bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macrophage Transplantation Fails to Improve Repair of Critical-Sized Calvarial Defects
Authors: Borrelli Mimi R. , Hu Michael S. , Hong Wan Xing , Oliver Jeremie D. , Duscher Dominik , Longaker Michael T. , Lorenz Hermann Peter 
Published: October 2019

Introduction:
Over 500,000 bone grafting procedures are performed every year in the United States for neoplastic and traumatic lesions of the craniofacial skeleton, costing $585 million in medical care. Current bone grafting procedures are limited, and full-thickness critical-sized defects (CSDs) of the adult human skull thus pose a substantial reconstructive challenge for the craniofacial surgeon. Cell-based strategies have been shown to safely and efficaciously accelerate the rate of bone formation in CSDs in animals. The authors recently demonstrated that supraphysiological transplantation of macrophages seeded in pullalan–collagen composite hydrogels significantly accelerated wound healing in wild type and diabetic mice, an effect mediated in part by enhancing angiogenesis. In this study, the authors investigated the bone healing effects of macrophage transplantation into CSDs of mice.

Methods:
CD1 athymic nude mice (60 days of age) were anesthetized, and unilateral full-thickness critical-sized (4 mm in diameter) cranial defects were created in the right parietal bone, avoiding cranial sutures. Macrophages were isolated from FVB-L2G mice and seeded onto hydroxyapatite-poly (lactic-co-glycolic acid) (HA-PLGA) scaffolds (1.0 × 106 cells per CSD). Scaffolds were incubated for 24 hours before they were placed into the CSDs. Macrophage survival was assessed using three-dimensional in vivo imaging system (3D IVIS)/micro-CT. Micro-CT at 0, 2, 4, 6, and 8 weeks was performed to evaluate gross bone formation, which was quantified using Adobe Photoshop. Microscopic evidence of bone regeneration was assessed at 8 weeks by histology. Bone formation and macrophage survival were compared at each time point using independent samples t tests.

Results:
Transplantation of macrophages at supraphysiological concentration had no effect on the formation of bones in CSDs as assessed by either micro-CT data at any time point analyzed (all P > 0.05). These results were corroborated by histology. 3D IVIS/micro-CT demonstrated survival of macrophages through 8 weeks.

Conclusion:
Supraphysiologic delivery of macrophages to CSDs of mice had no effect on bone formation despite survival of transplanted macrophages through to 8 weeks posttransplantation. Further research into the physiological effects of macrophages on bone regeneration is needed to assess whether recapitulation of these conditions in macrophage-based therapy can promote the healing of large cranial defects.
Outcomes of Surgical Management of Palatal Fistulae in Patients With Repaired Cleft Palate
Authors: Denadai Rafael , Zanco Guilherme Luis , Raposo-Amaral Cesar Augusto , Buzzo Celso Luiz , Raposo-Amaral Cassio Eduardo 
Published: October 2019

Background:
The palatal fistula is an important surgical challenge within the longitudinal follow-up of patients with repaired cleft palate as the success rate of palatal fistula reconstruction by adopting several surgical techniques is variable and often unsatisfactory. The purpose of this retrospective study was to report the clinical outcomes of an algorithm for the surgical management of palatal fistulae in patients with repaired cleft palate.

Methods:
Consecutive patients (n = 101) with repaired cleft palate and palatal fistula-related symptoms who were treated according to a specific algorithm between 2009 and 2017 were included. Based on the anatomical location (Pittsburgh fistula types II–V), amount of scarring (minimal or severe scarred palate), and diameter of the fistula (≤5 mm or >5 mm), 1 of 3 approaches (local flaps [62.4%], buccinator myomucosal flaps [20.8%], or tongue flaps [16.8%]) was performed. For clinical outcome assessment, symptomatic and anatomical parameters (fistula-reported symptoms and residual fistula, respectively) were combined as follows: complete fistula closure with no symptoms; asymptomatic narrow fistula remained; or failure to repair the fistula (“good,” “fair,” or “poor” outcomes, respectively). Surgical-related complication data were also collected.

Results:
Most patients (91.1%) presented “good” clinical outcomes, ranging from 86.2% to 100% (86.2%, 100%, and 100% for local flaps, buccinator flaps, and tongue flaps, respectively). All (8.9%) “fair” and “poor” outcomes were observed in fistulae reconstructed by local flaps. All “poor” (5%) outcomes were observed in borderline fistulae (4–5 mm). No surgical-related complications (dehiscence, infections, or necrosis) were observed, except for an episode of bleeding after the 1st stage of tongue flap-based reconstruction (1.0%).

Conclusion:
A high rate of fistula resolution was achieved using this algorithm for surgical management of palatal fistulae in patients with repaired cleft palate.
An Accurate Volumetric Analysis Method for Evaluating Outcomes of Alveolar Cleft Reconstruction
Authors: Liu Bing , Chen Shu X. , Li Bing H. , Yin Ning B. , Xiao Ran , Wang Yong Q. 
Published: October 2019

Abstract
An accurate volumetric analysis method for evaluating the outcomes of different types of alveolar cleft reconstruction is essential because it can help determine which graft material is more effective, confirm favorable times for alveolar bone grafting, and improve surgical techniques. This study aimed to introduce a novel method of precisely calculating the bone formation ratio using computer-aided engineering after surgery. A patient with a unilateral alveolar cleft who was treated with anterior iliac crest bone grafting was enrolled in this study. Helical computed tomography scans were performed preoperatively and 12 months postoperatively. The Digital Imaging and Communications in Medicine (DICOM) data were reconstructed as three-dimensional images and saved in the STL format by using Mimics software. STL data were processed by Geomagic Wrap 2017, using the Boolean operation, the newly formed bone of the alveolar was segmented by identifying the differences between the preoperative and the postoperative three-dimensional images. For this patient, the mean volume of the newly formed bone was 0.387 cm3, the morphology was clear, the bone formation ratio was 41.4%, the mean time required for calculating the newly formed bone volume was 23 minutes, and the bone survival ratio was 38.7%. This method is a clinically practical, accurately measurement and time-saving method to evaluate the outcome of alveolar cleft reconstruction. Both the volumetric assessment and morphological analysis of the newly formed bone could be determined in a precise manner.
Identification of Stress Fields in a Customized Mandibular Reconstruction Based on a Photoelastic Model
Authors: Moreno-Garibaldi Pablo , Beltrán-Fernández Juan-Alfonso , Yescas-Hernandez Jorge-Arturo , González-Rebattu Mauricio , Carrera-Espinoza Rafael , Hernández-Gómez Luis-Héctor , López-Liévano Daniel-Ramon , Pava-Chipol Nefi-David , Pava-Chipol Joel Francisco , Urriolagoitia-Calderon Guillermo Manuel 
Published: October 2019

AbstractTumors, trauma and infections are the main reasons for subjecting a patient to a bone reconstruction made with the use of bone grafts or prosthetic elements, using for example components such as osteosynthesis plates, meshes and screws for their stabilization.This study focuses on the photoelastic analysis of a customized prosthesis of the jaw for a patient diagnosed with osteonecrosis. A resin model was manufactured as follows: DICOM files were processed in ScanIP software to obtain an STL file that was used to generate an antagonist model of the healthy section of the jaw using CATIA software, then, models were printed in Acrylonitrile Butadiene Styrene (ABS). Following the resin casting technique, the printed model of the jaw was used to construct a resin model, which is tested to determine its mechanical behavior.After carrying out the photoelastic analysis, it was found that the assembly process generates stress concentration zones. Here, the stress reaches a maximum value after the application of a bite force of 130.9 N in the premolars. In this study near the premolars, 3 stress concentration zones were identified and overlap of stress fields is reveled.The results show the importance of planning in the design and assembly process to obtain the best results in the reconstruction, reducing in this way the risk of a surgical reoperation due to problems of rupture or loosening of the prosthesis.
Management of Congenital Melanocytic Nevus on Face Using Multiple Re-expansion Method: Aesthetic and Psychosocial Results
Authors: Lee Hojune , Eom Yeseul , Oh Kap Sung 
Published: October 2019

Background:
Congenital giant melanocytic nevus on the face is a challenging condition, especially in the pediatric population. It can produce significant cosmetic deformity with negative psychosocial effects in pediatric patients even after treatment. The objective of this study was to report aesthetic and psychosocial results in the management of congenital melanocytic nevus on the face using multiple reexpansion.

Methods:
Data of 6 patients with congenital melanocytic nevus on the face who underwent excision and multiple reexpansion at our center from September 2004 to August 2017, were retrospectively reviewed. To evaluate aesthetic outcomes, preoperative and final photographs of each patient were reviewed by 3 other plastic surgeons and 4 laypersons. For comparison, 6 other patients who were treated with conventional surgery during the same period were reviewed. After final reconstruction surgery, the authors surveyed patients’ satisfaction via telephone.

Results:
Six patients were followed up for an average of 87.66 months (range, 55–123 months). The mean number of tissue expander insertions was 3.33 and the mean number of total expanders inserted was 4.83. Complication associated with expander exposure occurred in 1 patient during the fifth expansion. The average score of aesthetic outcome in the multiple reexpansion group was superior to that of the conventional group (2.60 versus 2.10, P = 0.03). During the telephone survey, patients did not rate their appearance as positive, although they were comparatively satisfied with the surgical procedure.

Conclusion:
Considering the low rate of malignancy involving congenital melanocytic nevus in childhood, multiple reexpansion is an attractive option to obtain better results compared with other reconstructive methods.
Applications of artificial intelligence in neuro-oncology
Authors: Aneja Sanjay , Chang Enoch , Omuro Antonio 
Published: October 2019

Purpose of review
To discuss recent applications of artificial intelligence within the field of neuro-oncology and highlight emerging challenges in integrating artificial intelligence within clinical practice.

Recent findings
In the field of image analysis, artificial intelligence has shown promise in aiding clinicians with incorporating an increasing amount of data in genomics, detection, diagnosis, classification, risk stratification, prognosis, and treatment response. Artificial intelligence has also been applied in epigenetics, pathology, and natural language processing.

Summary
Although nascent, applications of artificial intelligence within neuro-oncology show significant promise. Artificial intelligence algorithms will likely improve our understanding of brain tumors and help drive future innovations in neuro-oncology.
HRT Atlas v1.1 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets
Authors: Hounkpe Bidossessi Wilfried , Chenou Francine , Lima Franciele , de Paula Erich Vinicius 
Published: October 2019

AbstractHousekeeping (HK) genes are constitutively expressed genes that are required for the maintenance of basic cellular functions. Despite their importance in the calibration of gene expression, as well as the understanding of many genomic and evolutionary features, important discrepancies have been observed in studies that previously identified these genes. Here, we present Housekeeping Transcript Atlas (HRT Atlas v1.0, www.housekeeping.unicamp.br) a web-based database which addresses some of the previously observed limitations in the identification of these genes, and offers a more accurate database of human and mouse HK genes and transcripts. The database was generated by mining massive human and mouse RNA-seq data sets, including 12,482 and 507 high-quality RNA-seq samples from 82 human non-disease tissues/cells and 15 healthy tissues/cells of C57BL/6 wild type mouse, respectively. User can visualize the expression and download lists of 2,158 human HK transcripts from 2,176 HK genes and 3,024 mouse HK transcripts from 3,277 mouse HK genes. HRT Atlas also offers the most stable and suitable tissue selective candidate reference transcripts for normalization of qPCR experiments. Specific primers and predicted modifiers of gene expression for some of these HK transcripts are also proposed. HRT Atlas has also been integrated with regulatory elements from Epiregio server. All of these resources can be accessed and downloaded from any computer or small device web browsers.
Cell segmentation-free inference of cell types fromin situtranscriptomics data
Authors: Park Jeongbin , Choi Wonyl , Tiesmeyer Sebastian , Long Brian , Borm Lars E. , Garren Emma , Nguyen Thuc Nghi , Tasic Bosiljka , Codeluppi Simone , Graf Tobias , Schlesner Matthias , Stegle Oliver , Eils Roland , Ishaque Naveed 
Published: October 2019

AbstractMultiplexed fluorescencein situhybridization techniques have enabled cell-type identification, linking transcriptional heterogeneity with spatial heterogeneity of cells. However, inaccurate cell segmentation reduces the efficacy of cell-type identification and tissue characterization. Here, we present a novel method called Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation (SSAM), a robust cell segmentation-free computational framework for identifying cell-types and tissue domains in 2D and 3D. SSAM is applicable to a variety ofin situtranscriptomics techniques and capable of integrating prior knowledge of cell types. We apply SSAM to three mouse brain tissue images: the somatosensory cortex imaged by osmFISH, the hypothalamic preoptic region by MERFISH, and the visual cortex by multiplexed smFISH. We found that SSAM detects regions occupied by known cell types that were previously missed and discovers new cell types.
The transcriptional landscape of the murine middle ear epithelium in vitro
Authors: Mulay Apoorva , Chowdhury Md Miraj K , James Cameron , Bingle Lynne , Bingle Colin D 
Published: October 2019

AbstractOtitis media (OM) is the most common paediatric disease and leads to significant morbidity. Although understanding of underlying disease mechanisms is hampered by complex pathophysiology, it is clear that epithelial abnormalities underpin the disease. The mechanisms underpinning epithelial remodelling in OM remain unclear. We recently described a novel in vitro model of mouse middle ear epithelial cells (mMEECs) that undergoes mucociliary differentiation into the varied epithelial cell populations seen in the middle ear cavity. We now describe genome wide gene expression profiles of mMEECs as they undergo differentiation. We compared the gene expression profiles of original (uncultured) middle ear cells, confluent cultures of undifferentiated cells (day 0 of ALI) and cells that had been differentiated for 7 days at an ALI. >5000 genes were differentially expressed among the three groups of cells. Approximately 4000 genes were differentially expressed between the original cells and day 0 of ALI culture. The original cell population was shown to contain a mix of cell types, including contaminating inflammatory cells that were lost on culture. Approximately 500 genes were upregulated during ALI induced differentiation. These included some secretory genes and some enzymes but most were associated with the process of ciliogenesis. Our in vitro model of differentiated murine middle ear epithelium exhibits a transcriptional profile consistent with the mucociliary epithelium seen within the middle ear. Knowledge of the transcriptional landscape of this epithelium will provide a basis for understanding the phenotypic changes seen in murine models of OM.
Sequential and efficient neural-population coding of complex task information
Authors: Koay Sue Ann , Charles Adam S. , Thiberge Stephan Y. , Brody Carlos D. , Tank David W. 
Published: October 2019

SummaryRecent work has highlighted that many types of variables are represented in each neocortical area. How can these many neural representations be organized together without interference, and coherently maintained/updated through time? We recorded from large neural populations in posterior cortices as mice performed a complex, dynamic task involving multiple interrelated variables. The neural encoding implied that correlated task variables were represented by uncorrelated neural-population modes, while pairs of neurons exhibited a variety of signal correlations. This finding relates to principles of efficient coding for task-specific information, with neural-population modes as the encoding unit, and applied across posterior cortical regions and layers 2/3 and 5. Remarkably, this encoding function was multiplexed with sequential neural dynamics as well as reliably followed changes in task-variable correlations through time. We suggest that neural circuits can implement time-dependent encoding in a simple way by using random sequential dynamics as a temporal scaffold.
Neuro-Computational Foundations of Moral Preferences
Authors: Ugazio Giuseppe , Grueschow Marcus , Polania Rafael , Lamm Claus , Tobler Philippe N. , Ruff Christian C. 
Published: October 2019

AbstractMoral preferences pervade many aspects of our lives, dictating how we ought to behave, whom we can marry, and even what we eat. Despite their relevance, one fundamental question remains unanswered: Where do individual moral preferences come from? It is often thought that all types of preferences reflect properties of domain-general neural decision mechanisms that employ a common “neural currency” to value choice options in many different contexts. This assumption, however, appears at odds with the observation that many humans consider it intuitively wrong to employ the same scale to compare moral value (e.g., of a human life) with material value (e.g., of money). In this paper, we directly challenge the common-currency hypothesis by comparing the neural mechanisms that represent moral and financial subjective values. In a study combining fMRI with a novel behavioral paradigm, we identify neural representations of the subjective values of human lives or financial payoffs by means of structurally identical computational models. Correlating isomorphic model variables from both domains with brain activity reveals specific patterns of neural activity that selectively represent values in the moral (in the rTPJ) or financial (in the vmPFC) domain. Thus, our findings show that human lives and money are valued in distinct neural currencies, supporting theoretical proposals that human moral behavior is guided by processes that are distinct from those underlying behavior driven by personal material benefit.
Characterisation of an inflammation-related epigenetic score and its association with cognitive ability
Authors: Stevenson Anna J. , McCartney Daniel L. , Hillary Robert F. , Campbell Archie , Morris Stewart W. , Bermingham Mairead L. , Walker Rosie M. , Evans Kathryn L. , Boutin Thibaud S. , Hayward Caroline , McRae Allan F. , McColl Barry W. , Spires-Jones Tara L. , McIntosh Andrew M. , Deary Ian J. , Marioni Riccardo E. 
Published: October 2019

ABSTRACTResults from large cohort studies investigating the association between inflammation and cognition have been mixed, possibly due to methodological disparities. However, a key issue in research utilising inflammatory biomarkers is their typically phasic responses. C-reactive protein (CRP) is widely used to investigate the association between chronic inflammation and cognition, but its plasma concentrations can markedly deviate in response to acute infection. Recently a large-scale epigenome-wide association study identified DNA methylation correlates of CRP. DNA methylation is thought to be relatively stable in the short term, marking it as a potentially useful signature of exposure. Here, we generate an epigenetic CRP score and investigate its trajectories with age, and associations with cognitive ability, in comparison to serum CRP in two cohorts: a longitudinal study of older adults (the Lothian Birth Cohort 1936, n=889) and a large, cross-sectional cohort (Generation Scotland, n=7,028).We identified differing trajectories of serum CRP across the cohorts, with no homogeneous trends seen with age. Conversely, the epigenetic score was consistently found to increase with age, and to do so more rapidly in males compared to females. Higher levels of serum CRP were found to associate with poorer cognition in Lothian Birth Cohort 1936, but not in Generation Scotland. However, a consistent negative association was identified between cognition and the epigenetic score in both cohorts. Furthermore, the epigenetic score accounted for a greater proportion of variance in cognitive ability.Our results suggest that epigenetic signatures of acute inflammatory markers may provide an enhanced signature of chronic inflammation, allowing for more reliable stratification of individuals, and thus clearer inference of associations with incident health outcomes.
Impact of higher-order network structure on emergent cortical activity
Authors: Nolte Max , Gal Eyal , Markram Henry , Reimann Michael W. 
Published: October 2019

ABSTRACTSynaptic connectivity between neocortical neurons is highly structured. The network structure of synaptic connectivity includes first-order properties that can be described by pairwise statistics, such as strengths of connections between different neuron types and distance-dependent connectivity, and higher-order properties, such as an abundance of cliques of all-to-all connected neurons. The relative impact of first- and higher-order structure on emergent cortical network activity is unknown. Here, we compare network structure and emergent activity in two neocortical microcircuit models with different synaptic connectivity. Both models have a similar first-order structure, but only one model includes higher-order structure arising from morphological diversity within neuronal types. We find that such morphological diversity leads to more heterogeneous degree distributions, increases the number of cliques, and contributes to a small-world topology. The increase in higher-order network structure is accompanied by more nuanced changes in neuronal firing patterns, such as an increased dependence of pairwise correlations on the positions of neurons in cliques. Our study shows that circuit models with very similar first-order structure of synaptic connectivity can have a drastically different higher-order network structure, and suggests that the higher-order structure imposed by morphological diversity within neuronal types has an impact on emergent cortical activity.