bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesenteric Panniculitis With Lupus Demonstrated on 18F-FDG PET/CT
Authors: Bourgeois Sophie , Van den Eeckhaut Anja , De Geeter Frank 
Published: October 2018

Abstract
We describe the 18F-FDG PET/CT findings in a rare case of mesenteric panniculitis caused by systemic lupus. A previous CT had raised suspicion of a space-occupying lesion in the left hypochondrium in a context of aspecific constitutional symptoms and inflammatory parameters. The diagnosis of panniculitis was confirmed at laparoscopic biopsy directed by the PET findings. Follow-up 18F-FDG PET/CT after 1 month of corticosteroid therapy showed complete disappearance of the abdominal hypermetabolic foci.
Idiopathic Inflammatory Myopathy and Antisynthetase Syndrome
Authors: Fernández-Rodríguez Paula , Martín-Marcuartu Juan José , Jiménez-Hoyuela Jose Manuel 
Published: October 2018

Abstract
We present a 44-year-old woman with scapular and pelvic muscle weakness, joint inflammation, and fever. Bone scintigraphy showed high uptake in proximal regions of upper and lower limbs, suspecting inflammatory myopathy and polyarticular damage. These features were the clue to request other complementary tests such as anti–aminoacyl-tRNA-synthetase antibodies and chest CT, which showed interstitial lung disease, defining an antisynthetase syndrome. Therefore, BS allows an earlier diagnosis of inflammatory muscle disease and to identify the optimal site for muscle biopsy. BS is an important step to reach a prompt diagnosis of antisynthetase syndrome for establishing an early treatment.
Imaging Characteristics of a Bladder Wall Paraganglioma
Authors: Bosserman Andrew John , Dai Dong , Lu Yang 
Published: October 2018

Abstract
A 65-year-old man with a history of hypertension and nephrolithiasis presented with flank pain. Urographic CT demonstrated a 1.7-cm nodule arising from the bladder wall. The patient was referred for cystourethroscopy. During the procedure, the patient became hypertensive while under general anesthesia. No biopsy or resection was performed. To work up for possible bladder paraganglioma, a 123I-MIBG scan was ordered, and the patient was referred to endocrinology. On SPECT/CT images, the bladder nodule demonstrates marked uptake of MIBG radiotracer, confirming the diagnosis of a genitourinary paraganglioma arising from the bladder wall.
Vascularized Tissue Reconstruction in Previously Irradiated Sarcoma Defects
Authors: Azzi Alain Joe , Zhou Sarah , Safran Tyler , Xu Liqin , Alnaif Nayif , Zadeh Teanoosh 
Published: October 2018

Introduction
Radiation therapy (RT) is recommended for appropriately selected sarcoma patients to minimize the risk of local recurrence and to maximize outcomes of disease-free survival and function. The purpose of this study was to confirm the safety of vascularized tissue reconstruction in recently irradiated sarcoma defects.

Methods
A retrospective review of all patients treated by the senior author for sarcoma reconstruction from January 2005 to July 2017 was performed. Two independent reviewers collected data from both electronic and paper medical records. Patients were included if they underwent flap reconstruction (pedicled or free) following sarcoma resection. The safety of neoadjuvant RT was compared with a control group with no previous irradiation using χ2 analysis.

Results
Fifty-seven patients were included in the study; 35 patients were included in the preoperative RT group, and 22 patients were included in the control group (no previous irradiation). There was no significant difference in wound complications between the 2 groups (infection, dehiscence, hematoma, and seroma). Microvascular complications (arterial thrombosis, venous thrombosis, partial/total flap loss) were also comparable in the free tissue transfer subgroup.

Conclusions
The current study demonstrates the safety of both pedicled and free flap reconstruction in previously irradiated sarcoma defects. Judicious selection of reconstructive technique and recipient vessels is crucial in obtaining optimal outcomes given the devastating effects of RT on native tissues.
Complex Ventral Hernia Repair in the Class III Morbidly Obese Patient
Authors: Oleck Nicholas C. , Liu Farrah C. , Conway Michael , Kalish Eric , Belgrade Joseph , Santoro Peter , Zabel David 
Published: October 2018

Introduction
Patients undergoing complex ventral hernia repair (VHR) often present with significant medical comorbidities, the most prevalent of which is obesity. Although recent advancements in abdominal wall reconstruction techniques have provided the general hernia patient population with markedly improved recurrence and postoperative complication rates, many patients have been precluded from these procedures owing to excessive body mass index (BMI). In this study, we investigate the viability of complex ventral hernia repair with epigastric artery perforator sparing skin incisions, component separation, and wide-spanning retrorectus mesh reinforcement for patients with BMI of greater than or equal to 40 kg/m2 (class III obesity).

Methods
A single surgeon retrospective review of our prospectively maintained database was performed. We restricted this data to class III morbidly obese patients undergoing open VHR with component muscle separation and wide-spanning mesh reinforcement.

Results
Between 2010 and 2017, 131 patients met the inclusion criteria for our study. The mean patient BMI was 46.7 kg/m2. Operative wounds were categorized according to the National Healthcare Safety Network Wound Class Definitions. There was no statistically significant association between wound class and postoperative complication rates. After our implementation of epigastric artery perforator sparing skin incisions in 2013, significantly less wound breakdown was observed (26.3%) as opposed to before (49.0%) (P < 0.01). Furthermore, significantly less cases required return to the operating room after this technique was implemented (31.3%) as compared with before (60.8%) (P < 0.001). Postoperatively, 28 patients developed an infection requiring antibiotic treatment (21.4%), and the overall hernia recurrence rate was 5.3%. Three patients expired.

Conclusions
Complex VHR with abdominal wall reconstruction may be a viable option for class III morbidly obese patients. Preliminary data suggest that implementation of epigastric artery perforator sparing skin incisions may reduce the risk of postoperative wound complications, and we have demonstrated hernia recurrence and wound complications comparable with those seen in the general population.
Lacrimal Injury After Rhinoplasty
Authors: Jafaripour Masoud , Kashfi Seyed Abolfazl 
Published: October 2018

Abstract
Lacrimal injury is very uncommon after osteotomy in rhinoplasty. We present 2 cases of lacrimal injury after osteotomy in rhinoplasty and present the steps to managing such an injury. These cases were finally treated with endoscopic dacryocystorhinostomy. We concluded that osteotomies must be at least 3 mm from the medial canthus or medial to the line from the medial canthus to the alar base. Also, it is recommended that osteotome blades be sharpened before each osteotomy.
Novel diamond shuttle to deliver flexible bioelectronics with reduced tissue compression
Authors: Na Kyounghwan , Sperry Zachariah J. , Lu Jiaao , Vöröslakos Mihaly , Parizi Saman S. , Bruns Tim M. , Yoon Euisik , Seymour John P. 
Published: October 2018

AbstractThe ability to deliver flexible biosensors through the toughest membranes of the central and peripheral nervous system is an important challenge in neuroscience and neural engineering. Bioelectronic devices implanted through dura mater and thick epineurium would ideally create minimal compression and acute damage as they reach the neurons of interest. We demonstrate that a three-dimensional diamond shuttle can be easily made with a vertical support to deliver ultra-compliant polymer microelectrodes (4.5 μm thick) in-vivo through dura mater and thick epineurium. The diamond shuttle has 54% less cross-sectional area than an equivalently stiff silicon shuttle, which we simulated will result in a 37% reduction in blood vessel damage. We also discovered that higher frequency oscillation of the shuttle (200 Hz) significantly reduced tissue compression regardless of the insertion speed, while slow speeds also independently reduced tissue compression. Insertion and recording performance are demonstrated in rat and feline models, but the large design space of these tools are suitable for research in a variety of animal models and nervous system targets.
netome: a computational framework for metabolite profiling and omics network analysis
Authors: Rahnavard Ali , Hitchcock Daniel , Pacheco Julian Avila , Deik Amy , Dennis Courtney , Jeanfavre Sarah , Pierce Kerry , Bullock Kevin , Costliow Zach , Clish Clary B. 
Published: October 2018

AbstractSummaryAdvances in metabolomics technologies have enabled comprehensive analyses of associations between metabolites and human disease and have provided a means to study biochemical pathways and processes in detail using model systems. Liquid chromatography tandem mass spectrometry (LC-MS) is an analytical technique commonly used by metabolomics labs to measure hundreds of metabolites of known identity and thousands of “peaks” from yet to be identified compounds that are tracked by their measured masses and chromatographic retention times. netome is a computational framework that provides tools for analyzing processed LC-MS data. In this framework, we develop and provide various computational resources including individual software modules to inspect and adjust trends in raw data, align unknown peaks between separately acquired data sets, and to remove redundancies in nontargeted LC-MS data arising from multiple ionization products of a single metabolite. These tools are deployed through computing resources such as web servers and virtual machines with detailed documentation in order to support researchers.Availability and implementationnetome is publicly available with extensive documentation and support via issue tracker at https://broadinstitute.github.io/netome under the MIT license. netome includes a set of computational methods that have been designed to execute quality control and post-raw data processing tasks for metabolomics data (e.g. scaling and clustering metabolite abundances), as well as statistical association testing in a network manner (e.g., testing relationship between metabolites and microbes). Each individual tool is available with source code, workshop-oriented documentation which includes instructions for installation and using tools with demonstration examples, and a web server with all services. We also provide a complete image of the netome package with all pre-installed dependencies and support for Google Compute Engine and Amazon EC2. All tools and related services are maintained, and upon new developments, new modules will be added to the environment.Contactrah@broadinstitute.org, clary@broadinstitute.orgSupplementary informationSupplementary data are available at Bioinformatics online.
Cannabis Use in Youth is Associated with Limited Alterations in Brain Structure
Authors: Scott J. Cobb , Rosen Adon F. G. , Moore Tyler M. , Roalf David R. , Satterthwaite Theodore D. , Calkins Monica E. , Ruparel Kosha , Gur Raquel E. , Gur Ruben C. 
Published: October 2018

ABSTRACTFrequent cannabis use during adolescence has been associated with alterations in brain structure. However, studies have featured relatively inconsistent results, predominantly from small samples, and few studies have examined less frequent users to shed light on potential brain structure differences across levels of cannabis use. In this study, high-resolution T1-weighted MRIs were obtained from 781 youth aged 14-21 years who were studied as part of the Philadelphia Neurodevelopmental Cohort. This sample included 147 cannabis users (109 Occasional [≤1-2 times per week] and 38 Frequent [≥ 3 times per week] Users) and 634 cannabis Non-Users. Several structural neuroimaging measures were examined in whole brain analyses, including gray and white matter volumes, cortical thickness, and gray matter density. Established procedures for stringent quality control were conducted, and two automated neuroimaging software processing packages were used to ensure robustness of results. There were no significant differences by cannabis group in global or regional brain volumes, cortical thickness, or gray matter density, and no significant group by age interactions were found. Follow-up analyses indicated that values of structural neuroimaging measures by cannabis group were similar across regions, and any differences among groups were likely of a small magnitude. In sum, structural brain metrics were similar among adolescent and young adult cannabis users and non-users. Our data converge with prior large-scale studies suggesting small or limited associations between cannabis use and structural brain measures in youth. Detailed studies of vulnerability to structural brain alterations and longitudinal studies examining long-term risk are indicated.
Oxytocin-mediated social preference and socially reinforced reward learning in the miniature fishDanionella cerebrum
Authors: Penalva-Tena Ariadne , Bedke Jacob , Gaudin Adam , Barrios Joshua P. , Bertram Erin P.L. , Douglass Adam D. 
Published: October 2018

SummaryIntegrative studies of the diverse neuronal networks that govern social behavior are hindered by the lack of methods to record neural activity comprehensively across the entire brain. The recent development of the miniature fishDanionella cerebrumas a model organism offers one potential solution, as the small size and optical transparency of these animals makes it possible to visualize circuit activity throughout the nervous system1–4. Here, we establish the feasibility of usingDanionellaas a model for social behavior and socially reinforced learning by showing that adult fish exhibit strong affiliative tendencies, and that social interactions can serve as the reinforcer in an appetitive conditioning paradigm. Fish exhibited an acute ability to identify conspecifics and distinguish them from closely related species, which was mediated by both visual and particularly olfactory cues. These behaviors were abolished by pharmacological and genetic interference with oxytocin signaling, demonstrating the conservation of key neural mechanisms observed in other vertebrates5–11. Our work validatesDanionellaas a tool for understanding the social brain in general, and its modulation by neuropeptide signaling in particular.
Daphnia stressor database: Taking advantage of a decade ofDaphnia‘-omics’ data for gene annotation
Authors: Ravindran Suda Parimala , Lüneburg Jennifer , Gottschlich Lisa , Tams Verena , Cordellier Mathilde 
Published: October 2018

AbstractGene expression patterns help to measure and characterize the effect of environmental perturbations at the cellular and organism-level. Complicating interpretation is the presence of uncharacterized or “hypothetical” gene functions for a large percentage of genomes. This is particularly evident inDaphniagenomes, which contains many regions coding for “hypothetical proteins” and are significantly divergent from many of the available arthropod model species, but might be ecologically important. In the present study, we developed a gene expression database, theDaphniastressor database (http://www.daphnia-stressordb.uni-hamburg.de/dsdbstart.php), built from 90 published studies onDaphniagene expression. Using a comparative genomics approach, we used the database to annotateD. galeatatranscripts. The extensive body of literature available forDaphniaspecies allowed to associate stressors with gene expression patterns. We believe that our stressor based annotation strategy allows for better understanding and interpretation of the functional role of the understudied hypothetical or uncharacterizedDaphniagenes, thereby increasing our understanding ofDaphnia’s genetic and phenotypic variability.
Programmed DNA elimination of germline development genes in songbirds
Authors: Kinsella Cormac M. , Ruiz-Ruano Francisco J. , Dion-Côté Anne-Marie , Charles Alexander J. , Gossmann Toni I. , Cabrero Josefa , Kappei Dennis , Hemmings Nicola , Simons Mirre J. P. , Camacho Juan P. M. , Forstmeier Wolfgang , Suh Alexander 
Published: October 2018

SummaryGenomes can vary within individual organisms. Programmed DNA elimination leads to dramatic changes in genome organisation during the germline–soma differentiation of ciliates1, lampreys2, nematodes3,4, and various other eukaryotes5. A particularly remarkable example of tissue-specific genome differentiation is the germline-restricted chromosome (GRC) in the zebra finch which is consistently absent from somatic cells6. Although the zebra finch is an important animal model system7, molecular evidence from its large GRC (>150 megabases) is limited to a short intergenic region8 and a single mRNA9. Here, we combined cytogenetic, genomic, transcriptomic, and proteomic evidence to resolve the evolutionary origin and functional significance of the GRC. First, by generating tissue-specific de-novo linked-read genome assemblies and re-sequencing two additional germline and soma samples, we found that the GRC contains at least 115 genes which are paralogous to single-copy genes on 18 autosomes and the Z chromosome. We detected an amplification of ≥38 GRC-linked genes into high copy numbers (up to 308 copies) but, surprisingly, no enrichment of transposable elements on the GRC. Second, transcriptome and proteome data provided evidence for functional expression of GRC genes at the RNA and protein levels in testes and ovaries. Interestingly, the GRC is enriched for genes with highly expressed orthologs in chicken gonads and gene ontologies involved in female gonad development. Third, we detected evolutionary strata of GRC-linked genes. Developmental genes such as bicc1 and trim71 have resided on the GRC for tens of millions of years, whereas dozens have become GRC-linked very recently. The GRC is thus likely widespread in songbirds (half of all bird species) and its rapid evolution may have contributed to their diversification. Together, our results demonstrate a highly dynamic evolutionary history of the songbird GRC leading to dramatic germline–soma genome differences as a novel mechanism to minimise genetic conflict between germline and soma.
Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis
Authors: Zeng Xiangrui , Fang Zhou , Ma Tianzhou , Lin Chien-Wei , Tseng George C. 
Published: October 2018

AbstractMotivationPathway analysis provides a knowledge-driven approach to interpret differentially expressed genes associated with disease status. Many tools have been developed to analyze a single study. When multiple studies of different conditions are jointly analyzed, novel integrative tools are needed. In addition, pathway redundancy issue introduced by combining public pathway databases hinders knowledge discovery.Methods and ResultsWe present a meta-analytic integration tool, Comparative Pathway Integrator (CPI), to address these issues using adaptively weighted Fisher’s method to discover consensual and differential enrichment patterns, consensus clustering to reduce pathway redundancy, and a novel text mining algorithm to assist interpretation of the pathway clusters. We applied CPI to jointly analyze six psychiatric disorder transcriptomic studies to demonstrate its effectiveness, and found functions confirmed by previous biological studies as well novel enrichment patterns.AvailabilityCPI is accessible online: http://tsenglab.biostat.pitt.edu/software.htm.Contactxiangruz@andrew.cmu.edu
Correlation between the oral microbiome and brain resting state connectivity in smokers
Authors: Lin Dongdong , Hutchison Kent E. , Portillo Salvador , Vegara Victor , Ellingson Jarrod M. , Liu Jingyu , Krauter Kenneth S. , Carroll-Portillo Amanda , Calhoun Vince D. 
Published: October 2018

AbstractRecent studies have shown a critical role of the gastrointestinal microbiome in brain and behavior via the complex gut–microbiome–brain axis, however, the influence of the oral microbiome in neurological processes is much less studied, especially in response to the stimuli in the oral microenvironment such as smoking. Additionally, given the complex structural and functional networks in brain system, our knowledge about the relationship between microbiome and brain function in specific brain circuits is still very limited. In this pilot work, we leveraged next generation microbial sequencing with functional neuroimaging techniques to enable the delineation of microbiome-brain network links as well as their relationship to cigarette smoking. Thirty smokers and 30 age- and sex- matched non-smokers were recruited for measuring both microbial community and brain functional networks. Statistical analyses were performed to demonstrate the influence of smoking on the abundance of the constituents within the oral microbial community and functional network connectivity among brain regions as well as the associations between microbial shifts and the brain functional network connectivity alternations. Compared to non-smokers, we found a significant decrease in beta diversity (p = 6×10−3) in smokers and identified several classes (Betaproteobacteria, Spirochaetia, Synergistia, and Mollicutes) as having significant alterations in microbial abundance. Taxonomic analyses demonstrate that the microbiota with altered abundance are mainly involved in pathways related to cell processes, DNA repair, immune system, and neurotransmitters signaling. One brain functional network connectivity component was identified to have a significant difference between smokers and nonsmokers (p = 0.033), mainly including connectivity between brain default network and other task-positive networks. The brain functional component was also significantly associated with some smoking related oral microbiota, suggesting a potential link between smoking-induced oral microbiome dysbiosis and brain functional connectivity, possibly through immunological and neurotransmitter signaling pathways. This work is the first attempt to link oral microbiome and brain functional networks, and provides support for future work in characterizing the role of oral microbiome in mediating smoking effects on brain activity.
Roles of Polycomb gene EED in pathogenesis and prognosis of acute myeloid leukemia and diffuse large B cell lymphoma
Authors: Yu Wenhua , Du Haiwei 
Published: October 2018

AbstractIn this study, we performed correlation analysis of polycomb gene EED and hematologic malignancies using the omics and clinical data of acute myeloid leukemia (LAML) and diffuse large B-Cell lymphoma (DLBC) from TCGA database. We found that: (1) High EED mRNA level was associated with poor prognosis and high CALGB cytogenetics risk of LAML patients. (2) EED mRNA level in DLBC cancer cells was higher than control cells. (3) EED gene expression could be regulated by both copy number alterations and DNA methylation. (4) Additionally, there were different EED co-expression genes nets in the two kinds of hematologic malignancies. In all, we confirmed that there are potential clinical significance of EED gene in pathogenesis and prognosis of hematologic malignancies.