bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated PET/MRI With 68Ga-DOTATATE and 18F-FDG in Pheochromocytomas and Paragangliomas
Authors: Xu Si , Pan Yu , Zhou Jinxin , Ju Huijun , Zhang Yifan 
Published: February 2022

Purpose
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors with metastatic potential. Both 68Ga-DOTATATE and 18F-FDG PET/CT scans have been demonstrated to have important roles in imaging PPGLs, but less is known about the performance of PET/MRI for PPGLs. The study is aimed to investigate whether diffusion-weighted imaging–MRI (DWI-MRI) has an added value to PET imaging in the identification of PPGL lesions by means of integrated PET/MRI.

Methods
Eleven patients who underwent both 18F-FDG and 68Ga-DOTATATE PET/MRI within 2 weeks were retrospectively included in the study. A total of 56 PPGL lesions were analyzed, and lesion-based detection rates of 68Ga-DOTATATE PET, 18F-FDG PET, DWI-MRI, and PET/MRI were calculated and compared, respectively.

Results

68Ga-DOTATATE PET was superior to 18F-FDG PET and DWI-MRI in imaging PPGLs with a lesion-based detection rate of 96.4% (54/56) (95% confidence interval [CI], 87.7%–99.6%), 85.7% (48/56) (95% CI, 76.3%–95.2%), and 89.3% (50/56) (95% CI, 80.9%–97.6%), respectively. PET/MRI with DWI could improve the detection rate of 68Ga-DOTATATE and 18F-FDG PET alone up to 100% in metastatic PPGLs. Lesions of PPGL demonstrated markedly higher tracer uptake in 68Ga-DOTATATE PET than in 18F-FDG PET (P = 0.009 for primary lesion, P = 0.033 for metastases).

Conclusions

68Ga-DOTATATE PET showed a higher detection rate than 18F-FDG for PPGLs. In integrated PET/MRI, MRI had an added value to 18F-FDG PET but not much to 68Ga-DOTATATAE PET in identifying PPGL lesions.
Unusual Radiotracer Deposition to the Forearm After Intrahepatic Injection of 99mTc-Macroaggregated Albumin Using a Transradial Approach
Authors: Mugweru Jon , Elman Shana , Rieter William J. , Gutjahr Christopher , Elojeimy Saeed 
Published: February 2022

Abstract
Arterial mapping and 99mTc-macroaggregated albumin (99mTc-MAA) hepatic perfusion imaging are routinely performed before 90Y radioembolization of hepatic tumors. These procedures serve multiple purposes, including an anatomical survey of hepatic arterial anatomy, interrogating expected microsphere distribution to avoid nontargeted embolization during therapy, and evaluating for possible hepatopulmonary shunting. We present a case where 99mTc-MAA planar images revealed unexpected soft tissue uptake within the left forearm, an unexpected complication that may result from residual 99mTc-MAA in the catheter being expelled as the catheter is removed, which is particularly important to avoid during the 90Y radioembolization procedure given the risk for associated radionecrosis.
Pediatric Plastic Surgery Operating Room Block-Time Utilization: A Casualty of Illness
Authors: Maliha Samantha G. , Bruce Madeleine K. , Anstadt Erin A. , Roy Eva , Pfaff Miles J. , Goldstein Jesse A. , Losee Joseph E. 
Published: February 2022

Background:
Optimizing operating room (OR) utilization is a critical component of health care system efficiency. The purpose of our study was to analyze the extent of OR cancellation and its effect on raw utilization of OR block time allotted to surgeons in the pediatric plastic surgery department.

Methods:
The authors retrospectively reviewed the cases of 4 plastic surgeons at a tertiary pediatric hospital between 2018 and 2019. Data collected included patient demographics, type of surgery, time of cancellation, reason for cancellation, length of surgery, and minutes of block time allotted to each surgeon per year. Percent of cases canceled, scheduled times lost, and block times lost were calculated.

Results:
Surgeons A, B, C, and D scheduled 170, 416, 305, and 474 cases, respectively. Overall, 7% of cases were canceled, 9.1% of scheduled time was lost, and a total of 5.1% of block time was lost due to cancellation. Patients of surgeon A and D were more likely to cancel due to reasons classified as ‘‘other,’’ including causes such as failure of nil per os or a family’s last-minute decision to forego elective surgery (33.3% and 37.2%, respectively), whereas patients of surgeon B and C were more likely to cancel due to illness (67.9% and 36.4%, respectively).

Conclusions:
Cancellations negatively impact raw utilization times; if fewer cases are performed, allotted block times are redistributed. Communication with patients in the week prior to surgery may allow for earlier identification of likely cancellations. Future directions include exploring whether particular surgeon characteristics are linked to rate of cancellations.
Uncovering the Pathogenesis of Orofacial Clefts Using Bioinformatics Analysis
Authors: Dong Xinxin , Meng Teng , Lei Liu 
Published: February 2022

Objective:
Many genes have been found to be associated with the occurrence of the orofacial clefts (OFC). The links between these pathogenic genes are rarely studied. In this study, bioinformatics analysis were performed in order to find associations between OFC- related genes and provide new ideas for etiology study of OFCs.

Methods:
Orofacial clefts-related genes were searched and identified from the Online Mendelian Inheritance of Man (OMIM.org). These genes were then analyzed by bioinformatics methods, including protein–protein interaction network, functional enrichment analysis, module analysis, and hub genes analysis.

Results:
After searching the database of OMIM.org and removing duplicate results, 279 genes were finally obtained. These genes were involved to 369 pathways in biological process, 56 in cell component, 64 in molecular function, and 45 in the Kyoto Encyclopedia of Genes and Genomes. Most identified genes were significantly enriched in embryonic appendage morphogenesis (29.17%), embryonic limb morphogenesis (6.06%), and limb development (4.33%) for biological process (Fig. 5A); ciliary tip (42.86%), MKS complex (28.57%), ciliary basal body (14.29%), and ciliary membrane (14.29%) for cell component. The top 10 hub genes were identified, including SHH, GLI2, PTCH1, SMAD4, FGFR1, BMP4, SOX9, SOX2, RUNX2, and CDH1.

Conclusions:
Bioinformatics methods were used to analyze OFC- related genes in this study, including hub gene identifying and analysis, protein – protein interaction network construction, and functional enrichment analysis. Several potential mechanisms related to occurrence of OFCs were also discussed. These results may be helpful for further studies of the etiology of OFC.
Reconciling GenBank names with standardized avian taxonomies to improve linkage between phylogeny and phenotype
Authors: Hosner Peter A. , Zhao Min , Kimball Rebecca T. , Braun Edward L. , Burleigh J. Gordon 
Published: February 2022

ABSTRACTBiodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequence data from around the globe, facilitating biodiversity research. However, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have led to widespread scientific name changes. Taxonomic instability, or “splits, lumps, and shuffles”, present logistical challenges to large-scale biodiversity research because species or populations may be listed under different names in different data sources, or because different species or populations may be listed under previous names. Consequently, distributional and trait data are often difficult to link directly to DNA sequence data without extensive and time consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize all avian names in use in NCBI GenBank, a primary source of genetic data, to a widely-used and regularly-updated avian taxonomy: eBird/Clements. Of 14,341 avian species or subspecies names used by GenBank, 11,031 names directly matched an eBird/Clements name, which were linked to over 6 million nucleotide sequences. For the remaining unique avian names in GenBank, we used Avibase’s taxonomic concepts, taxonomic descriptions in Cornell’s Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names were linked to over 600,000 nucleotide sequences, approximately 9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under two or more GenBank names. Our avian GenBank naming reconciliation is open source and available at GitHub, where it can be updated to correspond with future annual eBird/Clements taxonomic updates.LAY SUMMARY– 23% of avian names on GenBank do not match eBird/Clements, a widely-used standardized avian taxonomy– 600,000 nucleotide sequences on GenBank are associated with names that do not match eBird/Clements– 10% of eBird/Clements names have nucleotide sequences listed under multiple GenBank names– We provide an open source taxonomic reconciliation to mitigate difficulties associated with non-standardized name use for GenBank data
Host origin is a determinant of parallel evolution between influenza virus gene segments
Authors: Jones Jennifer E. , Lakdawala Seema S. 
Published: February 2022

AbstractSeveral emerging influenza viruses, including H7N9 and H5N6 viruses, trace their origins to reassortment with H9N2 viruses that contributed internal gene segments. However, the evolutionary constraints governing reassortment of H9N2 viruses remain unknown. In seasonal human influenza A viruses, gene segments evolve in parallel at both the gene and protein levels. Here, we demonstrate that parallel evolution in human H3N2 viruses differs from avian H9 viruses, with both genes and proteins of avian H9 viruses characterized by high phylogenetic divergence. Strikingly, protein trees corresponding to avian H9 polymerase subunits diverge despite known functional constraints on polymerase evolution. Gene divergence was consistent across avian H9 isolates from different continents, suggesting that parallel evolution between H9 gene segments is not dependent on regionally defined lineages. Instead, parallel evolution in H9 viruses was dependent upon host origin. Our study reveals the role of the host in parallel evolution of influenza gene segments and suggests that high reassortment potential in avian species may be a consequence of evolutionary flexibility between gene segments.
Semantic overlap protects from interference by restoring encoding mechanisms
Authors: Moore Isabelle L. , Long Nicole M. 
Published: February 2022

AbstractOverlap between experiences can have both facilitative and detrimental effects for memory. Our aim was to establish whether overlap along one dimension (e.g. contextual, semantic, temporal) can counteract overlap-driven interference along another dimension. We hypothesized that semantic overlap facilitates episodic memory formation by modulating encoding mechanisms. We recorded scalp electroencephalography (EEG) while human participants performed a free recall task. Half of the items from late in each study list semantically overlapped with an item presented earlier in the list. We find that semantic overlap selectively improves memory and influences the neural signals engaged during the study of late list items. Relative to other recalled items, late list items that are later recalled consecutively with semantically overlapping items elicited increased high frequency activity and decreased low frequency activity, a hallmark of successful encoding. Our findings demonstrate that semantic overlap can protect from interference due to temporal overlap by modulating encoding mechanisms.Statement of RelevancExperiences can overlap along different dimensions, including contextual, semantic, and tempo-ral. We tested the hypothesis that semantic overlap – shared meaning between experiences – may protect from interference due to temporal overlap, when experiences occur close together in time. Although evidence suggests that attention and/or encoding resources diminish across a series of study items presented in close temporal proximity, we find that semantic overlap can enable recovery of these encoding resources. Specifically, items that would typically be forgotten due to interference are better remembered and recruit distinct neural mechanisms when they share meaning with an earlier study item. These findings indicate that encoding mechanisms can be modulated by the degree of semantic overlap between two experiences. More broadly, our results suggest that experiences do not exist in isolation, rather that a prior experience can directly influence the neural mechanisms recruited to process a current experience.
Post marketing surveillance for Microwave Treatment of Plantar and Common Warts in Adults
Authors: Bristow Ivan , Joshi Shailesh , Williamson Jonathan , Ardern-Jones Michael 
Published: February 2022

AbstractA handheld microwave device (Swift®, Emblation Limited) has been licenced and available for clinical use since 2016 in the fields of podiatry and dermatology and has been extensively used in treating cutaneous warts. As part of post marketing surveillance by the manufacturer, an online 79-item survey was distributed to podiatry clinics in the United Kingdom with a Swift® device. A total of 126 clinics responded (59.6%). 6998 adults (<65 years) underwent wart treatment with microwave (81.9% plantar warts; 18.1% common, non-plantar warts). The median efficacy rate was reported as 79.2% (65.9 - 87.5%) and 82.3% (71.4 - 100%) respectively. In older adults (over 65 years) efficacy rates were similar for both sites: plantar (73.2%, 50-90%, n=1232) and non-plantar (80.0%, 42.1-100%, n=276). A median of three treatments was required to bring about resolution. Sub-group analysis of the data revealed good clearance rates in patients with diabetes (79.6%), but less in immunocompromised individuals (61.3%) and those with autoimmune disease (58.6%). Overall, mean user satisfaction was rated as “very satisfied” on a 10-point scale (n=93 practices). A small number of adverse events were reported including blistering, superficial ulceration and poor healing were reported (n=7). Despite the limitations of a post-marketing questionnaire survey, these data provide good evidence of the safety and efficacy for Swift® microwave treatment of cutaneous warts.What is already known about this topic?Microwave treatment has shown to be effective in the treatment of cutaneous warts.What does the study add?This survey of clinics using SWIFT microwave treatments reports on the effectiveness and safety of the device in the treatment of 8506 adult patients with common and plantar warts.Responding user clinics reporting efficacy with good clearance rates and low levels of adverse events demonstrating microwave is a safe and effective treatment for plantar and common warts.
Algorithmic Identification of Potentially High Risk Abdominal Presentations (PHRAPs) to the Emergency Department: A Clinically-Oriented Machine Learning Approach
Authors: Kuzma Richard S , Saraswathula Varun , Moon Kathryn R , Kelz Rachel R , Friedman Ari B 
Published: February 2022

AbstractBackgroundOlder adults presenting to emergency departments (EDs) with abdominal pain have been shown to be at high risk of subsequent morbidity and mortality. Yet, such presentations are poorly studied in national databases. Claims databases do not record the patient’s symptoms at the time of presentation to the ED, but rather the diagnosis after testing and evaluation, limiting study of care and outcomes for these high risk abdominal presentations.ObjectivesWe sought to develop an algorithm to define a patient population with potentially high risk abdominal presentations (PHRAPs) using only variables commonly available in claims data.Research DesignTrain a machine learning model to predict abdominal pain chief complaints using the National Hospital Ambulatory Medical Care Survey (NHAMCS), a nationally-representative database of abstracted ED medical records.SubjectsAll patients contained in NHAMCS data from 2013-2018. 2013-2017 were used for predictive modeling and 2018 was used as a hold-out test set.MeasuresPositive predictive value and sensitivity of the predictive algorithm against a hold-out test set of NHAMCS patients the algorithm was blinded to during training. Predictions were assessed for agreement with either a chief complaint of abdominal pain (contained in “Reason for Visit 1”), or an expanded definition intended to capture visits which were for abdominal concerns. These included secondary or tertiary complaints of abdominal pain or other abdominal conditions, other abdominal-related chief complaint (e.g. nausea or diarrhea, but not pain), discharge diagnosis of an abdominal condition, or reception of an abdominal CT or ultrasound.ResultsAfter validation on a hold-out data set, a gradient boosting machine (GBM) was the best best-performing machine learning model, but a logistic regression model had similar performance and may be more explainable and useful to future researchers. The GBM predicted a chief complaint of abdominal pain with a positive predictive value of 0.60 (95% CI of 0.56, 0.64) and a sensitivity of 0.29 (95% CI of (0.27, 0.32). Nearly all false positives still exhibited signs of “abdominal concerns” for patients: using the expanded definition of “abdominal concern” the model had a PPV of >0.99 (95% CI of 0.99, 1.00) and sensitivity of 0.12 (95% CI of 0.11, 0.13).ConclusionThe algorithm we report defines a patient population with abdominal concerns for further study of treatment and outcomes to inform the development of clinical pathways.
Unique neural coding of crucial versus irrelevant plant odors in a hawkmoth
Authors: Bisch-Knaden Sonja , Rafter Michelle A. , Knaden Markus , Hansson Bill S. 
Published: February 2022

AbstractThe sense of smell is pivotal for nocturnal moths to locate feeding and oviposition sites. However, these crucial resources are often rare and their bouquets are intermingled with volatiles emanating from surrounding ‘background’ plants. Here we asked if the olfactory system of female hawkmoths, Manduca sexta, could differentiate between crucial and background cues. To answer this question, we collected nocturnal headspaces of numerous plants in a natural habitat of M. sexta. We analyzed the chemical composition of these headspaces, and used them as stimuli in physiological experiments at the antenna and in the brain. The intense odors of floral nectar sources evoked strong responses in virgin and mated female moths, most likely enabling the localization of profitable flowers at a distance. Bouquets of larval host plants and most background plants, in contrast, were subtle, thus potentially complicating host identification. However, despite being subtle, antennal responses and brain activation patterns evoked by the smell of larval host plants were clearly different from those evoked by other plants. Interestingly, this difference was even more pronounced in the antennal lobe of mated females, revealing a status-dependent tuning of their olfactory system towards oviposition sites. Our study suggests that female moths possess unique neural coding strategies to find not only conspicuous floral cues but also inconspicuous bouquets of larval host plants within a complex olfactory landscape.
FoxP3 can fold into two distinct dimerization states with divergent functional implications for T cell homeostasis
Authors: Leng Fangwei , Zhang Wenxiang , Ramirez Ricardo N. , Leon Juliette , Zhong Yi , van der Veeken Joris , Rudensky Alexander Y. , Benoist Christophe , Hur Sun 
Published: February 2022

AbstractFoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrate that, unlike other known forkhead TFs, FoxP3 forms a head-to-head dimer using a unique linker (Runx1-binding region, RBR) preceding the forkhead domain. Head-to-head dimerization confers distinct DNA-binding specificity and creates a docking site for the cofactor Runx1. RBR is also important for proper folding of the forkhead domain, as truncation of RBR induces domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impairs FoxP3 function, as demonstrated with the disease-causing mutation R337Q, while a swap-suppressive mutation largely rescues R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap-dimerization with impaired functions.
Recombination-aware Phylogeographic Inference Using the Structured Coalescent with Ancestral Recombination
Authors: Guo Fangfang , Carbone Ignazio , Rasmussen David A. 
Published: February 2022

AbstractMovement of individuals between populations or demes is often restricted, especially between geographically isolated populations. The structured coalescent provides an elegant theoretical framework for describing how movement between populations shapes the genealogical history of sampled individuals and thereby structures genetic variation within and between populations. However, in the presence of recombination an individual may inherit different regions of their genome from different parents, resulting in a mosaic of genealogical histories across the genome, which can be represented by an Ancestral Recombination Graph (ARG). In this case, different genomic regions may have different ancestral histories and so different histories of movement between populations. Recombination therefore poses an additional challenge to phylogeographic methods that aim to reconstruct the movement of individuals from genealogies, although also a potential benefit in that different loci may contain additional information about movement. Here, we introduce the Structured Coalescent with Ancestral Recombination (SCAR) model, which builds on recent approximations to the structured coalescent by incorporating recombination into the ancestry of sampled individuals. The SCAR model allows us to infer how the migration history of sampled individuals varies across the genome from ARGs, and improves estimation of key population genetic parameters such as population sizes, recombination rates and migration rates. Using the SCAR model, we explore the potential and limitations of phylogeographic inference using full ARGs. We then apply the SCAR to lineages of the recombining fungusAspergillus flavussampled across the United States to explore patterns of recombination and migration across the genome.