bluuebunny/crossref_metadata_2025_split huggingface dataset:
Full Facial Allotransplantation Including the Temporomandibular Joints: A Radiologic and Anatomical Cadaveric Study
Authors: Nunez-Villaveiran Teresa , Fahradyan Vahe , Dalla Pozza Edoardo , Rezaei Majid , Drake Richard L. , Jellema Lyman M. , García-de-Lorenzo Abelardo , Papay Frank A. , Bassiri Gharb Bahar , Rampazzo Antonio 
Published: May 2020

Background:
Facial allotransplantation including the temporomandibular joints may improve the functional outcomes in face transplant candidates who have lost or damaged this joint.

Methods:
Linear and angular measurements were taken in 100 dry skulls and mandibles and in 100 three-dimensionally–reconstructed facial computed tomographic scans to determine the variability of the temporomandibular joint, glenoid fossa, and mandible. A vascular study was performed in six fresh cadaveric heads, followed by harvest of the face allograft in three heads. Next, four heads were used for mock transplantation (two donors and two recipients). The full facial allograft included four different segments: a Le Fort III, a mandibular tooth-bearing, and two condyle and temporomandibular joint–bearing segments. Statistical analysis was performed using SAS software.

Results:
In only one-third of the skulls, the condylar shape was symmetric between right and left sides. There was a wide variability in the condylar coronal (range, 14.3 to 23.62 mm) and sagittal dimensions (range, 5.64 to 10.96 mm), medial intercondylar distance (range, 66.55 to 89.91 mm), and intercondylar angles (range, 85.27 to 166.94 degrees). This high variability persisted after stratification by sex, ethnicity, and age. The temporomandibular joint was harvested based on the branches of the superficial temporal and maxillary arteries. The design of the allograft allowed fixation of the two condyle and temporomandibular joint–bearing segments to the recipient skull base, preserving the articular disk-condyle-fossa relationship, and differences were adjusted at the bilateral sagittal split osteotomy sites.

Conclusion:
Procurement and transplantation of a temporomandibular joint–containing total face allograft is technically feasible in a cadaveric model.
Quality and Safety in Health Care, Part LXXI
Authors: Harolds Jay A. 
Published: May 2020

Abstract
Peer review can be utilized to increase the quality of care for patients by upgrading the performance of all the providers by identifying learning opportunities. Peer review can identify providers whose care is below the standard of care and recommend actions to correct the situation. Peer review is also important to satisfy requirements of the government and The Joint Commission. Ongoing professional practice evaluation and focused professional practice evaluation have been required since 2008 to help insure that providers are rendering excellent care, and the results of these evaluation procedures are also utilized in privileging decisions.
Food and Drug Administration Safety Communication on the Use of Transvaginal Mesh in Pelvic Organ Prolapse Repair Surgery: The Impact of Social Determinants of Health
Authors: Mao Jialin , Chughtai Bilal , Ibrahim Said , Sedrakyan Art 
Published: May 2020

Objective
This study was to examine the impact of the July 2011 Food and Drug Administration (FDA) safety communication on the use of transvaginal mesh in pelvic organ prolapse (POP) repair by patients’ race and ethnicity.

Methods
We conducted an observational cohort study of women undergoing POP repairs in 2008 to 2015 in New York State. We examined the changes in transvaginal mesh use in POP repairs before and after the FDA communication by patients’ race and ethnicity. Piecewise logistic regression models were used to assess the trends of mesh use, adjusting for patient characteristics. We performed a subgroup analysis of the trends of transvaginal mesh use by racial groups, stratifying by patients’ neighborhood socioeconomic status.

Results
We included 49,848 women (78% white, 7% black, and 15% Hispanic) with an average ± SD age of 60.2 ± 13.0 years. After the safety communication, the use of transvaginal mesh in POP repairs decreased among white women (odds ratio [OR], 0.45; 95% confidence interval [CI], 0.41–0.50) and African Americans (OR, 0.48; 95% CI, 0.35–0.67) but remained stable among Hispanic women (OR, 0.88; 95% CI, 0.70–1.11). Only in the subgroup of patients from high-income areas, there was a trend toward decreasing mesh use among Hispanic patients after 2011 (OR, 0.71; 95% CI, 0.49–1.04).

Conclusions
The communications related to the safety of transvaginal mesh did not have an equal impact across racial groups. Mesh use decreased among white and African American women but not among Hispanic women after the 2011 FDA safety communication. Particular attention is warranted for patients from disadvantaged groups, especially low-income minorities, when disseminating medical device safety messages.
A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways
Authors: Lorenzo-Redondo Ramon , Nam Hannah H. , Roberts Scott C. , Simons Lacy M. , Jennings Lawrence J. , Qi Chao , Achenbach Chad J. , Hauser Alan R. , Ison Michael G. , Hultquist Judd F. , Ozer Egon A. 
Published: May 2020

ABSTRACTBackgroundThe rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID- 19), has been accompanied by the emergence of distinct viral clades, though their clinical significance remains unclear. Here, we aimed to investigate the phylogenetic characteristics of SARS-CoV-2 infections in Chicago, Illinois and assess their relationship to clinical parameters.MethodsWe performed whole-genome sequencing of SARS-CoV-2 isolates collected from COVID-19 patients in a Chicago healthcare system in mid-March, 2020. Using these and other publicly available sequences, we performed phylogenetic, phylogeographic, and phylodynamic analyses. Patient data was assessed for correlations between demographic or clinical characteristics and virologic features.FindingsThe 88 SARS-CoV-2 genome sequences in our study separated into three distinct phylogenetic clades. Clade 1 was most closely related to viral sequences from New York, and showed evidence of rapid expansion across the US, while Clade 3 was most closely related to those in Washington state. Clade 2 was localized primarily to the Chicago area with limited evidence of expansion elsewhere. At the time of diagnosis, patients infected with Clade 1 viruses had significantly higher average viral loads in their upper airways relative to patients infected with Clade 2 viruses, independent of time to symptom onset and disease severity.InterpretationThese results show that multiple variants of SARS-CoV-2 are circulating in the Chicago area that differ in their relative viral loads in patient upper airways. These data suggest that differences in virus genotype impact viral load and may in turn influence viral transmission and spread.FundingDixon Family Translational Research Award, Northwestern University Clinical and Translational Sciences Institute (NUCATS), National Institute of Allergy and Infectious Diseases (NIAID)
Determinants of cardiac adverse events of chloroquine and hydroxychloroquine in 20 years of drug safety surveillance reports
Authors: Cohen Isaac V. , Makunts Tigran , Moumedjian Talar , Issa Masara , Abagyan Ruben 
Published: May 2020

AbstractChloroquine (CQ) and hydroxychloroquine (HCQ) are on the World Health Organization’s List of Essential Medications for treating non-resistant malaria, rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). In addition, both drugs are currently used off-label in hospitals worldwide and in numerous clinical trials for the treatment of SARS-CoV-2 infection. However, CQ and HCQ use has been associated with cardiac side effects, which is of concern due to the higher risk of COVID-19 complications in patients with heart related disorders, and increased mortality associated with COVID-19 cardiac complications. In this study we analyzed over thirteen million adverse event reports form the United States Food and Drug Administration Adverse Event Reporting System to confirm and quantify the association of cardiac side effects of CQ and HCQ. Additionally, we identified several confounding factors, including male sex, NSAID coadministration, advanced age, and prior diagnoses contributing to the risk of drug related cardiotoxicity. These findings may help guide therapeutic decision making and ethical trial design for COVID-19 treatment.
SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi Associated Microorganisms
Authors: Kang Jee Eun , Ciampi Antonio , Hijri Mohamed 
Published: May 2020

AbstractArbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface and inside their mycelia, resulting in a metagenome when whole genome sequencing (WGS) data are obtained from sequencing AMF cultivatedin vivo.The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this article, we introduce a novel bioinformatics program, SeSaMe, designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of three consecutive codon DNA 9-mers encoding for an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The average correct prediction percentages of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 65% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. The program provides a means for estimating not only taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, the program enables users to study the symbiotic roles of associated microorganisms. SeSaMe can be applicable to other microorganisms as well as soil metagenomes. It is freely available atwww.journal.comandwww.fungalsesame.org.
Automated assessment of COVID-19 pulmonary disease severity on chest radiographs using convolutional Siamese neural networks
Authors: Li Matthew D. , Arun Nishanth Thumbavanam , Gidwani Mishka , Chang Ken , Deng Francis , Little Brent P. , Mendoza Dexter P. , Lang Min , Lee Susanna I. , O’Shea Aileen , Parakh Anushri , Singh Praveer , Kalpathy-Cramer Jayashree 
Published: May 2020

ABSTRACTPurposeTo develop an automated measure of COVID-19 pulmonary disease severity on chest radiographs (CXRs), for longitudinal disease evaluation and clinical risk stratification.Materials and MethodsA convolutional Siamese neural network-based algorithm was trained to output a measure of pulmonary disease severity on anterior-posterior CXRs (pulmonary x-ray severity (PXS) score), using weakly-supervised pretraining on ~160,000 images from CheXpert and transfer learning on 314 CXRs from patients with COVID-19. The algorithm was evaluated on internal and external test sets from different hospitals, containing 154 and 113 CXRs respectively. The PXS score was correlated with a radiographic severity score independently assigned by two thoracic radiologists and one in-training radiologist. For 92 internal test set patients with follow-up CXRs, the change in PXS score was compared to radiologist assessments of change. The association between PXS score and subsequent intubation or death was assessed.ResultsThe PXS score correlated with the radiographic pulmonary disease severity score assigned to CXRs in the COVID-19 internal and external test sets (ρ=0.84 and ρ=0.78 respectively). The direction of change in PXS score in follow-up CXRs agreed with radiologist assessment (ρ=0.74). In patients not intubated on the admission CXR, the PXS score predicted subsequent intubation or death within three days of hospital admission (area under the receiver operator characteristic curve=0.80 (95%CI 0.75-0.85)).ConclusionA Siamese neural network-based severity score automatically measures COVID-19 pulmonary disease severity in chest radiographs, which can be scaled and rapidly deployed for clinical triage and workflow optimization.SUMMARYA convolutional Siamese neural network-based algorithm can calculate a continuous radiographic pulmonary disease severity score in COVID-19 patients, which can be used for longitudinal disease evaluation and clinical risk stratification.KEY RESULTSA Siamese neural network-based severity score correlates with radiologist-annotated pulmonary disease severity on chest radiographs from patients with COVID-19 (ρ=0.84 and ρ=0.78 in internal and external test sets respectively).The direction of change in the severity score in follow-up radiographs is concordant with radiologist assessment (ρ=0.74).The admission chest radiograph severity score can help predict subsequent intubation or death within three days of admission (receiver operator characteristic area under the curve=0.80).
The adaptability of H9N2 avian influenza A virus to humans: A comparative docking simulation study
Authors: Xu Hengyue , Qian Jiaqiang , Song Yifan , Ming Dengming 
Published: May 2020

AbstractInfluenza A virus, the H9N2 subtype, is an avian influenza virus that has long been circulating in the worldwide poultry industry and is occasionally found to be transmissible to humans. Evidence from genomic analysis suggests that H9N2 provides the genes for the H5N1 and H7N9 subtypes, which have been found to infect mammals and pose a threat to human health. However, due to the lack of a structural model of the interaction between H9N2 and host cells, the mechanism of the extensive adaptability and strong transformation capacity of H9N2 is not fully understood. In this paper, we collected 40 representative H9N2 virus samples reported recently, mainly in China and neighboring countries, and investigated the interactions between H9N2 hemagglutinin and the mammalian receptor, the polysaccharide α-2,6-linked lactoseries tetrasaccharide c, at the atomic level using docking simulation tools. We categorized the mutations of studied H9N2 hemagglutinin according to their effects on ligand-binding interactions and the phylogenetic analysis. The calculations indicated that all the studied H9N2 viruses can establish a tight binding with LSTc although the mutations caused a variety of perturbations to the local conformation of the binding pocket. Our calculations suggested that a marginal equilibrium is established between the conservative ligand-receptor interaction and the conformational dynamics of the binding pocket, and it might be this equilibrium that allows the virus to accommodate mutations to adapt to a variety of environments. Our results provided a way to understand the adaptive mechanisms of H9N2 viruses, which may help predict its propensity to spread in mammals.
Playing the piano with a robotic third thumb: Assessing constraints of human augmentation
Authors: Shafti Ali , Haar Shlomi , Mio Renato , Guilleminot Pierre , Faisal A. Aldo 
Published: May 2020

AbstractContemporary robotics gives us mechatronic capabilities for augmenting human bodies with extra limbs. However, how our motor control capabilities pose limits on such augmentation is an open question. We developed a Supernumerary Robotic 3rd Thumbs (SR3T) with two degrees-of-freedom controlled by the user’s body to endow them with an extra contralateral thumb on the hand. We demonstrate that a pianist can learn to play the piano with 11 fingers within an hour. We then evaluate 6 naïve and 6 experienced piano players in their prior motor coordination and their capability in piano playing with the robotic augmentation. We show that individuals’ augmented performance could be predicted by our new custom motor coordination assessment, the Human Augmentation Motor Coordination Assessment (HAMCA) performed pre-augmentation. Our work demonstrates how supernumerary robotics can augment humans in skilled tasks and that individual differences in their augmentation capability are predictable by their individual motor coordination abilities.
Automatic mapping of multiplexed social receptive fields by deep learning and GPU-accelerated 3D videography
Authors: Ebbesen Christian L. , Froemke Robert C. 
Published: May 2020

AbstractSocial interactions powerfully impact the brain and the body, but high-resolution descriptions of these important physical interactions are lacking. Currently, most studies rely on labor-intensive methods such as manual annotation. Scalable and objective tracking methods are required to understand the neural circuits underlying social behavior. Here we describe a hardware/software system and analysis pipeline that combines 3D videography, deep learning, physical modeling, and GPU-accelerated robust optimization, with automatic analysis of neuronal receptive fields recorded in interacting mice. Our system is capable of fully automatic multi-animal tracking with minimal errors (including in complete darkness) during complex, spontaneous social encounters, together with simultaneous electrophysiological recordings. We capture posture dynamics of multiple unmarked mice with high spatiotemporal precision (~2 mm, 60 frames/s). A generative model revealed the multiplexed ‘social receptive field’ of neurons in barrel cortex. This approach could be broadly useful for neurobehavioral studies of multiple animals interacting in complex low-light environments.
Single cell RNA sequencing reveals regulation of fetal ovary development in the monkey (Macaca fascicularis)
Authors: Zhao Zheng-Hui , Li Chun-Yang , Meng Tie-Gang , Wang Yan , Liu Wen-Bo , Li Ang , Cai Yi-Jun , Hou Yi , Schatten Heide , Wang Zhen-Bo , Sun Qing-Yuan , Sun Qiang 
Published: May 2020

ABSTRACTGerm cells are vital for reproduction and heredity. However, the mechanisms underlying female germ cell development in primates, especially in late embryonic stages, remain elusive. Here, we performed single-cell RNA sequencing of 12471 cells from whole fetal ovaries, and explored the communications between germ cells and niche cells. We depicted the two waves of oogenesis at single cell resolution and demonstrated that progenitor theca cells exhibit similar characteristics to Leydig cells in fetal monkey ovaries. Notably, we found thatZGLP1displays differentially expressed patterns between mouse and monkey, which is not overlapped withNANOGin monkey germ cells, suggesting its role in meiosis entry but not in activating oogenic program in primates. Furthermore, the majority of germ cell clusters that highly expressedPRDM9andSPO11might undergo apoptosis after cyst breakdown, leading to germ cell attrition. Overall, our work provides new insights into the molecular and cellular basis of primate fetal ovary development at single-cell resolution.
A two-stage diffusion modeling approach to the compelled-response task
Authors: Diederich Adele , Colonius Hans 
Published: May 2020

AbstractThe issue of how perception and motor planning interact to generate a given choice between actions is a fundamental question in both psychology and neuroscience. Salinas and colleagues have developed a behavioral paradigm, the compelled-response task, where the signal that instructs the subject to make an eye movement is given before the cue that indicates which of two possible target choices is the correct one. When the cue is given rather late, the participant must guess and make an uninformed random choice. Perceptual performance can be tracked as a function of the amount of time during which sensory information is available. In Salina’s accelerated race-to-threshold model, two variables race against each other to a threshold, at which a saccade is initiated. The source of random variability is in the initial state of information buildup across trials. This implies that incorrect decisions are due to the inertia of the racing variables that have, at the start, sampled a constant buildup in the “wrong” direction. Here we suggest an alternative, non-time-homogeneous two-stage-diffusion model that is able to predict both response time distributions and choice probabilities with a few easy-to-interpret parameters and without assuming cross-trial parameter variability. It is falsifiable at the level of qualitative features already, e.g. predicting bimodal RT distributions for particular gap times. It connects the compelled-response paradigm with an approach to decision making that has been uniquely successful in describing both behavioral and neural data in a variety of experimental settings for the last 40 years.
Organizing Pneumonia of COVID-19: Time-dependent Evolution and Outcome in CT Findings
Authors: Wang Yan , Jin Chao , Wu Carol C. , Zhao Huifang , Liang Ting , liu Zhe , Jian Zhijie , Li Runqing , Wang Zekun , Li Fen , Zhou Jie , Cai Shubo , Liu Yang , Li Hao , Li Zhongyi , Liang Yukun , Zhou Heping , Wang Xibin , Ren Zhuanqin , Yang Jian 
Published: May 2020

AbstractObjectiveAs a pandemic, a most-common pattern resembled organizing pneumonia (OP) has been identified by CT findings in novel coronavirus disease (COVID-19). We aimed to delineate the evolution of CT findings and outcome in OP of COVID-19.Materials and Methods106 COVID-19 patients with OP based on CT findings were retrospectively included and categorized into non-severe (mild/common) and severe (severe/critical) groups. CT features including lobar distribution, presence of ground glass opacities (GGO), consolidation, linear opacities and total severity CT score were evaluated at three time intervals from symptom-onset to CT scan (day 0-7, day 8-14, day>14). Discharge or adverse outcome (admission to ICU or death), and pulmonary sequelae (complete absorption or lesion residuals) on CT after discharge were analyzed based on the CT features at different time interval.Results79(74.5%) patients were non-severe and 103(97.2%) were discharged at median day 25 (range, day 8-50) after symptom-onset. Of 67 patients with revisit CT at 2-4 weeks after discharge, 20(29.9%) had complete absorption of lesions at median day 38 (range, day 30-53) after symptom-onset. Significant differences between complete absorption and residuals groups were found in percentages of consolidation (1.5% vs. 13.8%, P=0.010), number of involved lobe >3 (40.0% vs. 72.5%, P=0.030), CT score >4 (20.0% vs. 65.0%, P=0.010) at day 8-14.ConclusionsMost OP cases had good prognosis. Approximately one-third of cases had complete absorption of lesions during 1-2 months after symptom-onset while those with increased frequency of consolidation, number of involved lobe>3, and CT score >4 at week 2 after symptom-onset may indicate lesion residuals on CT.
Estimation of the Final Size of the COVID-19 Epidemic in Balochistan, Pakistan
Authors: Arif Muhammad , Kakar Aftab , Larik Ehsan 
Published: May 2020

AbstractCOVID-19 is a new disease that is spreading very fast in Pakistan. Cases have been reported from all the provinces in Pakistan including Balochistan. The first two confirmed cases in Pakistan had travel history from Iran to Pakistan, The some of the initial cases were quarantine at Taftan boarder in Balochistan, hence SIR model is used to predict the magnitude of the disease in Balochistan from May 2020 on wards when lock down and other social distancing measures were loosen up by the government of Balochistan. Our Prediction model shows that about 30,00000 individuals in Balochistan will be infected by 5th of July 2020.Over all 25% of the total population of Balochistan will be affected by this disease with 98% (2940,000) recovery rate by the end of 15th July 2020.