bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-time Assessment of Neurology Residents’ Perceptions of Inappropriate Consults
Authors: Gentile Caroline , Loebel Emma , Sanky Charles , Krieger Stephen 
Published: November 2020

Background:
We sought to characterize perceptions of inappropriate neurology consults of neurology residents (NR) and requesting providers (RP) immediately following the consult interaction.

Methods:
Student investigators were embedded in the Mount Sinai neurology consult service for 4 weeks in May/June 2018. For each consecutive neurology consult the NR’s real-time attitudes toward the consult were evaluated with a survey using Likert scales. A similar survey was immediately administered to the RP who called the consult. Response scores for each attribute were dichotomized and data were analyzed descriptively in SPSS.

Results:
Data from 69 consults were collected. NRs perceived 45% of consults as inappropriate and 82% of all consults as low urgency. When NRs perceived a consult as inappropriate, they felt more resistance (r=−0.79). NRs also felt more resistant when they thought that the RP could have cared for the patient without the consult (r=0.79). NRs felt that perceived medicolegal risk highly influenced the RP’s decision to call a consult in 36% of cases. Of these “high liability” consults, NRs considered 76% inappropriate and 100% low urgency.

Conclusions:
NRs were more likely to rate consults as inappropriate if they were also perceived as low urgency, strongly influenced by liability concerns, or unnecessary due to belief that the RP could have cared for the patient without the consult. Our findings suggest a discrepancy in how NRs and RPs perceive neurology consult appropriateness, and help to elucidate potential drivers of these perceptions that could be barriers to education and to interdisciplinary care.
Review of Outcomes in Prepectoral Prosthetic Breast Reconstruction with and without Surgical Mesh Assistance
Authors: DeLong Michael R. , Tandon Vickram J. , Bertrand Anthony A. , MacEachern Mark , Goldberg Mytien , Salibian Arthur , Pusic Andrea L. , Festekjian Jaco H. , Wilkins Edwin G. 
Published: November 2020

Background:
In the past decade, surgeons have increasingly advocated for a return to prepectoral breast reconstruction with claims that surgical mesh (including acellular dermal matrix) can reduce complication rates. However, numerous surgical and implant advancements have occurred in the decades since the initial prepectoral studies, and it is unclear whether mesh is solely responsible for the touted benefits.

Methods:
The authors conducted a systematic review of all English language articles reporting original data for prepectoral implant-based breast reconstruction. Articles presenting duplicate data were excluded. Complications were recorded and calculated on a per-breast basis and separated as mesh-assisted, no-mesh prior to 2006, and no-mesh after 2006 (date of first silicone gel–filled breast implant approval). Capsular contracture comparisons were adjusted for duration of follow-up.

Results:
A total of 58 articles were included encompassing 3120 patients from 1966 to 2019. The majority of the included studies were retrospective case series. Reported complication outcomes were variable, with no significant difference between groups in hematoma, infection, or explantation rates. Capsular contracture rates were higher in historical no-mesh cohorts, whereas seroma rates were higher in contemporary no-mesh cohorts.

Conclusions:
Limited data exist to understand the benefits of surgical mesh devices in prepectoral breast reconstruction. Level I studies with an appropriate control group are needed to better understand the specific role of mesh for these procedures. Existing data are inconclusive but suggest that prepectoral breast reconstruction can be safely performed without surgical mesh.
Muscle Spindles in the Levator Palpebrae Superioris Muscle of Human Adults
Authors: Takahashi Yasuhiro , Ohmichi Yusuke , Lee Patricia Ann L. , Naito Munekazu , Nakano Takashi , Kakizaki Hirohiko 
Published: November 2020

Abstract
In this experimental anatomic study, the authors examined the number and distribution of muscle spindles in the levator palpebrae superioris (LPS) muscle of human adults. This study included 11 orbits from 11 cadavers (mean age at death, 81.9 years). The LPS muscles were harvested and equally divided into 5 sections using transverse incisions. Muscle spindles were counted in each section. Consequently, muscle spindles were identified in 4 (36.4%) of the 11 orbits studied. One to 4 muscle spindles were identified in each of these 4 orbits. All muscle spindles were found in the most proximal section (the muscle origin), and no muscle spindles were identified in the other sections. The results indicate that the LPS muscle is associated with a smaller number of muscle spindles as compared with the rest of the extraocular muscles. Since higher muscle spindle numbers are associated with finer motor movements, eyelid opening does not seem to require much precision, compared to ocular movement.
Healing Adjuncts in Craniofacial Surgery: Review of Dietary Vitamins and Supplements
Authors: Spielman Amanda F. , Epstein Anabel , Jabori Sinan , Mathew Prakash , Thaller Seth 
Published: November 2020

Background:
In the United States, the use of herbal supplements on a regular basis ranges from 32% to 97%. Prevalence of supplement use is particularly elevated after facial surgery. It has been reported as high as 50%. Unfortunately, there is a paucity of literature on the dietary use of supplements. They are not regulated by the FDA. Often, they are not reported by patients. This study examines the role of dietary supplements as adjuncts to healing in craniofacial and facial aesthetic surgeries.

Methods:
A comprehensive literature review was conducted using MEDLINE, PubMed, and EMBASE. Databases were screened for papers describing the use of supplements in craniofacial procedures in adult patients using relevant search terms. Data on criteria, outcomes, and patient satisfaction were collected.

Results:
A total of 19 articles were selected from the 806 identified. Fifteen different supplements or combinations of supplements have been studied for use in facial surgeries. Of these 15 supplements, the following demonstrated potential healing benefits: dry ivy leaf extract, Nazalzem ointment (vitamin A and dexpanthenol), combination nasal sprays (phospholipids, fatty acids, vitamin A, and vitamin E), Saireito pills, topical olive oil, yunnan baiyao, melilotus extract, arnica, and combination arnica and ledum. Arnica is the most commonly studied supplement in a variety of facial operations.

Conclusions:
There is ample evidence to support a role for the use of certain dietary supplements to optimize wound healing in craniofacial and facial aesthetic surgery. Controlled diet and use of appropriate supplements may have a synergistic beneficial effect on wound healing following craniofacial surgery. However, there is a need for additional reporting to allow for the creation of stronger guidelines and increased patient screening, reporting, and compliance.
Clinical Application of Carving Template With 3D Reconstruction Technique for Personalized and Precise Treatment of Traumatic Ear Defects
Authors: Song Yupeng , Yang Qinghua , Jiang Haiyue , Dong Weiwei 
Published: November 2020

Abstract
We explored the clinical application of a 3-dimensional (3D) digital reconstruction technique for personalized and precise traumatic ear defect treatment. A 3D scanner was used to obtain 3D images of the unaffected ear. The data were converted into an ear contour model through mirroring using the software, and imported to a rapid prototyping 3D printer to construct an ipsilateral ear model. For treating different types of ear defect patients with individualized treatment programs, the defective ear model was constructed with individualized autogenous costal cartilage carving. We constructed ipsilateral ear defect models in 16 cases and rebuilt the auricular with >10 outer ear substructure units, maintaining a stable cranial angle. At the 6-month follow-up, the reconstructed ear was similar to the unaffected one, and the patient satisfaction was high. Based on a paired t test, the differences in the width of both auricles was statistically significant, with P values of 0.023, respectively. The differences in the P values of the auricle length, circumference and height, at 0.261, 0.333, and 0.197, respectively, were not statistically significant. Compared to the model utilizing the traditional 2D film template of the ear, the 3D reconstruction technology was more intuitive and stereoscopic, and the personalized ear reconstruction was accurate. Thus, 3D digital technology can avail the most suitable personalized treatment for various traumatic ear defects. It can assist in precisely engraving the reconstructed cartilage stent and objectively analyzing the postoperative results. The therapeutic effect was significant.
Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island
Authors: Sun Jia , Guo Jiaying , Lin Ta-Hui , Feng Xuejin , Zhang Rui 
Published: November 2020

A Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10–50 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and in the presence of 0–9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family

Erythrobacteraceae

, namely

Croceibacterium atlanticum

(96.1 %),

Pelagerythrobacter marensis

(96.0 %),

Tsuneonella rigui

(96.0 %) and

Altericroceibacterium xinjiangense

(96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), C16 : 0, C17 : 1
ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family

Erythrobacteraceae

, with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).
Deconstructing the mouse olfactory percept through an olfactory ethological atlas
Authors: Manoel Diogo , Makhlouf Melanie , Arayata Charles J. , Sathappan Abbirami , Da’as Sahar , Abdelrahman Doua , Selvaraj Senthil , Hasnah Reem , Mainland Joel D. , Gerkin Richard C. , Saraiva Luis R. 
Published: November 2020

ABSTRACTOdor perception in non-humans is poorly understood. Here, we generated the most comprehensive murine olfactory ethological atlas to date, consisting of behavioral responses to a diverse panel of 73 odorants, including 12 at multiple concentrations. These data revealed that the mouse behavior is incredibly diverse, and changes in response to odor identity and intensity. Using only behavioral responses, ~30% of the 73 odorants could be identified with high accuracy (>96%) by a trained classifier. Mouse behavior occupied a low-dimensional space, consistent with analyses of human olfactory perception. While mouse olfactory behavior is difficult to predict from the corresponding human olfactory percept, three fundamental properties are shared: odor valence is the primary axis of olfactory perception; the physicochemical properties of odorants can predict the olfactory percept; and odorant concentration quantitatively and qualitatively impacts olfactory perception. These results provide a template for future comparative studies of olfactory percepts among species.
Identification and phenotype of MAIT cells in cattle and their response to bacterial infections
Authors: Edmans Matthew D. , Connelley Timothy K. , Jayaraman Siddharth , Vrettou Christina , Vordermeier Martin , Mak Jeffrey Y. W. , Liu Ligong , Fairlie David P. , Maze Emmanuel Atangana , Chrun Tiphany , Klenerman Paul , Eckle Sidonia B. G. , Tchilian Elma , Benedictus Lindert 
Published: November 2020

AbstractMucosal-associated invariant T (MAIT) cells are a population of innate-like T cells that utilise a semi-invariant T cell receptor (TCR) α chain and are restricted by the highly conserved antigen presenting molecule MR1. MR1 presents microbial riboflavin biosynthesis derived metabolites produced by bacteria and fungi. Consistent with their ability to sense ligands derived from bacterial sources, MAIT cells have been associated with the immune response to a variety of bacterial infections, such asMycobacterium spp.,Salmonella spp. and Escherichia coli. To date, MAIT cells have been studied in humans, non-human primates and mice. However, they have only been putatively identified in cattle by PCR based methods; no phenotypic or functional analyses have been performed. Here, we identified a MAIT cell population in cattle utilising MR1 tetramers and high-throughput TCR sequencing. Phenotypic analysis of cattle MAIT cells revealed features highly analogous to those of MAIT cells in humans and mice, including expression of an orthologous TRAV1-TRAJ33 TCR α chain, an effector memory phenotype irrespective of tissue localisation, and expression of the transcription factors PLZF and EOMES. We determined the frequency of MAIT cells in peripheral blood and multiple tissues, finding that cattle MAIT cells are enriched in mucosal tissues as well as in the mesenteric lymph node. Cattle MAIT cells were responsive to stimulation by 5-OP-RU and riboflavin biosynthesis competent bacteriain vitro. Furthermore, MAIT cells in milk increased in frequency in cows with mastitis. Following challenge with virulentMycobacterium bovis, a causative agent of bovine tuberculosis and a zoonosis, peripheral blood MAIT cells expressed higher levels of perforin. Thus MAIT cells are implicated in the immune response to two major bacterial infections in cattle. These data suggest that MAIT cells are functionally highly conserved and that cattle are an excellent large animal model to study the role of MAIT cells in important zoonotic infections.
Proteobacteria encode diverse flg22 peptides that elicit varying immune responses inArabidopsis thaliana
Authors: Cheng Janis H.T. , Bredow Melissa , Monaghan Jacqueline , diCenzo George C. 
Published: November 2020

ABSTRACTBacterial flagellin protein is a potent microbe-associated molecular pattern. Immune responses are triggered by a 22 amino acid epitope derived from flagellin, known as flg22, upon detection by the pattern recognition receptor FLAGELLIN-SENSING2 (FLS2) in multiple plant species. However, increasing evidence suggests that flg22 epitopes of several bacterial species are not universally immunogenic to plants. We investigated whether flg22 immunogenicity systematically differs between classes of the phylum Proteobacteria, using a dataset of 2,470 flg22 sequences. To predict which species encode highly immunogenic flg22 epitopes, we queried a custom motif (11[ST]xx[DN][DN]xAGxxI21) in the flg22 sequences, followed by sequence conservation analysis and protein structural modelling. These data led us to hypothesize that most flg22 epitopes of the γ- and β-Proteobacteria are highly immunogenic, whereas most flg22 epitopes of the α-, δ-, and ε-Proteobacteria are weakly to moderately immunogenic. To test this hypothesis, we generated synthetic peptides representative of the flg22 epitopes of each proteobacterial class, and we monitored their ability to elicit an immune response inArabidopsis thaliana. Flg22 peptides of the γ- and β-Proteobacteria triggered strong oxidative bursts, whereas peptides from the ε-, δ-, and α-Proteobacteria triggered moderate, weak, or no response, respectively. These data suggest flg22 immunogenicity is not highly conserved across the phylum Proteobacteria. We postulate that sequence divergence of each taxonomic class was present prior to the evolution of FLS2, and that the ligand specificity ofA. thalianaFLS2 was driven by the flg22 epitopes of the γ- and β-proteobacteria, a monophyletic group containing many common phytopathogens.
Navigating the amino acid sequence space between functional proteins using a deep learning framework
Authors: Bitard-Feildel Tristan 
Published: November 2020

AbstractMotivationShedding light on the relationships between protein se-quences and functions is a challenging task with many implications in protein evolution, diseases understanding, and protein design. Protein sequence / function space is however hard to comprehend due to its com-plexity. Generative models help to decipher complex systems thanks to their abilities to learn and recreate data specificity. Applied to protein sequences, they can point out relationships between protein positions and functions capture the sequence patterns associated with functions or navigate through uncharted area of molecular evolution.ResultsIn this study, an unsupervised generative approach based on adversarial auto-encoder (AAE) is proposed to generate and explore new sequences with respect to their functions thanks to the prior distribution allowing a continuous exploration of the latent space. AAEs are tested on three protein families known for their multiple functions. Clustering re-sults on the encoded sequences from the latent space computed by AAEs display high level of homogeneity regarding the protein sequence func-tions. The study also reports and analyzes for the first time two sampling strategies based on latent space interpolation and latent space arithmetic to generate intermediate protein sequences sharing sequential and functional properties of original sequences issued from different families and functions. Generated sequences by interpolation between latent space data points demonstrate the ability of the AAE to generalize and to pro-duce meaningful biological sequences from an evolutionary uncharted area of the biological sequence space. Finally, 3D structure models generated by comparative modelling between different combinations of structures of different sub-families and of generated sequences from latent space or sub-family sequences point out to the ability of the latent space arithmetic to successfully transfer functional properties between sub-families. All in all this study confirms the ability of deep learning frameworks to model biological complexity and bring new tools to explore amino acid sequence and functional spaces.AvailabilityCode and data used for this study are freely available at https://github.com/T-B-F/aae4seq.Contacttristan@bitardfeildel.frSupplementary informationSupplementary data are available at online.
Inferring species interactions from ecological survey data: a mechanistic approach to predict quantitative food webs of seed-feeding by carabid beetles
Authors: Pocock Michael J.O. , Schmucki Reto , Bohan David A. 
Published: November 2020

AbstractEcological networks are valuable for ecosystem analysis but their use is often limited by a lack of data because many types of ecological interaction, e.g. predation, are short-lived and difficult to observe or detect. There are different methods for inferring the presence of interactions, which we lack methods to predict interaction strengths and so use weighted network analysis.Here, we develop a trait-based approach suitable for creating quantitative networks, i.e. with varying interaction strengths. We developed the method for seed-feeding carabid ground beetles (Coleoptera: Carabidae) although the principles can be applied to other interactions.We used existing literature data from experimental seed-feeding trials to predict a per-individual interaction cost index based on carabid and seed size with frequency-dependent prey selection and assuming bottom up control. This was scaled up to the population level to create predicted inferred weighted networks using the abundance of carabids and seeds in samples from arable fields and energetic intake rates of carabids from the literature. From these weighted networks, we also calculated a novel measure of predation pressure.We applied it to existing ecological survey data from 255 arable fields with carabid data from pitfall traps and plant seeds from seed rain traps. Analysis of these inferred networks led to testable hypotheses about how networks and predation pressure varied amongst fields.Inferred networks are valuable because (i) they provide null models for the structuring of food webs to test against empirical species interaction data, e.g. DNA analysis of carabid gut regurgitates, and (ii) they allow weighted inferred networks to be constructed whenever we can estimate interactions between species and have ecological census data available. This would permit network analysis even at times and in places when interactions were not directly assessed.
DeepCorn: A Semi-Supervised Deep Learning Method for High-Throughput Image-Based Corn Kernel Counting and Yield Estimation
Authors: Khaki Saeed , Pham Hieu , Han Ye , Kuhl Andy , Kent Wade , Wang Lizhi 
Published: November 2020

AbstractThe success of modern farming and plant breeding relies on accurate and efficient collection of data. For a commercial organization that manages large amounts of crops, collecting accurate and consistent data is a bottleneck. Due to limited time and labor, accurately phenotyping crops to record color, head count, height, weight, etc. is severely limited. However, this information, combined with other genetic and environmental factors, is vital for developing new superior crop species that help feed the world’s growing population. Recent advances in machine learning, in particular deep learning, have shown promise in mitigating this bottleneck. In this paper, we propose a novel deep learning method for counting on-ear corn kernels in-field to aid in the gathering of real-time data and, ultimately, to improve decision making to maximize yield. We name this approach DeepCorn, and show that this framework is robust under various conditions and can accurately and efficiently count corn kernels. We also adopt a semi-supervised learning approach to further improve the performance of our proposed method. Our experimental results demonstrate the superiority and effectiveness of our proposed method compared to other state-of-the-art methods.