bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-Dimensional Bioprinting: Role in Craniomaxillary Surgery Ethics and Future
Authors: Gupta Nimish , Agarwal Shreya 
Published: May 2020

Abstract
Three-dimensional (3D) printing and bioprinting is gaining lot of momentum, especially in surgical specialties. These two technologies have wide array of applications in presurgical, surgical, and in vitro scenarios. Bioprinting can generate customized patient specific tissue engineered from specialized cells. This technology can be a gold standard in reconstructive and regenerative surgeries, if used in regulated and ethical environment. This communication focuses on basics of these technologies, their role in surgical specialties, ethical issues specific to these technologies, and its future.
Facial Reconstruction Based on Combined Three-Dimensional Printing and Microsurgical Free Transfer
Authors: Horta Ricardo , Frias Francisca , Jarnalo Mariana , Teixeira Sergio , Silva Pedro , Oliveira Isabel , Silva Alvaro 
Published: May 2020

Abstract
There are patients with craniofacial deformity that can lead to extensive bone loss and severe disfigurement. Autologous reconstruction may be challenging in these patients, and it is usually associated with flap donor area morbidity and unfavorable aesthetic and functional results. A 51-year-old patient with human immunodeficiency virus infection, developed in the context of immunosuppression a fulminant fungal rhino-sinusitis with the need for surgical debridement, and in consequence extensive destruction of the nasal cavity and upper jaw, resulting in severe disfigurement due to nasal deformity and maxillary collapse. Human immunodeficiency virus disease was controlled and the complex craniofacial defect was posteriorly reconstructed with direct 3-dimensional (3D) printing combined with microsurgical free tissue transfer. The 3D facial implant, in titanium, was individualized and fabricated based on computed tomography images of the patient. A radial forearm free flap was used since a soft-tissue defect was anticipated after scar release and implant placement. It allowed simultaneous coverage of the palate, the anterior surface of maxilla and intranasal lining. The flap survived despite flap venous congestion in the postoperative period probably facilitated because of the complex 3D flap configuration and pedicle tunneling into the neck. After 9 months, the patient showed a tremendous aesthetic and functional improvement. The 3D printing was useful in our patient with craniofacial reconstruction. Its combination with free tissue transfer may improve the surgeon's armamentarium when dealing with complex patients.
Improvised Explosive Device Blast Injuries to the Craniofacial Region: Wound Characteristics and Management
Authors: Arya Saurabh , Jose Anson , Rawat Aditi 
Published: May 2020

Abstract
Improvised explosive device blast injuries frequently report at our center and showed the maximum amount of contamination and damage, both in the facial soft tissues and the skeletal tissues with impregnation of splinters with size ranging from 2 mm to 10 mm. Should splinters be always explored is questionable and varies with every case. The reconstruction in such cases was done with titanium mini-plates along with extensive use of local vascular flaps for soft tissue repair in majority of the cases. Soldier who sustained splinter injuries wrt orbital floor were managed with splinter exploration using C-arm and orbital floor reconstruction using titanium mesh.
Tenosynovial Giant Cell Tumor in an Infant
Authors: Shahriari Shawhin , Ederle Ashley , Botros James , Elwood Hillary , Shetty Anil 
Published: May 2020

Abstract
In this report, the authors describe a child presenting at 6 months old with a rapidly expanding extracranial left temporal mass concerning for malignancy. The mass was successfully treated at 16 months with radical surgical excision. The patient was found to have a tenosynovial giant cell tumor, diffuse type, completely encased by the temporalis muscle. To our knowledge, this is the first report of a case of diffuse type tenosynovial giant cell tumor in the temporalis muscle, without articular involvement, presenting in an infant.
Nasopharynx Hairy Polyp as a Cause of Stridor in Newborn
Authors: Freni Francesco , Nicastro Viviana , Costanzo Daria , Zagaria Annamaria , Galletti Bruno 
Published: May 2020

Abstract
Hairy polyps are histological benign lesions derived from 2 germinal layers which arise during fetal period, they can occur anywhere in the body. When they are localized in the oropharynx or nasopharynx can lead to upper airway obstruction in infants.
We describe a case of a 2-days-old full-term female with intermittent upper airway obstruction, stridor, and feeding difficulty. Endoscopic and radiologic exams show a mass localized in nasopharynx, which was excised with a transnasal endoscopic approach resolving her respiratory difficulties.
Histology confirmed the diagnosis of hairy polyp, a mass composed by an external layer of mature skin and a core with subcutaneous mature fibro fatty tissue, mature skeletal muscle, and cartilage.
This report has an important value for the readers because, for a good functional result and an excellent prognosis, an accurate clinic and radiologic diagnose, with subsequent surgical complete resection should be performed.
Repairing Cranial Defect With Autogenous Mandibular Outer Plate
Authors: Xu Shixing , Niu Feng , Chen Ying , Jin Qi , Gui Lai 
Published: May 2020

Background:
Autogenous bone is the best material in cranioplasty because of biological advantages. Previously, skull, rib, ilium, and fibula have been used in the reconstruction of cranial defects. However, the application of autologous mandibular outer plate in the treatment of skull defect is rarely reported. This study evaluated the application of the autogenous mandibular outer plate in the reconstruction of cranial defect.

Methods:
Eleven patients who underwent cranioplasty with mandibular outer plate were recruited. Three-dimensional tomography data were collected to calculate the preoperative, immediate postoperative, and long-term follow-up volume of the bone graft area and donor bone site, and then the absorption rate and the regeneration rate of autogenous bone were analyzed.

Results:
The majority of the patients were satisfied with the reconstructive outcome. There are statistical differences in the volumetric measurements of the bone graft area and bone donor site at different time periods (P<0.05). The mean absorptivity of mandibular outer plate implanted in the cranial defect area was (17.30 ± 5.03)% after 3 to 24 months postoperatively, the average regeneration rate of mandibular outer plate volume was (41.65 ± 9.85)% at the same period.

Conclusion:
This report shows that the cranioplasty with mandibular outer plate bone graft may be an optional surgical procedure.
COVID-19 Pandemic and Otologic Surgery
Authors: Cetinkaya Erdem Atalay 
Published: May 2020

Abstract
All around world, the COVID-19 pandemic is accelerating, and any insight we can learn from our colleagues who have either encountered or are currently going through this will be used to protect our patients, our medical staff, and ourselves. No one knows to the best of our understanding whether or not COVID-19 includes the respiratory mucosal lining the middle ear and mastoid air cell system-but it seems probable they do. Since the rest of the airways are affected, and so is the nose and nasopharynx, it seems possible that the lining of the Eustachian tube, middle ear and mastoid air cell system would all be polluted. Viral particle aerosolization, which can occur otologic surgery using powered instruments and they remain in the air for at least 3 hours. Powered air purifying respirators are supplied even shorter than N95 masks, but strongly believed they are important for our team safety and protection. This mini review provides fundamental knowledge on otologic surgery feasibility in the COVID-19 pandemic from an objective perspective.
naturaList: a package to classify occurrence records in levels of confidence in species identification
Authors: Rodrigues Arthur Vinicius , Nakamura Gabriel , Duarte Leandro 
Published: May 2020

AbstractThere is a big volume of occurrence records available in biodiversity databases, but researchers should guarantee its quality before use it in scientific studies. A problem that might compromise the quality of occurrence data is species misidentification. We address this issue by presentingnaturaList, a R package designed to classify species occurrence data according to identification reliability.naturaListallows to classify species occurrences up to six levels of confidence in species identification, and to filter occurrence data accordingly. The highest level of confidence is assigned to records identified by a specialist, whose name must be provided by the user. The other five levels of confidence are derived from the occurrence data. We demonstratenaturaListfunctions using occurrences ofAlsophila setosa, a tree fern species from Atlantic Forest, as example. We classified and filtered data in grid cells in order to maintain only the highest-level records in each cell. Then we selected only those records classified in the two highest levels of confidence.From 323 occurrences ofAlsophila setosadisplaying geographic coordinates, 69 (21%) were identified by a specialist. After filtering the highest-level records inside grid cells, 102 records remained. From these grid cell filtered data, 38 occurrences (37%) were classified into the highest confidence level. Three records were removed using an interactive map module, due to falling in sea sites or outside the native range size of the species. Since we selected only records classified in the two highest levels of confidence, the final dataset contained 94 occurrence records.naturaListguarantees the reproducibility of occurrence data processing and cleaning. Macroecologists, biogeographers and taxonomists might benefit from usingnaturaListpackage to evaluate the quality of species identification in occurrence data and by identify sites that need evaluation of taxonomic classification of species.
Hippocampal theta oscillations support successful associative memory formation
Authors: Kota Srinivas , Rugg Michael D. , Lega Bradley C. 
Published: May 2020

1.AbstractModels of memory formation posit that recollection as compared to familiarity-based memory depends critically on the hippocampus, which binds features of an event to its context. For this reason, the contrast between study items that are later recollected versus those that are recognized on the basis of familiarity should reveal electrophysiological patterns in the hippocampus selectively involved in associative memory encoding. Extensive data from studies in rodents support a model in which theta oscillations fulfill this role, but results in humans results have not been as clear. Here, we employed an associative recognition memory procedure to identify hippocampal correlates of successful associative memory encoding and retrieval in patients undergoing intracranial EEG monitoring. We identified a dissociation between 2– 5 Hz and 5–9 Hz theta oscillations, by which 2–5 Hz oscillations uniquely were linked with successful associative memory in both the anterior and posterior hippocampus. These oscillations exhibited a significant phase reset that also predicted successful associative encoding, distinguished recollected from familiar items at retrieval, and contributed to reinstatement of encoding-related patterns that distinguished these items. Our results provide direct electrophysiological evidence that 2–5 Hz hippocampal theta oscillations support the encoding and retrieval of memories based on recollection but not familiarity.2.Significance StatementExtensive fMRI evidence suggests that the hippocampus plays a selective role in recollection rather than familiarity, during both encoding and retrieval. However, there is little or no electrophysiological evidence that speaks to whether the hippocampus is selectively involved in recollection. Here, we used intracranial EEG from human participants engaged in an associative recognition paradigm. The findings suggest that oscillatory power and phase reset in the hippocampus are selectively associated with recollection rather than familiarity-based memory judgements. Furthermore, reinstatement of oscillatory patterns in the hippocampus was stronger for successful recollection than familiarity. Collectively, the findings support a role for hippocampal theta oscillations in human episodic memory.
Evaluating single-cell cluster stability using the Jaccard similarity index
Authors: Tang Ming , Kaymaz Yasin , Logeman Brandon , Eichhorn Stephen , Liang ZhengZheng S. , Dulac Catherine , Sackton Timothy B. 
Published: May 2020

AbstractMotivationOne major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor, and the resolution parameters, among others.ResultsHere, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat, and estimation of cluster stability using the Jaccard similarity index. The Snakemake workflow takes advantage of high-performance computing clusters and dispatches jobs in parallel to available CPUs to speed up the analysis. The scclusteval package provides functions to facilitate the analysis of the output, including a series of rich visualizations.AvailabilityR package scclusteval:https://github.com/crazyhottommy/scclustevalSnakemake workflow:https://github.com/crazyhottommy/pyflow_seuratv3_parameterContacttsackton@g.harvard.edu,tangming2005@gmail.comSupplementary informationSupplementary data are available atBioinformaticsonline.
The timing and impact of psychiatric, cognitive and motor abnormalities in Huntington’s disease
Authors: McAllister Branduff , Gusella James F. , Landwehrmeyer G. Bernhard , Lee Jong-Min , MacDonald Marcy E. , Orth Michael , Rosser Anne E. , Williams Nigel M. , Holmans Peter , Jones Lesley , Massey Thomas H. 
Published: May 2020

AbstractObjectiveTo assess the prevalence, timing and functional impact of psychiatric, cognitive and motor abnormalities in Huntington’s disease (HD) gene carriers, we analysed retrospective clinical data from individuals with manifest HD.MethodsClinical features of HD patients were analysed for 6316 individuals in the European REGISTRY study from 161 sites across 17 countries. Data came from clinical history and the patient-completed Clinical Characteristics Questionnaire that assessed eight symptoms: motor, cognitive, apathy, depression, perseverative/obsessive behavior, irritability, violent/aggressive behavior, and psychosis. Multiple logistic regression was used to analyse relationships between symptoms and functional outcomes.ResultsThe initial manifestation of HD is increasingly likely to be motor, and less likely to be psychiatric, as age at presentation increases, and is independent of pathogenic CAG repeat length. The Clinical Characteristics Questionnaire captures data on non-motor symptom prevalence that correlate specifically with validated clinical measures. Psychiatric and cognitive symptoms are common in HD gene carriers, with earlier onsets associated with longer CAG repeats. 42.4% of HD patients reported at least one psychiatric or cognitive symptom before motor symptoms, with depression most common. Each non-motor symptom was associated with significantly reduced total functional capacity scores.ConclusionsPsychiatric and cognitive symptoms are common and functionally debilitating in HD gene carriers. They require recognition and targeting with clinical outcome measures and treatments. However, as it is impossible to distinguish confidently between non-motor symptoms arising from HD and primary psychiatric disorders, particularly in younger pre-manifest patients, non-motor symptoms should not be used to make a clinical diagnosis of HD.
A Deep Feature Learning Approach for Mapping the Brain’s Microarchitecture and Organization
Authors: Balwani Aishwarya H. , Dyer Eva L. 
Published: May 2020

AbstractModels of neural architecture and organization are critical for the study of disease, aging, and development. Unfortunately, automating the process of building maps of microarchitectural differences both within and across brains still remains a challenge. In this paper, we present a way to build data-driven representations of brain structure using deep learning. With this model we can build meaningful representations of brain structure within an area, learn how different areas are related to one another anatomically, and use this model to discover new regions of interest within a sample that share similar characteristics in terms of their anatomical composition. We start by training a deep convolutional neural network to predict the brain area that it is in, using only small snapshots of its immediate surroundings. By requiring that the network learn to discriminate brain areas from these local views, it learns a rich representation of the underlying anatomical features that allow it to distinguish different brain areas. Once we have the trained network, we open up the black box, extract features from its last hidden layer, and then factorize them. After forming a low-dimensional factorization of the network’s representations, we find that the learned factors and their embeddings can be used to further resolve biologically meaningful subdivisions within brain regions (e.g., laminar divisions and barrels in somatosensory cortex). These findings speak to the potential use of neural networks to learn meaningful features for modeling neural architecture, and discovering new patterns in brain anatomy directly from images.
Metabolic scaling has diversified among species, despite an evolutionary constraint within species
Authors: Beaman Julian E. , Ortiz-Barrientos Daniel , Monro Keyne , Hall Matthew D. , White Craig R. 
Published: May 2020

AbstractMetabolic rate scales disproportionally with body mass, such that the energetic cost of living is relatively lower in larger organisms. Theory emphasises the importance of fixed physical constraints on metabolic scaling, yet empirical data are lacking with which to assess how evolutionary processes (e.g. mutation, drift, selection) contribute to the observed variation in metabolic scaling across the tree of life. Using a large-scale quantitative genetic study of growth in cockroaches, we show that ontogenetic metabolic scaling is evolutionarily constrained due to an absence of additive genetic variation in juvenile metabolic rate and mass. Using a phylogenetic analysis, we also show that ontogenetic metabolic scaling is more similar among closely related species than among distant relatives, suggesting that the constraints on metabolic scaling are subject to change during lineage diversification. Our results are consistent with growing evidence that there is strong stabilising selection on combinations of mass and metabolic rate within species.
Language impairment with a microduplication in 1q42.3q43
Authors: Benítez-Burraco Antonio , Fernández-Urquiza Maite , Jiménez-Romero Mª Salud 
Published: May 2020

ABSTRACTDeletions and duplications of the distal region of the long arm of chromosome 1 are associated with brain abnormalities and developmental delay. Because duplications are less frequent than deletions, no detailed account of the cognitive profile of the affected people is available, particularly, regarding their language (dis)abilities. In this paper we report on the cognitive and language features of a girl with one of the smallest interstitial duplications ever described in this region, affecting to 1q42.3q43 (arr[hg19] 1q42.3q43(235,963,632-236,972,276)x3). Standardized tests as well as the analysis of her language use in natural settings suggest that the proband’s speech is severely impaired, exhibiting dysarthric-like features, with speech problems also resulting from a phonological deficit boiling down to a verbal auditory memory deficit. Lexical and grammatical knowledge are also impaired, impacting negatively on both expressive and receptive abilities, seemingly as a consequence of the phonological deficit. Still, her pragmatic abilities seem to be significantly spared, granting her a good command on the principles governing conversational exchanges. In silico analyses (literature mining, network analysis) and in vitro analyses (microarray) point to several genes as potential candidates for the observed deficits in the language domain. These include one gene within the duplicated region (LYST), one predicted functional partner (CMIP), and three genes outside the 1q42.3q43 region, which are all highly expressed in the cerebellum:DDIT4andSLC29A1, found strongly downregulated in the proband compared to their healthy parents, andCNTNAP3, found strongly upregulated.
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability
Authors: Salifou Kader , Burnard Callum , Basavarajaiah Poornima , Helsmoortel Marion , Mac Victor , Depierre David , Grasso Giuseppa , Franckhauser Céline , Beyne Emmanuelle , Contreras Xavier , Dejardin Jérôme , Rouquier Sylvie , Cuvier Olivier , Kiernan Rosemary 
Published: May 2020

AbstractThe MRN-MDC1 complex plays a central role in the DNA damage response (DDR) and repair. Using Proteomics of Isolated Chromatin Fragments (PICh), we identified DDR factors, such as MDC1, among those that become highly associated with a genomic locus upon transcriptional activation. Purification of endogenous MDC1, in the absence of exogenous DNA damage, revealed its interaction with factors involved in gene expression and co-transcriptional RNA processing, in addition to DDR factors. ChIP-seq analysis showed that MDC1 interacting factors, MRE11 and NBS1 subunits of MRN, were co-localized throughout the genome and notably at TSSs and gene bodies of actively transcribing genes. Blockade of transcriptional elongation showed that binding of MRN was dependent on the RNAPII transcriptional complex rather than transcriptionper se. Depletion of MRN increased RNAPII abundance at TSSs and gene bodies of MRE11/NBS1-bound genes. Prolonged exposure of cells to either MRE11- or NBS1-depletion led to single nucleotide polymorphism formation across actively transcribing, MRE11 or NBS1 target genes. These data support a model by which association of the MRN complex with the transcriptional machinery constitutively scans active genes for transcription-induced DNA damage to preserve the integrity of the coding genome.