during acute HIV-infection to include selection. Simulations of this model were used to fit a global mutational fitness effects distribution (MFED) to sequencing data of theenvgene of individuals with acute HIV infection. Measures of sharing between viral populations were used as summary statistics to compare the data to the simulations. We confirm that evolution during acute infection is significantly different from neutral. The distribution of mutational fitness effects is best fit by distribution with a low, but significant fraction of beneficial mutations and a high fraction of deleterious mutations. While most mutations are neutral or deleterious in this model, about 5% of mutations is beneficial. These beneficial mutations will, on average, result in a small but significant increase in fitness. When assuming no epistasis, this indicates that at the moment of transmission HIV is near, but not on the fitness peak for early infection.
Genetic Analysis of Lodging in Diverse Maize Hybrids
Authors: Larsson Sara J. , Peiffer Jason A. , Edwards Jode W. , Ersoz Elhan S. , Flint-Garcia Sherry , Holland James B. , McMullen Michael D. , Tuinstra Mitchell R. , Romay M. Cinta , Buckler Edward S. 
Published: September 2017

ABSTRACTDamage caused by lodging is a significant problem in corn production that results in estimated annual yield losses of 5-20%. Over the past 100 years, substantial maize breeding efforts have increased lodging resistance by artificial selection. However, less research has focused on understanding the genetic architecture underlying lodging. Lodging is a problematic trait to evaluate since it is greatly influenced by environmental factors such as wind, rain, and insect infestation, which make replication difficult. In this study over 1,723 diverse inbred maize genotypes were crossed to a common tester and evaluated in five environments over multiple years. Natural lodging due to severe weather conditions occurred in all five environments. By testing a large population of genetically diverse maize lines in multiple field environments, we detected significant correlations for this highly environmentally influenced trait across environments and with important agronomic traits such as yield and plant height. This study also permitted the mapping of quantitative trait loci (QTL) for lodging. Several QTL identified in this study overlapped with loci previously mapped for stalk strength in related maize inbred lines. QTL intervals mapped in this study also overlapped candidate genes implicated in the regulation of lignin and cellulose synthesis.
Drosophila beta-Tubulin 97EF is upregulated at low temperature and stabilizes microtubules
Authors: Myachina Faina , Bosshardt Fritz , Bischof Johannes , Kirschmann Moritz , Lehner Christian F. 
Published: September 2017

Summary statementEctotherms thrive within an often remarkable temperature range. At low temperature,betaTub97EF, a beta-tubulin paralog stabilizing microtubules, is upregulated in a tissue-specific manner in the flyDrosophila melanogaster.AbstractCells in ectotherms function normally within an often wide temperature range. As temperature dependence is not uniform across all the distinct biological processes, acclimation presumably requires complex regulation. The molecular mechanisms coping with the disruptive effects of temperature variation are still poorly understood. Interestingly, one of five different beta-tubulin paralogs,betaTub97EF, was among the genes up-regulated at low temperature in culturedDrosophilacells. As microtubules are known to be cold-sensitive, we analyzed whetherbetaTub97EFprotects microtubules at low temperatures. During development at the optimal temperature (25°C),betaTub97EFwas expressed in a tissue-specific pattern primarily in the gut. There, as well as in hemocytes, expression was increased at low temperature (14°C). WhilebetaTub97EFmutants were viable and fertile at 25°C, their sensitivity within the well-tolerated range was slightly enhanced during embryogenesis specifically at low temperatures. Changing beta-tubulin isoform ratios in hemocytes demonstrated that beta-Tubulin 97EF has a pronounced microtubule stabilizing effect. Moreover,betaTub97EFis required for normal microtubule stability in the gut. These results suggest thatbetaTub97EFup-regulation at low temperature contributes to acclimation by stabilizing microtubules.
Highly expressed genes evolve under strong epistasis from a proteome-wide scan inE. coli
Authors: Girard Eric , Dasmeh Pouria , Serohijos Adrian W.R. 
Published: September 2017

ABSTRACTEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes inE. coliusing several hundreds of orthologs for each gene within the classGammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.
Functional characterization of theABFgene family in upland cotton (Gossypium hirsutumL.)
Authors: Kerr Tyson C. C. , Abdel-Mageed Haggag , Kang MiYoung , Cryer Dakota , Allen Randy D. 
Published: September 2017

AbstractThe AREB/ABF bZIP transcription factors play a pivotal role in abscisic acid-dependent abiotic stress-responsive gene expression. Despite the perennial damage and reduced productivity that result from water-deficit and unpredictable early season temperature fluctuations, these critical genes have not been previously examined in upland cotton (Gossypium hirsutum). Here, we report the isolation of theG. hirsutum ABFhomologs, characterization of their expression patterns in response to abiotic stress treatments, and examination of their functions through heterologous ectopic expression inArabidopsis. As expected for an allotetraploid,G. hirsutum ABFhomologs are present in the genome as homeologous pairs. These genes are differentially expressed, both among the homologs and within the homeologous pairs, in response to exogenous abscisic acid (ABA) application, dehydration, and chilling temperatures. Furthermore, heterologous ectopic expression of many of theG. hirsutum ABFgenes inArabidopsisconferred increased tolerance to water deficit and osmotic stress, as well as cold tolerance, in a gene specific manner. These results indicate theG. hirsutum ABFhomologs are functional inArabidopsisand, as in other species, are likely to play an essential role in the abiotic stress response.HighlightTheGossypium hirsutum ABFhomeologs are differentially expressed in response to abiotic stress, and their ectopic expression inArabidopsiscan confer increased water deficit tolerance.