bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propionibacterium acnes Septic Pericarditis in a Patient With Sarcoidosis and Acne
Authors: Kapinos Piotr , El Khoury Marc Y 
Published: August 2017

Abstract

Propionibacterium acnes has been recently recognized as a common cause of pericarditis in both immunocompetent and immunocompromised hosts. It is frequently missed on routine cultures because of its slow growth. We present the first case of infective pericarditis caused by P. acnes in a man with acne and severe sarcoidosis. This case emphasizes the importance of considering this microorganism as a causative agent of pericarditis in this setting.
Extensively Drug-Resistant Pseudomonas aeruginosa Sternal Osteomyelitis
Authors: Buchanan Patrick J. , Lee Teng C. , Venugopalan Veena , Tremblay Elizabeth E. , Cannella Anthony P. , Leyngold Mark M. 
Published: August 2017

Background
Sternal wound infection continues to be the leading complication after median sternotomy. With the growing concern of multidrug-resistant and extensively drug-resistant (XDR) bacterial infections, sternal wound reconstruction is a critical step in successfully healing these patients. The use of a rectus abdominis muscle flap for coverage of the lower one third of sternal wounds as well as objectively optimizing antimicrobial therapy has revolutionized the field of sternal wound reconstruction, yet both practices are not well documented within the literature.

Clinical Scenario
A 72-year-old man developed an XDR Pseudomonas aeruginosa infection of his sternum after median sternotomy. The sternal wound was successfully reconstructed using a dual flap approach of bilateral pectoralis major myocutaneous flaps and a rectus abdominis muscle flap. Because of the antibiotic susceptibility profile and patient allergy profile, parental tobramycin and high-dose continuous-infusion meropenem were used to treat the osteomyelitis; meropenem serum concentrations were obtained via mass spectroscopy to optimize bactericidal activity.

Conclusions
Osteomyelitis secondary to XDR P. aeruginosa is exceedingly rare in the literature. Individuals with this type of infection can be successfully treated with aggressive surgical debridement, subsequent reconstruction using bilateral pectoralis major myocutaneous flaps and a rectus abdominis muscle flap for coverage of the sternal wound, and both guided and targeted parental antibiotics. Lastly, the innovative use of antibiotic concentrations was instrumental in targeting the appropriate dose of antimicrobials in this patient.
Invasive Pulmonary Aspergillosis and Methicillin-Resistant Staphylococcus aureus Associated With Influenza A Infection
Authors: Ballal Megana L. , Shirvanian Shant , Halai Umme-Aiman , Graber Christopher J. , Betancourt Jaime 
Published: August 2017

Abstract
Bacterial superinfection is a known complication of influenza infection, with Streptococcus pneumoniae and Staphylococcus aureus often being the offending pathogens. In recent decades, there has been an increased prevalence of superinfection with Aspergillus in seemingly immunocompetent hosts. We describe a fatal case of influenza complicated by simultaneous methicillin-resistant S. aureus pneumonia and invasive pulmonary aspergillosis.
Qualitative and Quantitative Evaluation of Structural Myocardial Alterations by Grating-Based Phase-Contrast Computed Tomography
Authors: Notohamiprodjo Susan , Webber Nicole , Birnbacher Lorenz , Willner Marian , Viermetz Manuel , Herzen Julia , Marschner Mathias , Mayr Doris , Bartsch Harald , Saam Tobias , Auweter Sigrid , Pfeiffer Franz , Reiser Maximilian F. , Hetterich Holger 
Published: August 2017

Objectives
Grating-based phase-contrast computed tomography (gb-PCCT) relies on x-ray refraction instead of absorption to generate high-contrast images in biological soft tissue. The aim of this study was to evaluate the potential of gb-PCCT for the depiction of structural changes in heart disease.

Materials and Methods
Four human heart specimens from patients with hypertensive disease, ischemic disease, dilated heart disease, and cardiac lipomatosis were examined. The gb-PCCT setup consisted of an x-ray tube (40 kV, 70 mA), grating-interferometer, and detector, and allowed simultaneous acquisition of phase- and absorption-contrast data. With histopathology as the standard of reference, myocardium (MC), fibrotic scar (FS), interstitial fibrosis (IF), and fatty tissue (FT) were visually and quantitatively evaluated. Systematic differences in absorption- and phase-contrast Hounsfield units (HU

abs
and HU

p
) were assessed.

Results
Thirteen corresponding cross-sections were included, and MC, FS, IF, and FT were found in 13 (100%), 4 (30.8%), 7 (53.8%), and 13 (100%) cross-sections, respectively. Mean HU

p
/HU

abs
were 52.5/54.1, 86.6/69.7, 62.4/62.3, and −38.6/−258.9 for MC, FS, IF, and FT, respectively. An overlap in HU

abs
was observed for MC and IF (P = 0.84) but not for HU

p
(P < 0.01). Contrast-to-noise ratios were significantly higher in phase- than in absorption-contrast for MC/FT (35.4 vs 7.8; P < 0.01) and for MC/FS (12.3 vs 0.2; P < 0.01).

Conclusions
Given its superior soft tissue contrast, gb-PCCT is able to depict structural changes in different cardiomyopathies, which can currently not be obtained by x-ray absorption-based imaging methods. If current technical limitations can be overcome, gb-PCCT may evolve as a powerful tool for the anatomical assessment of cardiomyopathy.
Optic Disc Drusen in Children: The Copenhagen Child Cohort 2000 Eye Study
Authors: Malmqvist Lasse , Li Xiao Qiang , Eckmann Christina L. , Skovgaard Anne M. , Olsen Else M. , Larsen Michael , Munch Inger C. , Hamann Steffen 
Published: August 2017

Background:
Optic disc drusen (ODD) are seen in up to 2.4% of the general population, but the etiology and pathophysiology of the condition is still unknown. The purpose of this study was to determine the prevalence of ODD in a population-based child cohort and to determine if scleral canal diameter and fetal birth and pubertal parameters are associated with the presence of ODD.

Methods:
This observational, longitudinal population-based birth cohort study, with a nested case–control, included 1,406 children. Eye examinations were performed when the children were between 11 and 12 years of age. Assessment was performed of optical coherence tomography (OCT) scans from 1,304 children with gradable enhanced depth imaging scans of the optic disc.

Results:
ODD in one or both eyes were found in 13 (1.0%) of all children. All but one of the cases were found in children with scleral canal diameter in the lowest quartile (1,182–1,399 μm) in the nested case–control study. Children with ODD had a mean disc diameter of 1,339 μm (interquartile range, 30 μm), whereas it was 1,508 μm (interquartile range, 196 μm) in the 130 controls without ODD (P < 0.001). No differences in sex, birth weight, refractive error, and Tanner stages (of puberty) were found between children with and without ODD.

Conclusions:
The prevalence of ODD was 1% in a large child cohort examined by OCT. ODD was found only in eyes with a narrow scleral canal, which is consistent with the hypothesis that ODD might arise as a consequence of retinal nerve fiber congestion in the scleral canal.
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarianSchmidtea mediterranea
Authors: Cheng Li-Chun , Tu Kimberly C. , Seidel Chris W. , Robb Sofia M.C. , Guo Fengli , Alvarado Alejandro Sánchez 
Published: August 2017

AbstractThe epidermis is essential for animal survival, providing both a protective barrier and cellular sensor to external environments. The generally conserved embryonic origin of the epidermis, but the broad morphological and functional diversity of this organ across animals is puzzling. We define the transcriptional regulators underlying epidermal lineage differentiation in the planarianSchmidtea mediterranea,an invertebrate organism that, unlike fruitflies and nematodes, continuously replaces its epidermal cells. We find thatSmed-p53, SoxandPaxtranscription factors are essential regulators of epidermal homeostasis, and act cooperatively to regulate genes associated with early epidermal precursor cell differentiation, including a tandemly arrayed novel gene family(prog)of secreted proteins. Additionally, we report on the discovery of distinct and previously undescribed secreted organelles whose production is dependent on the transcriptional activity ofsoxP-3,and which we term Hyman vesicles.
Effects of partial selfing on the equilibrium genetic variance, mutation load and inbreeding depression under stabilizing selection
Authors: Abu Awad Diala , Roze Denis 
Published: August 2017

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100041).The mating system of a species is expected to have important effects on its genetic diversity. In this paper, we explore the effects of partial selfing on the equilibrium genetic varianceVg, mutation loadLand inbreeding depressionδunder stabilizing selection acting on a arbitrary numbernof quantitative traits coded by biallelic loci with additive effects. Overall, our model predicts a decrease in the equilibrium genetic variance with increasing selfing rates; however, the relationship between self-fertilization and the variables of interest depends on the strength of associations between loci, and three different regimes are observed. When theU/nratio is low (whereUis the total haploid mutation rate on selected traits) and effective recombination rates are sufficiently high, genetic associations between loci are negligible and the genetic variance, mutation load and inbreeding depression are well predicted by approximations based on single-locus models. For higher values ofU/nand/or lower effective recombination, moderate genetic associations generated by epistasis tend to increaseVg,Landδ, this regime being well predicted by approximations including the effects of pairwise associations between loci. For yet higher values ofU/nand/or lower effective recombination, a different regime is reached under which the maintenance of coadapted gene complexes reducesVg,Landδ. Simulations indicate that the values ofVg,Landδare little affected by assumptions regarding the number of possible alleles per locus.
Novel Magnetic Resonance Imaging strategy targeting Neurotensin Receptors in detection of Prostate Cancer
Authors: Desai Mitul , Tam Neville N.C. , Carraway Robert. , Ho Shuk-Mei , Ferris Craig. , King Jean. 
Published: August 2017

ABSTRACTProstate cancer is the second leading cause of all male cancer deaths. One of the factors present in malignant prostate cells and shown to support its metastatic growth is the neuropeptide neurotensin (NT). The primary goal of the present study was to establish the feasibility of using a newly developed paramagnetic receptor ligand for NT and non-invasive ultrahigh-field magnetic resonance (MR) imaging to visualize prostate cancer in rodents. Orthotropic xenografts were initiated in six-week old male BALB/cnu/nuathymic mice (n = 28) by intra-prostatic (ventral lobe) inoculation of human prostate cancer cells (10μL of PC3 cells (106/100μl)). Palpable tumors developed within 30-60 days. A micro-imager utilized in these studies was an actively shielded 9.4T, 89 mm bore, Oxford superconducting magnet with a 100 gauss/cm gradient system. Prior to contrast injection, T2 weighted anatomy scans were done to localize the tumor with a spin-echo multi-slice sequence with TR: 2000 TE: 40 and NEX: 1 in both coronal and axial planes. The paramagnetic ligand data sets were collected with a spin-echo, T1 weighted pulse sequence (MSME): TR 300 msec; TE 5 msec; NEX 4 in both axial and coronal planes. The data sets were taken initially at 5-min intervals post contrast injection for the first half hour and then at 15 min intervals for the next 1.5-2 hours for a time series analyses. The temporal distribution of MR signal intensity in various regions were determined in the absence and presence of NT. Our results confirm that the novel NT molecule was protected from enzymatic degradation and capable of forming a high affinity paramagnetic NT ligand with an extended half-life. During the imaging studies, the signal intensity increased by 200 % in the region of the tumor. This increase in signal intensity approached maximum binding within 30 minutes and remained visible for 1 hour post-injection of the contrast agent. Taken together, these findings suggest that it is feasible to detect and image prostate cancer using a paramagnetic NT ligand and the emergence of the NT receptor ligand that may be used as a diagnostic marker for prostate cancer in humans.
P-values and confidence intervals: not fit for purpose?
Authors: Pharoah Paul D.P. , Jones Michelle R. , Kar Siddartha 
Published: August 2017

DeclarationsCompeting interests: All authors have completed theunified competing interest form and declare: no support from any organisation for the submitted work; no financial relationships with any organisations that might have an interest in the submitted work in the previous three years, no other relationships or activities that could appear to have influenced the submitted work.The lead author (the manuscript’s guarantor) affirms that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted.Ethical approval: not requiredDetails of funding: Not applicableStatement of independence of researchers from funders: Not applicablePatient involvement statement. Not applicable.Data sharing statement: Not applicable.
A unifying motif for spatial and directional surround suppression
Authors: Liu Liu D. , Miller Kenneth D. , Pack Christopher C. 
Published: August 2017

AbstractIn the visual system, the response to a stimulus in a neuron’s receptive field can be modulated by stimulus context, and the strength of these contextual influences vary with stimulus intensity. Recent work has shown how a theoretical model, the stabilized supralinear network (SSN), can account for such modulatory influences, using a small set of computational mechanisms. While the predictions of the SSN have been confirmed in primary visual cortex (V1), its computational principles apply with equal validity to any cortical structure. We have therefore tested the generality of the SSN by examining modulatory influences in the middle temporal area (MT) of the macaque visual cortex, using electrophysiological recordings and pharmacological manipulations. We developed a novel stimulus that can be adjusted parametrically to be larger or smaller in the space of all possible motion directions. We found, as predicted by the SSN, that MT neurons integrate across motion directions for low-contrast stimuli, but that they exhibit suppression by the same stimuli when they are high in contrast. These results are analogous to those found in visual cortex when stimulus size is varied in the space domain. We further tested the mechanisms of inhibition using pharmacologically manipulations of inhibitory efficacy. As predicted by the SSN, local manipulation of inhibitory strength altered firing rates, but did not change the strength of surround suppression. These results are consistent with the idea that the SSN can account for modulatory influences along different stimulus dimensions and in different cortical areas.Significance StatementVisual neurons are selective for specific stimulus features in a region of visual space known as the receptive field, but can be modulated by stimuli outside of the receptive field. The SSN model has been proposed to account for these and other modulatory influences, and tested in V1. As this model is not specific to any particular stimulus feature or brain region, we wondered whether similar modulatory influences might be observed for other stimulus dimensions and other regions. We tested for specific patterns of modulatory influences in the domain of motion direction, using electrophysiological recordings from MT. Our data confirm the predictions of the SSN in MT, suggesting that the SSN computations might be a generic feature of sensory cortex.
Genetically Targeted Ratiometric and Activated pH Indicator Complexes (TRApHIC) for Receptor Trafficking
Authors: Perkins Lydia A. , Yan Qi , Schmidt Brigitte F. , Kolodieznyi Dmytro , Saurabh Saumya , Larsen Mads Breum , Watkins Simon C. , Kremer Laura , Bruchez Marcel P. 
Published: August 2017

AbstractFluorescent protein based pH sensors are a useful tool for measuring protein trafficking through pH changes associated with endo-and exocytosis. However, commonly used pH sensing probes are ubiquitously expressed with their protein of interest throughout the cell, hindering the ability to focus on specific trafficking pools of proteins. We developed a family of excitation-ratiometric, activatable pH responsive tandem dyes, consisting of a pH sensitive Cy3 donor linked to a fluorogenic malachite green acceptor. These cell-excluded dyes are targeted and activated upon binding to a genetically expressed fluorogen activating protein, and are suitable for selective labeling of surface proteins for analysis of endocytosis and recycling in live cells using both confocal and superresolution microscopy. Quantitative profiling of the endocytosis and recycling of tagged β2-adrenergic receptor (B2AR) at a single vesicle level revealed differences among B2AR agonists, consistent with more detailed pharmacological profiling.
Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates
Authors: Tamura Koichiro , Tao Qiqing , Kumar Sudhir 
Published: August 2017

AbstractRelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It showed excellent performance in estimating divergence times for both simulated and empirical molecular sequence datasets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of datasets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between an evolutionary lineage and its descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be also useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.
Efficientin situbarcode sequencing using padlock probe-based BaristaSeq
Authors: Chen Xiaoyin , Sun Yu-Chi , Church George M , Lee Je Hyuk , Zador Anthony M 
Published: August 2017

AbstractCellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes trade off spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas manual cell picking has low throughput.In situsequencing could potentially achieve both high spatial resolution and high throughput, but currentin situsequencing techniques are inefficient at reading out cellular barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock probe-based technique forin situbarcode sequencing compatible with Illumina sequencing chemistry. BaristaSeq results in a five-fold increase in amplification efficiency, with a sequencing accuracy of at least 97%. BaristaSeq could be used for barcode-assisted lineage tracing, and to map long-range neuronal projections.Key PointsIn situsequencing by gap-filling padlock probes is limited by the strand displacement of DNA polymerasesIllumina sequencing chemistry offers superior signal-to-noise ratioin situcompared to sequencing by ligationBaristaSeq as an accurate method for barcode sequencingin situwith improved gap-filling efficiency
A plant receptor-like kinase promotes cell-to-cell spread of RNAi and is targeted by a virus
Authors: Rosas-Diaz Tabata , Zhang Dan , Fan Pengfei , Wang Liping , Ding Xue , Jiang Yuli , Jimenez-Gongora Tamara , Medina-Puche Laura , Zhao Xinyan , Feng Zhengyan , Zhang Guiping , Liu Xiaokun , Bejarano Eduardo R , Tan Li , Zhu Jian-Kang , Xing Weiman , Faulkner Christine , Nagawa Shingo , Lozano-Duran Rosa 
Published: August 2017

ABSTRACTRNA interference (RNAi) in plants can move from cell to cell, allowing for systemic spread of an anti-viral immune response. How this cell-to-cell spread of silencing is regulated is currently unknown. Here, we describe that the C4 protein fromTomato yellow leaf curl virushas the ability to inhibit the intercellular spread of RNAi. Using this viral protein as a probe, we have identified the receptor-like kinase (RLK) BARELY ANY MERISTEM 1 (BAM1) as a positive regulator of the cell-to-cell movement of RNAi, and determined that BAM1 and its closest homologue, BAM2, play a redundant role in this process. C4 interacts with the intracellular domain of BAM1 and BAM2 at the plasma membrane and plasmodesmata, the cytoplasmic connections between plant cells, interfering with the function of these RLKs in the cell-to-cell spread of RNAi. Our results identify BAM1 as an element required for the cell-to-cell spread of RNAi and highlight that signalling components have been co-opted to play multiple functions in plants.
Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics
Authors: Leggett Richard M. , Alcon-Giner Cristina , Heavens Darren , Caim Shabhonam , Brook Thomas C. , Kujawska Magdalena , Martin Samuel , Hoyles Lesley , Clarke Paul , Hall Lindsay J. , Clark Matthew D. 
Published: August 2017

ABSTRACTThe Oxford Nanopore MinION sequencing platform offers near real time analysis of DNA reads as they are generated, which makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics. We used the MinION platform for shotgun metagenomic sequencing and analysis of gut-associated microbial communities; firstly, we used a 20-species human microbiota mock community to demonstrate how Nanopore metagenomic sequence data can be reliably and rapidly classified. Secondly, we profiled faecal microbiomes from preterm infants at increased risk of necrotising enterocolitis and sepsis. In single patient time course, we captured the diversity of the immature gut microbiota and observed how its complexity changes over time in response to interventions, i.e. probiotic, antibiotics and episodes of suspected sepsis. Finally, we performed ‘real-time’ runs from sample to analysis using faecal samples of critically ill infants and of healthy infants receiving probiotic supplementation. Real-time analysis was facilitated by our new NanoOK RT software package which analysed sequences as they were generated. We reliably identified potentially pathogenic taxa (i.e.Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance (AMR) gene profiles within as little as one hour of sequencing. Antibiotic treatment decisions may be rapidly modified in response to these AMR profiles, which we validated using pathogen isolation, whole genome sequencing and antibiotic susceptibility testing. Our results demonstrate that our pipeline can process clinical samples to a rich dataset able to inform tailored patient antimicrobial treatment in less than 5 hours.