bluuebunny/crossref_metadata_2025_split huggingface dataset:
Left Occipital Craniotomy for Resection of Arteriovenous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F 
Published: January 2020

Abstract
Medial parieto-occipital arteriovenous malformations (AVMs) are fed by distal cortical posterior cerebral artery branches and are generally considered eloquent given the proximity to the calcarine fissure and paracentral lobule. This patient was a neurologically intact 12-yr-old girl with an incidentally discovered left occipital AVM. The patient underwent preoperative angiographic evaluation with embolization of a dominant posterior cerebral artery feeding vessel. The AVM was removed in the standard manner using circumdissection. Indocyanine green angiography was utilized to demonstrate disconnection of the AVM before sacrificing the draining veins. The AVM was removed entirely, as evidenced on postoperative angiography. The patient had a partial right hemianopsia after the operation but was otherwise neurologically intact. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Endoscopic Paramedian Sitting Craniotomy for Resection of a Dorsal Midbrain Cavernous Malformation: 2-Dimensional Operative Video
Authors: Choudhri Omar A , Glauser Gregory , Abdullah Kalil G , Lee John Y K 
Published: January 2020

Abstract
This case video demonstrates the surgical technique for resection of a cavernous malformation in the right dorsal midbrain. This video was deemed exempt by the University of Pennsylvania Institutional Review Board (IRB), as it is considered a case report, which does not require IRB approval or patient consent. The patient was a 57-yr-old male with cerebral cavernous malformation syndrome with multiple intracranial cavernomas. He was noticed to have progressively slowed speech with worsening confusion and drowsiness. On exam, the patient exhibited worsening in swallowing and upward gaze paresis, secondary to Parinaud phenomena. The patient was treated with microsurgical resection, utilizing stereotactic navigation and intraoperative neurophysiologic monitoring. Intraoperative view provided in the video was captured using a Karl Storz Endoscope (Karl Storz SE & Co KG, Tuttlingen, Germany). Postoperatively, the patient had worsening double vision, which improved on follow-up, in addition to improvement in sensorium and swallowing.
LEVELS OF EXPOSURE TO IONIZING RADIATION AMONG THE PERSONNEL ENGAGED IN CYCLOTRON OPERATION AND THE PERSONNEL ENGAGED IN THE PRODUCTION OF RADIOPHARMACEUTICALS, BASED ON RADIATION MONITORING SYSTEM
Authors: Biegała Michał , Jakubowska Teresa 
Published: January 2020

Abstract
This paper aims to determine the levels of exposure to neutron and photon radiation among the personnel engaged in cyclotron operation and the personnel engaged in the production of radiopharmaceuticals, with the use of the environmental radiation monitoring system (RMS) installed in the positron emission tomography laboratory. The annual exposures of employees operating the cyclotron measured with the use of the RMS system are: 1.39 ± 0.16 mSv in case of photon radiation and 2.61 ± 0.14 mSv in case of neutron radiation. In the case of employees in the radiopharmaceuticals’ production zone, the annual exposures measured by means of the RMS system are 0.15 ± 0.03 mSv in case of photon radiation and 0.11 ± 0.01 mSv in case of neutron radiation. The exposure levels among the personnel engaged in cyclotron operation and the personnel engaged in the production of radiopharmaceuticals are below the permissible radiation dose limits.
The language network reemerges during recovery from severe traumatic brain injury
Authors: Coffey Brian J. , Threlkeld Zachary D. , Bodien Yelena G. , Edlow Brian L. 
Published: January 2020

AbstractRegaining the ability to express and understand language is a key milestone for patients recovering from severe traumatic brain injury (TBI). However, the neurobiological correlates of language recovery after TBI have not been identified. We explored whether recovery of language in patients with acute severe TBI is associated with functional MRI (fMRI) changes within and outside the canonical language network (i.e. bilateral superior temporal gyri [STG] and inferior frontal gyri [IFG]). We consecutively enrolled 16 adult patients with acute severe TBI and performed fMRI assessment using a spoken language stimulus in the intensive care unit. Eight patients, all of whom recovered language function, returned for follow-up fMRI at median [interquartile range] 220.5 [189-473.5] days post-injury. Sixteen age- and sex-matched healthy subjects also completed the fMRI paradigm. Language function was behaviorally assessed immediately before fMRI using the Coma Recovery Scale-Revised and components of the Confusion Assessment Protocol. At follow-up, patients also completed the California Verbal Learning Test-II. We compared acute and follow-up fMRI responses by calculating mean Z-scores of suprathreshold voxels in bilateral STG and IFG regions-of-interest (ROI). We also performed a whole-brain analysis. Significant longitudinal increases to language stimuli were found in the left STG but not the right STG, left IFG, or right IFG. Whole-brain analysis revealed longitudinal changes in the right supramarginal and middle temporal gyri, regions known to be involved in language processing. Both acute and follow-up fMRI responses in patients were indistinguishable from those of healthy subjects at a stringent statistical threshold of Z ≥ 3.1. At lower statistical thresholds (e.g. Z ≥ 2.1) patients assessed acutely demonstrated decreased fMRI responses in right STG and IFG compared to healthy subjects. Collectively, these results provide initial evidence that responses in bihemispheric language-processing regions of cerebral cortex reemerge with recovery of language function in patients with severe TBI.
Therapeutic use of blood products for the treatment of autoimmune hemolytic anemia: A network meta-analysis protocol
Authors: Deng Jiawen 
Published: January 2020

ABSTRACTAutoimmune hemolytic anemia is a rare blood disorder that can result in anemic hypoxia. Currently, red blood cell (RBC) transfusion is the only effective method of treating this condition. We propose a network meta-analysis that investigates whether the use of different types of blood products (e.g. suspended RBC, leukoreduced RBC, washed RBC, etc.) can decrease adverse events, increase the rate of remission and improve lab results, including hemoglobin, RBC, reticulocyte counts, hematocrit and total bilirubin.
Uses of pathogen detection data to estimate vaccine direct effects in case-control studies
Authors: Lewnard Joseph A. 
Published: January 2020

ABSTRACTThe diagnosis of infectious disease syndromes such as fever, diarrhea, and pneumonia is complicated by the potential for shedding or carriage of putatively etiologic pathogens among individuals experiencing symptoms due to other causes. Symptomatic individuals among whom a pathogen is detected, but whose symptoms are caused by other factors, may be misclassified by diagnostic criteria based on pathogen detection. Case-control studies are commonly undertaken to estimate vaccine effectiveness, and present an opportunity to compare pathogen detection among individuals with and without clinically-relevant symptoms. Considering this study context, we derive simple estimators for the direct effects of vaccination on various aspects of host susceptibility. These include protection against acquisition of the pathogen of interest, and protection against progression of this pathogen to disease following acquisition. We assess the impact of test sensitivity on these estimators, and extend our framework to identify a “vaccine probe” estimator for pathogen-specific etiologic fractions. We also derive biases affecting vaccine effectiveness estimates under the test-negative design, an alternative approach using similar data. Our results provide strategies for estimation of pathogen-specific vaccine effectiveness in the absence a diagnostic gold standard. These approaches can inform the design and analysis of studies addressing numerous pathogens and vaccines.
Effect of nitrogen on fungal growth efficiency
Authors: Di Lonardo D.P. , van der Wal A. , Harkes P. , de Boer W. 
Published: January 2020

AbstractThe contribution of fungi to carbon (C) and nitrogen (N) cycling is related to their growth efficiency (amount of biomass produced per unit of substrate utilized). The concentration and availability of N influences the activity and growth efficiency of saprotrophic fungi. When N is scarce in soils, fungi have to invest more energy to obtain soil N, which could result in lower growth efficiencies. Yet, the effect of N on growth efficiencies of individual species of fungi in soil has not been studied extensively. In this study we investigated the influence of different concentrations of mineral N on the growth efficiency of two common soil fungi, Trichoderma harzanium and Mucor hiemalis in a soil-like environment. We hypothesized that a higher N availability will coincide with higher biomass production and growth efficiency. To test this, we measured fungal biomass production as well as the respiration fluxes in sand microcosms amended with cellobiose and mineral N at different C:N ratios. We found that for both fungal species lower C:N ratios resulted in the highest biomass production as well as the highest growth efficiency. This may imply that when N is applied concurrently with a degradable C source, a higher amount of N will be temporarily immobilized into fungal biomass.
Neural oscillations track the maintenance and proceduralization of novel instructions
Authors: Formica Silvia , González-García Carlos , Senoussi Mehdi , Brass Marcel 
Published: January 2020

AbstractHumans are capable of flexibly converting symbolic instructions into novel behaviors. Previous evidence and theoretical models suggest that the implementation of a novel instruction requires the reformatting of its declarative content into an action-oriented code optimized for the execution of the instructed behavior. While neuroimaging research focused on identifying the brain areas involved in such a process, the temporal and electrophysiological mechanisms remain poorly understood. These mechanisms, however, can provide information about the specific cognitive processes that characterize the proceduralization of information. In the present study, we recorded EEG activity while we asked participants to either simply maintain declaratively the content of novel S-R mappings or to proactively prepare for their implementation. By means of time-frequency analyses, we isolated the oscillatory features specific to the proceduralization of instructions. Implementation of the instructed mappings elicited stronger theta activity over frontal electrodes and suppression in mu and beta activity over central electrodes. On the contrary, activity in the alpha band, which has been shown to track the attentional deployment to task-relevant items, showed no differences between tasks. Together, these results support the idea that proceduralization of information is characterized by specific component processes such as orchestrating complex task settings and configuring the motor system that are not observed when instructions are held in a declarative format.HighlightsFrontal theta power is increased during instructions implementationAttentional orienting in WM is analogous across maintenance and implementationInstructions implementation involves motor recruitment
Urban colonization is driven by a mixture of evolutionarily conserved and labile traits
Authors: Duchene David A. , Pardo-Diaz Carolina , Iglesias-Carrasco Maider 
Published: January 2020

AbstractUrbanization is a fast and dramatic transformation of habitat that generally forces native fauna into novel ecological challenges. The biological prerequisites necessary to establish in urban areas have been widely studied, but the macroevolutionary characteristics of traits that allow urban colonization remain poorly understood. Urban colonization might be facilitated by traits that are evolutionarily conserved and which lead to a diversity of closely related species. Alternatively, urban colonization might be associated with labile traits that frequently arise and are lost. In a large data set from passerine birds, we find that urban colonization has a signal of highly labile traits, despite many traits associated with colonization being highly conserved. Urban colonization is associated with traits that allow faster speciation than non-urban-colonizing counterparts, and more frequently transition to non-urban trait states than in the opposite direction. Overall, the traits that facilitate urban colonization are a mix of highly conserved and labile traits and appear to provide an evolutionarily successful strategy.
Underground deserts below fertility islands? – Woody species desiccate lower soil layers in sandy drylands
Authors: Tolgyesi Csaba , Torok Peter , Habenczyus Alida Anna , Batory Zoltan , Orsolya Valko , Deak Balazs , Tothmeresz Bela , Erdos Laszlo , Kelemen Andras 
Published: January 2020

AbstractWoody plants in water-limited ecosystems affect their environment on multiple scales: locally, natural stands can create islands of fertility for herb layer communities compared to open habitats, but afforestation has been shown to negatively affect regional water balance and productivity. Despite these contrasting observations, no coherent multiscale framework has been developed for the environmental effects of woody plants in water-limited ecosystems. To link local and regional effects of woody species in a spatially explicit model, we simultaneously measured site conditions (microclimate, nutrient availability and topsoil moisture) and conditions of regional relevance (deeper soil moisture), in forests with different canopy types (long, intermediate and short annual lifetime) and adjacent grasslands in sandy drylands. All types of forests ameliorated site conditions compared to adjacent grasslands, although natural stands did so more effectively than managed ones. At the same time, all forests desiccated deeper soil layers during the vegetation period, and the longer the canopy lifetime, the more severe the desiccation in summer and more delayed the recharge after the active period of the canopy. We conclude that the site-scale environmental amelioration brought about by woody species is bound to co-occur with the desiccation of deeper soil layers, leading to deficient ground water recharge. This means that the cost of creating islands of fertility for sensitive herb layer organisms is an inevitable negative impact on regional water balance. The canopy type or management intensity of the forests affects the magnitude but not the direction of these effects. The outlined framework of the effects of woody species should be considered for the conservation, restoration, or profit-oriented use of forests as well as in forest-based carbon sequestration and soil erosion control projects in water-limited ecosystems.
Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra
Authors: Hartoyo Agus , Cadusch Peter J. , Liley David T. J. , Hicks Damien G. 
Published: January 2020

AbstractAlpha blocking, a phenomenon where the alpha rhythm is reduced by attention to a visual, auditory, tactile or cognitive stimulus, is one of the most prominent features of human electroencephalography (EEG) signals. Here we identify a simple physiological mechanism by which opening of the eyes causes attenuation of the alpha rhythm. We fit a neural population model to EEG spectra from 82 subjects, each showing different degrees of alpha blocking upon opening of their eyes. Although it is notoriously difficult to estimate parameters from fitting such models, we show that, by regularizing the differences in parameter estimates between eyes-closed and eyes-open states, we can reduce the uncertainties in these differences without significantly compromising fit quality. From this emerges a parsimonious explanation for the spectral changes between states: Just a single parameter,pei, corresponding to the strength of a tonic, excitatory input to the inhibitory population, is sufficient to explain the reduction in alpha rhythm upon opening of the eyes. When comparing parameter estimates across different subjects we find that the inferred differential change inpeifor each subject increases monotonically with the degree of alpha blocking observed. In contrast, other parameters show weak or negligible differential changes that do not scale with the degree of alpha attenuation in each subject. Thus most of the variation in alpha blocking across subjects can be attributed to the strength of a tonic afferent signal to the inhibitory cortical population.Author summaryOne of the most striking features of the human electroencephalogram (EEG) is the presence of neural oscillations in the range of 8-13 Hz. It is well known that attenuation of these alpha oscillations, a process known as alpha blocking, arises from opening of the eyes, though the cause has remained obscure. In this study we infer the mechanism underlying alpha blocking by fitting a neural population model to EEG spectra from 82 different individuals. Although such models have long held the promise of being able to relate macroscopic recordings of brain activity to microscopic neural parameters, their utility has been limited by the difficulty of inferring these parameters from fits to data. Our approach is to fit both eyes-open and eyes-closed EEG spectra together, minimizing the number of parameter changes required to transition from one spectrum to the other. Surprisingly, we find that there is just one parameter, the external input to the inhibitory neurons in cortex, that is responsible for attenuating the alpha oscillations. We demonstrate how the strength of this inhibitory input scales monotonically with the degree of alpha blocking observed over all 82 subjects.
EnhancerP-2L: A Gene regulatory site identification tool for DNA enhancer region using CREs motifs
Authors: Butt Ahmad Hassan , Alkhalaf Salem , Iqbal Shaukat , Khan Yaser Daanial 
Published: January 2020

AbstractEnhancers are DNA fragments that do not encode RNA molecules and proteins, but they act critically in the production of RNAs and proteins by controlling gene expression. Prediction of enhancers and their strength plays significant role in regulating gene expression. Prediction of enhancer regions, in sequences of DNA, is considered a difficult task due to the fact that they are not close to the target gene, have less common motifs and are mostly tissue/cell specific. In recent past, several bioinformatics tools were developed to discriminate enhancers from other regulatory elements and to identify their strengths as well. However the need for improvement in the quality of its prediction method requires enhancements in its application value practically. In this study, we proposed a new method that builds on nucleotide composition and statistical moment based features to distinguish between enhancers and non-enhancers and additionally determine their strength. Our proposed method achieved accuracy better than current state-of-the-art methods using 5-fold and 10-fold cross-validation. The outcomes from our proposed method suggest that the use of statistical moments based features could bear more efficient and effective results. For the accessibility of the scientific community, we have developed a user-friendly web server for EnhancerP-2L which will increase the impact of bioinformatics on medicinal chemistry and drive medical science into an unprecedented resolution. Web server is freely accessible athttp://www.biopred.org/enpred.
An Innovative Setup for High-Throughput Respirometry of Small Aquatic Animals
Authors: Drown M.K. , DeLiberto A.N. , Crawford D.L. , Oleksiak M.F. 
Published: January 2020

AbstractMetabolic rate is often measured as a phenotype in evolutionary genetics studies because it impacts organismal fitness, is repeatable and heritable, and is responsive to numerous environmental variables. Despite a wide body of literature about metabolic rates, key questions remain unanswered: 1) why do individuals from the same population exhibit up to three fold differences in metabolic rate, 2) how does metabolic rate change during an individual’s lifetime, and 3) what metabolic rate is advantageous in a specific environment? Current low throughput approaches to measure metabolic rate make it difficult to answer these and other relevant ecological and evolutionary questions that require a much larger sample size. Here we describe a scalable high-throughput intermittent flow respirometer (HIFR) design and use it to measure the metabolic rates of 20 aquatic animals simultaneously while reducing equipment costs and time by more than 50%.
Production location of the gelling agent Phytagel has a significant impact onArabidopsis thalianaseedling phenotypic analysis
Authors: Jacques Caitlin N. , Hulbert Anna K. , Westenskow Shelby , Neff Michael M. 
Published: January 2020

AbstractBackgroundRecently, it was found that 1% Phytagel plates used to conductArabidopsis thalianaseedling phenotypic analysis no longer reproduced previously published results. This Phytagel, which is produced in China (Phytagel C), has replace American-made Phytagel (Phytagel), which is no longer commercially available. In this study, we present the impact of Phytagel produced in the United States vs. China on seedling phenotypic analysis. As a part of this study, an alternative gelling agent has been identified that is capable of reproducing previously published seedling morphometrics.ResultsPhytagel and Phytagel C were investigated based on their ability to reproduce the subtle phenotype of thesob3-4 esc-8double mutant. Fluence-rate-response analysis of seedlings grown on 1% Phytagel C plates failed to replicate thesob3-4 esc-8subtle phenotype seen on 1% Phytagel. Furthermore, root penetrance analysis showed a significant difference betweensob3-4 esc-8seedlings grown on 1% Phytagel and 1% Phytagel C. It was also found that 1% Phytagel C was significantly harder than 1% Phytagel. As a replacement for Phytagel C, Gellan was tested. 1% Gellan was able to reproduce the subtle phenotype ofsob3-4 esc-8. Furthermore, there was no significant difference in root penetration of the wild type orsob3-4 esc-8seedlings between 1% Phytagel and 1% Gellan. This may be due to the significant reduction in hardness in 1% Gellan plates compared to 1% Phytagel plates. Finally, we tested additional concentrations of Gellan and found that seedlings on 0.6% Gellan looked more uniform while also being able to reproduce previously published results.ConclusionsPhytagel has been the standard gelling agent for several studies involving the characterization of subtle seedling phenotypes. After production was moved to China, Phytagel C was no longer capable of reproducing these previously published results. An alternative gelling agent, Gellan, was able to reproduce previously published seedling phenotypes at both 1% and 0.6% concentrations. The information provided in this manuscript is beneficial to the scientific community as whole, specifically phenomics labs, as it details key problematic differences between gelling agents that should be performing identically (Phytagel and Phytagel C).