bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pneumocystis PCR: It Is Time to Make PCR the Test of Choice
Authors: Doyle Laura , Vogel Sherilynn , Procop Gary W 
Published: September 2017

Abstract

Background
The testing strategy for Pneumocystis at the Cleveland Clinic changed from toluidine blue staining to polymerase chain reaction (PCR). We studied the differences in positivity rates for these assays and compared each with the detection of Pneumocystis in companion specimens by cytology and surgical pathology.

Methods
We reviewed the results of all Pneumocystis test orders 1 year before and 1 year after the implementation of a Pneumocystis-specific PCR. We also reviewed the corresponding cytology and surgical pathology results, if performed. Finally, we reviewed the medical records of patients with rare Pneumocystis detected by PCR in an effort to differentiate colonization vs true disease.

Results
Toluidine blue staining and surgical pathology had similar sensitivities and negative predictive values, both of which were superior to cytology. There was a &gt;4-fold increase in the annual detection of Pneumocystis by PCR compared with toluidine blue staining (toluidine blue staining: 11/1583 [0.69%] vs PCR: 44/1457 [3.0%]; chi-square P &lt; .001). PCR detected 1 more case than surgical pathology and was far more sensitive than cytology. Chart review demonstrated that the vast majority of patients with rare Pneumocystis detected were immunosuppressed, had radiologic findings supportive of this infection, had no other pathogens detected, and were treated for pneumocystosis by the clinical team.

Conclusion
PCR was the most sensitive method for the detection of Pneumocystis and should be considered the diagnostic test of choice. Correlation with clinical and radiologic findings affords discrimination of early true disease from the far rarer instances of colonization.
Effect of Xenon Anesthesia Compared to Sevoflurane and Total Intravenous Anesthesia for Coronary Artery Bypass Graft Surgery on Postoperative Cardiac Troponin Release
Authors: Hofland Jan , Ouattara Alexandre , Fellahi Jean-Luc , Gruenewald Matthias , Hazebroucq Jean , Ecoffey Claude , Joseph Pierre , Heringlake Matthias , Steib Annick , Coburn Mark , Amour Julien , Rozec Bertrand , Liefde Inge de , Meybohm Patrick , Preckel Benedikt , Hanouz Jean-Luc , Tritapepe Luigi , Tonner Peter , Benhaoua Hamina , Roesner Jan Patrick , Bein Berthold ,   for the Xenon-CABG Study Group
Published: September 2017

Abstract

Background
Ischemic myocardial damage accompanying coronary artery bypass graft surgery remains a clinical challenge. We investigated whether xenon anesthesia could limit myocardial damage in coronary artery bypass graft surgery patients, as has been reported for animal ischemia models.

Methods
In 17 university hospitals in France, Germany, Italy, and The Netherlands, low-risk elective, on-pump coronary artery bypass graft surgery patients were randomized to receive xenon, sevoflurane, or propofol-based total intravenous anesthesia for anesthesia maintenance. The primary outcome was the cardiac troponin I concentration in the blood 24 h postsurgery. The noninferiority margin for the mean difference in cardiac troponin I release between the xenon and sevoflurane groups was less than 0.15 ng/ml. Secondary outcomes were the safety and feasibility of xenon anesthesia.

Results
The first patient included at each center received xenon anesthesia for practical reasons. For all other patients, anesthesia maintenance was randomized (intention-to-treat: n = 492; per-protocol/without major protocol deviation: n = 446). Median 24-h postoperative cardiac troponin I concentrations (ng/ml [interquartile range]) were 1.14 [0.76 to 2.10] with xenon, 1.30 [0.78 to 2.67] with sevoflurane, and 1.48 [0.94 to 2.78] with total intravenous anesthesia [per-protocol]). The mean difference in cardiac troponin I release between xenon and sevoflurane was −0.09 ng/ml (95% CI, −0.30 to 0.11; per-protocol: P = 0.02). Postoperative cardiac troponin I release was significantly less with xenon than with total intravenous anesthesia (intention-to-treat: P = 0.05; per-protocol: P = 0.02). Perioperative variables and postoperative outcomes were comparable across all groups, with no safety concerns.

Conclusions
In postoperative cardiac troponin I release, xenon was noninferior to sevoflurane in low-risk, on-pump coronary artery bypass graft surgery patients. Only with xenon was cardiac troponin I release less than with total intravenous anesthesia. Xenon anesthesia appeared safe and feasible.
A Random-allocation Graded Dose–Response Study of Norepinephrine and Phenylephrine for Treating Hypotension during Spinal Anesthesia for Cesarean Delivery
Authors: Ngan Kee Warwick D. 
Published: September 2017

Abstract

Background
Norepinephrine has been investigated as a potential alterative to phenylephrine for maintaining blood pressure during spinal anesthesia for cesarean delivery with the advantage of less depression of maternal heart rate and cardiac output. However, the relative potencies of these two vasopressors have not been fully determined in this context.

Methods
In a random-allocation, graded dose–response study, 180 healthy patients undergoing spinal anesthesia for elective cesarean delivery received a single bolus of norepinephrine in one of six different doses ranging from 4 to 12 µg or phenylephrine in one of six different doses ranging from 60 to 200 µg to treat the first episode of hypotension. The magnitude of response was measured as the percentage of full restoration of systolic blood pressure to the baseline value. Dose–response analysis was performed using nonlinear regression to derive four-parameter logistic dose–response curves, which were compared to determine relative potency.

Results
Data were analyzed for 180 patients. The estimated ED50 values (dose giving a 50% response) were norepinephrine 10 µg (95% CI, 6 to 17 µg) and phenylephrine 137 µg (95% CI, 79 to 236 µg). The estimated relative potency ratio for the two drugs was 13.1 µg (95% CI, 10.4 to 15.8 µg).

Conclusions
Comparative dose–response analysis was completed for norepinephrine and phenylephrine given as a bolus to treat the first episode of hypotension in patients undergoing spinal anesthesia for cesarean delivery. The estimated dose equivalent to phenylephrine 100 µg was norepinephrine 8 µg (95% CI, 6 to 10 µg). These results may be useful to inform the design of future comparative studies.
Neural source dynamics of brain responses to continuous stimuli: speech processing from acoustics to comprehension
Authors: Brodbeck Christian , Presacco Alessandro , Simon Jonathan Z. 
Published: September 2017

AbstractHuman experience often involves continuous sensory information that unfolds over time. This is true in particular for speech comprehension, where continuous acoustic signals are processed over seconds or even minutes. We show that brain responses to such continuous stimuli can be investigated in detail, for magnetoencephalography (MEG) data by combining linear kernel estimation with minimum norm source localization. Previous research has shown that the requirement to average data over many trials can be overcome by modeling the brain response as a linear convolution of the stimulus and a kernel, or response function, and estimating a kernel that predicts the response from the stimulus. However, such analysis has been typically restricted to sensor space. Here we demonstrate that this analysis can also be performed in neural source space. We first computed distributed minimum norm current source estimates for continuous MEG recordings, and then computed response functions for the current estimate at each source element, using the boosting algorithm with cross-validation. Permutation tests can then assess the significance of individual predictor variables as well as features of the corresponding spatio-temporal response functions. We demonstrate the viability of this technique by computing spatio-temporal response functions for speech stimuli, using predictor variables reflecting acoustic, lexical and semantic processing. Results indicate that processes related to comprehension of continuous speech can be differentiated anatomically as well as temporally: acoustic information engaged auditory cortex at short latencies, followed by responses over the central sulcus and inferior frontal gyrus, possibly related to somatosensory/motor cortex involvement in speech perception; lexical frequency was associated with a left-lateralized response in auditory cortex and subsequent bilateral frontal activity; and semantic composition was associated with bilateral temporal and frontal brain activity. We conclude that this technique can be used to study the neural processing of continuous stimuli in time and anatomical space with the millisecond temporal resolution of MEG. This suggests new avenues for analyzing neural processing of naturalistic stimuli, without the necessity of averaging over artificially short or truncated stimuli.
Structural covariance of brain region volumes is associated with both structural connectivity and transcriptomic similarity
Authors: Yee Yohan , Fernandes Darren J. , French Leon , Ellegood Jacob , Cahill Lindsay S. , Vousden Dulcie A. , Noakes Leigh Spencer , Scholz Jan , van Eede Matthijs C. , Nieman Brian J. , Sled John G. , Lerch Jason P. 
Published: September 2017

AbstractAn organizational pattern seen in the brain, termedstructural covariance, is the statistical association of pairs of brain regions in their anatomical properties. These associations, measured across a population as covariances or correlations usually in cortical thickness or volume, are thought to reflect genetic and environmental underpinnings.Here, we examine the biological basis of structural volume covariance in the mouse brain. We first examined large scale associations between brain region volumes using an atlas-based approach that parcellated the entire mouse brain into 318 regions over which correlations in volume were assessed, for volumes obtained from 153 mouse brain images via high-resolution MRI. We then used a seed-based approach and determined, for 108 different seed regions across the brain and using mouse gene expression and connectivity data from the Allen Institute for Brain Science, the variation in structural covariance data that could be explained by distance to seed, transcriptomic similarity to seed, and connectivity to seed.We found that overall, correlations in structure volumes hierarchically clustered into distinct anatomical systems, similar to findings from other studies and similar to other types of networks in the brain, including structural connectivity and transcriptomic similarity networks. Across seeds, this structural covariance was significantly explained by distance (17% of the variation, up to a maximum of 49% for structural covariance to the visceral area of the cortex), transcriptomic similarity (13% of the variation, up to maximum of 28% for structural covariance to the primary visual area) and connectivity (15% of the variation, up to a maximum of 36% for structural covariance to the intermediate reticular nucleus in the medulla) of covarying structures. Together, distance, connectivity, and transcriptomic similarity explained 37% of structural covariance, up to a maximum of 63% for structural covariance to the visceral area. Additionally, this pattern of explained variation differed spatially across the brain, with transcriptomic similarity playing a larger role in the cortex than subcortex, while connectivity explains structural covariance best in parts of the cortex, midbrain, and hindbrain. These results suggest that both gene expression and connectivity underlie structural volume covariance, albeit to different extents depending on brain region, and this relationship is modulated by distance.
Accuracy of programs for the determination of HLA alleles from NGS data
Authors: Larjo Antti , Eveleigh Robert , Kilpeläinen Elina , Kwan Tony , Pastinen Tomi , Koskela Satu , Partanen Jukka 
Published: September 2017

AbstractThe human leukocyte antigen (HLA) genes code for proteins that play a central role in the function of the immune system by presenting peptide antigens to T cells. As HLA genes show extremely high genetic polymorphism, HLA typing on the allele level is demanding and is based on DNA sequencing. Determination of HLA alleles is warranted as many HLA alleles are major genetic factors that confer susceptibility to autoimmune diseases and is important for the matching of HLA alleles in transplantation. Here, we compared the accuracy of several published HLA-typing algorithms that are based on next generation sequencing (NGS) data. As genome screens are becoming increasingly routine in research, we wanted to test how well HLA alleles can be deduced from genome screens not designed for HLA typing. The accuracies were assessed using datasets consisting of NGS data produced using the ImmunoSEQ platform, including the full 4 Mbp HLA segment, from 94 stem cell transplantation patients and exome sequences from the 1000 Genomes collection. When used with the default settings none of the methods gave perfect results for all the genes and samples. However, we found that ensemble prediction of the results or modifications of the settings could be used to improve accuracy. Most of the algorithms did not perform very well for the exome-only data. The results indicate that the use of these algorithms for accurate HLA allele determination based on NGS data is not straightforward.
RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of holo-mycoheterotrophic plants
Authors: Schelkunov M.I. , Penin A.A. , Logacheva M.D. 
Published: September 2017

Summary• While photosynthesis is the most notable trait of plants, several lineages of plants (so-called holo-heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels.• Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllumandEpipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related holo-heterotrophic plants.• In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of bothEpipogiumspecies accumulated mutations twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed inH.monotropa.• Holo-heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.
Ldb1 and Rnf12-dependent regulation of Lhx2 controls the relative balance between neurogenesis and gliogenesis in retina
Authors: de Melo Jimmy , Venkataraman Anand , Clark Brian S. , Zibetti Cristina , Blackshaw Seth 
Published: September 2017

AbstractPrecise control of the relative ratio of retinal neurons and glia generated during development is essential for visual function. We show thatLhx2, which encodes a LIM-homeodomain transcription factor essential for specification and differentiation of retinal Müller glia, also plays a critical role in the development of retinal neurons. Overexpression ofLhx2, and its transcriptional coactivatorLdb1, triggers cell cycle exit and inhibits both Notch signaling and retinal gliogenesis.Lhx2/Ldb1overexpression also induced the formation of wide-field amacrine cells (wfACs). In contrastRnf12, which encodes a negative regulator of LDB1, is necessary for the initiation of retinal gliogenesis. We also show that LHX2 protein binds upstream of multiple neurogenic bHLH factors includingAscl1andNeurog2, which are necessary for suppression of gliogenesis and wfAC formation respectively, and activates their expression. Finally, we demonstrate that the relative level of the LHX2-LDB1 complex in the retina decreases in tandem with the onset of gliogenesis. These findings show that control ofLhx2function byLdb1andRnf12acts as a molecular mechanism underpinning the coordinated differentiation of neurons and Müller glia in postnatal retina.Significance StatementThe molecular mechanisms that control the ratio neurons and glia that are generated by neuronal progenitors remain unclear. Here we show that Lhx2, a transcription factor essential for retinal gliogenesis, also controls development of retinal neurons. The Lhx2 coactivator Ldb1 promotes Lhx2-dependent neurogenesis, while the Lhx2 corepressor Rnf12 is necessary and sufficient for retinal gliogenesis. Furthermore, Lhx2 directly regulates expression of bHLH factors that promote neural development, which are necessary for Lhx2-dependent neurogenesis. Finally, we show that levels of the LHX2-LDB1 complex, which activates transcription, drop as gliogenesis begins. Dynamic regulation of Lhx2 activity by Ldb1 and Rnf12 thus controls the relative levels of retinal neurogenesis and gliogenesis, and may have similar functions elsewhere in the developing nervous system.
Entorhinal cortex receptive fields are modulated by spatial attention, even without movement
Authors: Wilming Niklas , König Peter , König Seth , Buffalo Elizabeth A. 
Published: September 2017

AbstractGrid cells have been identified in the entorhinal cortex in a variety of species and allow for the precise decoding of position in space (1–7). Along with potentially playing an important role in navigation, grid cells have recently been hypothesized to make a general contribution to mental operations, including remembering the past and thinking about the future (8,9). A prerequisite for this hypothesis is that grid cell activity does not critically depend on physical movement. Directed attention, which contributes to virtually all mental operations and can be separated from physical movement provides a good test case to investigate this hypothesis. Overt attention in the form of fixational eye movements leads to grid-like firing fields in the monkey entorhinal cortex (3). Here we show that movement of covert attention, without any physical movement, also elicits spatial receptive fields with a triangular tiling of the space. In monkeys trained to maintain central fixation while covertly attending to a stimulus moving in the periphery we identified a significant population (20/141, 14% neurons at a FDR<5%) of entorhinal cells with spatially structured receptive fields. Further, we were able to identify a population of neurons that were labeled as grid cells on an individual basis. This contrast with our recordings obtained in the hippocampus, where grid-like representations were not observed. Our results provide compelling evidence that neurons in macaque entorhinal cortex do not rely on physical movement. Notably, these results support the notion that grid cells may be capable of serving a variety of different cognitive functions and suggest that grid cells are a versatile component of many neural algorithms.
SwarmSight: Real-Time Tracking of Insect Antenna Movements and Proboscis Extension Reflex using a Common Preparation and Conventional Hardware
Authors: Birgiolas Justas , Jernigan Christopher M. , Gerkin Richard C. , Smith Brian H. , Crook Sharon M. 
Published: September 2017

ABSTRACTMany scientifically and agriculturally important insects use antennae to detect the presence of volatile chemical compounds and extend their proboscis during feeding. The ability to rapidly obtain high-resolution measurements of natural antenna and proboscis movements and assess how they change in response to chemical, developmental, and genetic manipulations can aid the understanding of insect behavior. By extending our previous work on assessing aggregate insect swarm or animal group movements from natural and laboratory videos using video analysis software SwarmSight, we developed a novel, free, and open-source software module, SwarmSight Appendage Tracking (SwarmSight.org) for frame-by-frame tracking of insect antenna and proboscis positions from conventional web camera videos using conventional computers. The software processes frames about 120 times faster than humans, performs at better than human accuracy, and, using 30 frames-per-second videos, can capture antennal dynamics up to 15 Hz. We used the software to track the antennal response of honey bees to two odors and found significant mean antennal retractions away from the odor source about 1 s after odor presentation. We observed antenna position density heat map cluster formation and cluster and mean angle dependence on odor concentration.
Development of an integrated genomic map for a threatened Caribbean coral (Orbicella faveolata)
Authors: Snelling Jacob , Dziedzic Katherine , Guermond Sarah , Meyer Eli 
Published: September 2017

ABSTRACTGenomic methods are powerful tools for studying evolutionary responses to selection, but the application of these tools in non-model systems threatened by climate change has been limited by the availability of genomic resources in those systems. High-throughput DNA sequencing has enabled development of genome and transcriptome assemblies in non-model systems including reef-building corals, but the fragmented nature of early draft assemblies often obscures the relative positions of genes and genetic markers, and limits the functional interpretation of genomic studies in these systems. To address this limitation and improve genomic resources for the study of adaptation to ocean warming in corals, we’ve developed a genetic linkage map for the mountainous star coral,Orbicella faveolata. We analyzed genetic linkage among multilocus SNP genotypes to infer the relative positions of markers, transcripts, and genomic scaffolds in an integrated genomic map. To illustrate the utility of this resource, we tested for genetic associations with bleaching responses and fluorescence phenotypes, and estimated genome-wide patterns of population differentiation. Mapping the significant markers identified from these analyses in the integrated genomic resource identified hundreds of genes linked to significant markers, highlighting the utility of this resource for genomic studies of corals. The functional interpretations drawn from genomic studies are often limited by the availability of genomic resources linking genes to genetic markers. The resource developed in this study provides a framework for comparing genetic studies ofO. faveolataacross genotyping methods or references, and illustrates an approach for integrating genomic resources that may be broadly useful in other non-model systems.