bluuebunny/crossref_metadata_2025_split huggingface dataset:
YouTube™ as a Source of Information for Patients Regarding Dental Implant Failure: A Content Analysis
Authors: Özkan Enes , Acar Ahmet Hüseyin 
Published: March 2022

Abstract:
The aim of this study is to investigate the quality of the information YouTubeTM offers to patients concerning dental implant failure. YouTubeTM was searched systematically using the keyword ‘dental implant failure’. The first 100 videos were viewed by two independent researchers. For each video, its purpose, target audience and source were also recorded. A 10 point content scale (CS) was used to evaluate the video content. The Global Quality Scale (GQS) was also used to determine the quality of videos. Statistical analyses were performed using the Kruskal Wallis and Mann Whitney test and correlation coefficient analyses were performed using Spearman’s Rho. While 92.2% of the videos included in the study were uploaded by dentists/health institutions, only 3.1% were uploaded by laypersons. Of the videos, 40.6% were aimed at informing laypersons and 56.3% targetted professionals. The content which was discussed most (71.9%) was ‘definition of a dental implant’ followed by ‘reasons for failure’ (65.6%). The mean CS and GQS score of the videos were 3.75 ± 2.35 (moderate) and 2.07 ± 1.05 (generally poor), respectively. There was a positive correlation between the CS and GQS score (r = 0.620). The quality of information on YouTubeTM regarding dental implant failure was found inadequate. Thus, the information currently available online needs to be constantly checked and improved by professionals. In addition, clinicians should improve the ways in which they use YouTubeTM to better inform patients about the causes, risks and treatment choices involved with failed dental implants.
A Multidimensional Bioinformatic Platform for the Study of Human Response to Surgery
Authors: Eckhoff Austin M. , Connor Ashton A. , Thacker Julie K. M. , Blazer Dan G. , Moore Harvey G. , Scheri Randall P. , Lagoo-Deenadayalan Sandhya A. , Harpole David H. , Seymour Keri A. , Purves J. Todd , Ravindra Kadiyala V. , Southerland Kevin W. , Rocke Daniel J. , Gilner Jennifer B. , Parker Daniel C. , Bain James R. , Muehlbauer Michael J. , Ilkayeva Olga R. , Corcoran David L. , Modliszewski Jennifer L. , Devos Nicolas , Foster Matthew W. , Moseley M. Arthur , Dressman Holly K. , Chan Cliburn , Huebner Janet L. , Chasse Scott , Stempora Linda , Aschenbrenner Mary E. , Joshi Mary-Beth , Hollister Beth , Henao Ricardo , Barfield Richard T. , Ellison Mark A. , Bailey Sean , Woody Stephen , Huang Erich S. , Kirk Allan , Hwang E. Shelley 
Published: March 2022

Objective:
To design and establish a prospective biospecimen repository that integrates multi-omics assays with clinical data to study mechanisms of controlled injury and healing.

Background:
Elective surgery is an opportunity to understand both the systemic and focal responses accompanying controlled and well-characterized injury to the human body. The overarching goal of this ongoing project is to define stereotypical responses to surgical injury, with the translational purpose of identifying targetable pathways involved in healing and resilience, and variations indicative of aberrant peri-operative outcomes.

Methods:
Clinical data from the electronic medical record combined with large-scale biological data sets derived from blood, urine, fecal matter, and tissue samples are collected prospectively through the peri-operative period on patients undergoing 14 surgeries chosen to represent a range of injury locations and intensities. Specimens are subjected to genomic, transcriptomic, proteomic, and metabolomic assays to describe their genetic, metabolic, immunologic, and microbiome profiles, providing a multidimensional landscape of the human response to injury.

Results:
The highly multiplexed data generated includes changes in over 28,000 mRNA transcripts, 100 plasma metabolites, 200 urine metabolites, and 400 proteins over the longitudinal course of surgery and recovery. In our initial pilot dataset, we demonstrate the feasibility of collecting high quality multi-omic data at pre- and postoperative time points and are already seeing evidence of physiologic perturbation between timepoints.

Conclusions:
This repository allows for longitudinal, state-of-the-art geno-mic, transcriptomic, proteomic, metabolomic, immunologic, and clinical data collection and provides a rich and stable infrastructure on which to fuel further biomedical discovery.
Highly efficient protein expression of Plasmodium vivax surface antigen, Pvs25 by silkworm, Bombyx mori, and its biochemical analysis
Authors: Miyata Takeshi , Minamihata Kosuke , Kurihara Koichi , Kamizuru Yui , Gotanda Mari , Obayashi Momoka , Kitagawa Taiki , Sato Keita , Kimura Momoko , Oyama Kosuke , Ikeda Yuta , Tamaki Yukihiro , Lee Jae Man , Sakao Kozue , Hamanaka Daisuke , Kusakabe Takahiro , Tachibana Mayumi , Ibrahim Hisham R. 
Published: March 2022

AbstractPlasmodium vivax ookinete surface protein, Pvs25 is a transmission-blocking vaccine (TBV) candidate for malaria. Pvs25 has four EGF-like domains containing 22 cysteine residues forming 11 intramolecular disulfide bonds and this structural feature makes recombinant expression of Pvs25 difficult. In this study, we report the high expression of recombinant Pvs25 as a soluble form in silkworm, Bombyx mori. The Pvs25 protein was purified from hemolymphs of larvae and pupae by affinity chromatography. In the Pvs25 expressed by silkworm, no isoform with inappropriate disulfide bonds was found, requiring no further purification step which is necessary in case of Pichia pastoris based expressions systems. The Pvs25 from silkworm were confirmed to be the molecularly uniform by sodium dodecyl sulfate gel electrophoresis analysis and size exclusion chromatography analysis. To examine the immunogenicity, the Pvs25 from B. mori, was administered to BALB/c mice by the subcutaneous (s.c.) route with the oil adjuvant. The Pvs25 produced by silkworm induced potent and robust immune response, and the induced antisera correctly recognized P. vivax ookinetes in vitro, demonstrating the potency of Pvs25 from silkworm as a TBV candidate for malaria. This is the first study that to construct a mass production system for malaria TBV antigens by the silkworm to the best of our knowledge.
Deep learning on reflectance confocal microscopy improves Raman spectral diagnosis of basal cell carcinoma
Authors: Chen Mengkun , Feng Xu , Fox Matthew C. , Reichenberg Jason S. , Lopes Fabiana C.P.S. , Sebastian Katherine R. , Markey Mia K. , Tunnell James W. 
Published: March 2022

AbstractSignificanceRaman spectroscopy may be useful to assist Mohs micrographic surgery for skin cancer diagnosis; however, the specificity of Raman spectroscopy is limited by the high spectral similarity between tumors and normal tissues structures such as epidermis and hair follicles. Reflectance confocal microscopy (RCM) can provide imaging guidance with morphological and cytological details similar to histology. Combining Raman spectroscopy with deep-learning-aided RCM has the potential to improve the diagnostic accuracy of Raman without requiring additional input from the clinician.AimWe seek to improve the specificity of Raman for basal cell carcinoma (BCC) by integrating information from RCM images using an Artificial Neural Network.ApproachA Raman biophysical model was used in prior work to classify BCC tumors from surrounding normal tissue structures. 191 RCM images were collected from the same site as the Raman data and served as inputs to train two ResNet50 networks. The networks selected the hair structure images and epidermis images respectively within all the images corresponding to the positive predictions of the Raman Biophysical Model.ResultsDeep learning on RCM images removes 54% of false positive predictions from the Raman Biophysical Model result and keeps the sensitivity as 100%. The specificity was improved from 84.8% by using Raman spectra alone to 93.0% by integrating Raman spectra with RCM imagesConclusionsCombining Raman spectroscopy with deep-learning-aided RCM imaging is a promising tool to guide tumor resection surgery.
Transcytosis-mediated anterograde transport of TrkA receptors is necessary for sympathetic neuron development and function
Authors: Connor Blaine , Yamashita Naoya , Kuruvilla Rejji 
Published: March 2022

SummaryIn neurons, many membrane proteins, synthesized in cell bodies, must be efficiently delivered to axons to influence neuronal connectivity, synaptic communication, and repair. Previously, we found that axonal targeting of TrkA neurotrophin receptors in sympathetic neurons occurs via an atypical transport mechanism called transcytosis, which relies on TrkA interactions with PTP1B, a protein tyrosine phosphatase. Here, we generated TrkAR685A mice, where TrkA receptor signaling is preserved, but its PTP1B-dependent transcytosis is disrupted, to show that this mode of axonal transport is essential for sympathetic neuron development and autonomic function. TrkAR685A mice have decreased axonal TrkA levels in vivo, developmental loss of sympathetic neurons, and reduced innervation of targets. Postnatal TrkAR685A mice exhibit reduced pupil size and eyelid ptosis, indicative of sympathetic dysfunction. These findings establish the necessity of transcytosis in supplying TrkA receptors to sympathetic axons and highlight the physiological relevance of this axon targeting mechanism in the nervous system.
A new method to estimate the ecological niche throughn-dimensional hypervolumes that combines convex hulls and elliptical envelopes
Authors: Carrasco Jaime , Lisón Fulgencio , Jiménez Laura , Weintraub Andrés 
Published: March 2022

AbstractMethods that estimate the niche of a species by calculating a convex hull or an elliptical envelope have become popular due to their simplicity and interpretation, given Hutchinson’s conception of the niche as ann-dimensional hypervolume.It is well known that convex hulls are sensitive to outliers and do not have the ability to differentiate between regions of low and high concentration of presences, while the elliptical envelopes may contain large regions of niche space that are not relevant for the species. Thus, when the goal is to estimate the realized niche of the species, both methods may overestimate the niche.We present a methodology that combines both the convex hull and the elliptical envelope methods producing ann-dimensional hypervolume that better fits the observed density of species presences, making it a better candidate to model the realized niche. Our method, called the CHE approach, allows defining regions of iso-suitability as a function of the significance levels inherited from the method (Mahalanobis distance model, minimum covariance determinant, or minimum volume ellipsoid) used to fit an initial elliptical envelope from which we then discard regions not relevant for the species by calculating a convex hull.We applied the CHE approach to a case study of twenty-five species of bats present in the Iberian Peninsula, fitting a hypervolume for each species and comparing them to both the convex hulls and elliptical envelopes obtained with the same data and different values ofn. We show that as the number of variables used to define the niche space increases, both the convex hull and elliptical envelope models produce overly large hypervolumes, while the size of the hypervolume fitted with the CHE approach remains stable. As a consequence, similarity measures that account for the niche overlap among different species may be inflated when using convex hulls or elliptical envelopes to model the niche; something that does not occur under the CHE approach.
A rapid review of the effectiveness of alternative education delivery strategies in medical, dental, nursing and pharmacy education during the COVID-19 pandemic
Authors: Carrier Judith , Edwards Deborah , Tombs Michal , Riley Steve , Lewis Ruth , Gillen Elizabeth , Cooper Alison , Edwards Adrian 
Published: March 2022

AbstractBackgroundEducation delivery in higher education institutions was severely affected by the COVID-19 pandemic, with emergency remote teaching developed and adapted promptly for the circumstances. This rapid review investigated the effectiveness of alternative education delivery strategies during the pandemic for medical, dental, nursing and pharmacy students, to help plan and adapt further education provision.MethodsWe included 23 primary studies in undergraduate education, all published in 2020-2021, no relevant UK-based or postgraduate studies were found. Included studies comprised 10 single cohort descriptive; 11 comparative descriptive; and two RCTs. There was considerable variability in terms of students, type of distance learning, platforms used and outcome measures.ResultsIn medicine (n=14), self-reported competency and confidence, and demonstrable suturing skills were achieved through participating in remote learning. However, lower levels of knowledge were obtained by students who received virtual or blended learning compared to in-person teaching (low-very low confidence). Using bespoke interactive platforms in undergraduate medical training was superior to standard video (low confidence) or ‘textbook’ presentations (very low confidence).In dentistry (n=2), remote learning led to knowledge gained (low confidence), but self-reported practical and interpersonal skills were lower with remote rather than in-person learning (very low confidence).In nursing (n=3), remote learning, when compared to in-person, resulted in similar knowledge and self-reported competency levels (very low confidence) pre-COVID, but confidence was higher when learning or assessment was conducted virtually (low confidence).In pharmacy (n=4), virtual learning was associated with higher skills, but lower knowledge compared to in-person, pre-COVID; self-reported competency and confidence scores were similar between the two groups (very low confidence).ConclusionsRemote teaching was valued, and learning was achieved, but the comparative effectiveness of virtual versus in-person teaching is less clear. Supplementary alternative or in-person practical sessions may be required post-emergency to address learning needs for some disadvantaged student groups.
Biologically-derived neoproteoglycans for profiling protein-glycosaminoglycan interactions
Authors: Porell Ryan N. , Follmar Julianna L. , Purcell Sean C. , Timm Bryce , Laubach Logan K. , Kozirovskiy David , Thacker Bryan E. , Glass Charles A. , Gordts Philip L. S. M. , Godula Kamil 
Published: March 2022

AbstractGlycosaminoglycans (GAGs) are a class of highly negatively charged membrane associated and extracellular matrix polysaccharides involved in the regulation of myriad biological functions, including cell adhesion, migration, signaling and differentiation, among others. GAGs are typically attached to core proteins, termed proteoglycans (PGs), and can engage >500 binding proteins, making them prominent relays for sensing external stimuli and transducing cellular responses. However, their unique substructural protein-recognition domains that confer their binding specificity remain elusive. While the emergence of glycan arrays has rapidly enabled the profiling of ligand specificities of a range of glycan-binding proteins, their adaptation for the analysis of GAG-binding proteins has been considerably more challenging. Current GAG-microarrays primarily employ synthetically defined oligosaccharides, which capture only a fraction of the structural diversity of native GAG polysaccharides. Augmenting existing array platforms to include GAG structures purified from tissues or produced in cells with engineered glycan biosynthetic pathways may significantly advance the understanding of structure-activity relationships in GAG-protein interactions. Here, we demonstrate an efficient and tunable strategy to mimic cellular proteoglycan architectures by conjugating biologically-derived GAG chains to a protein scaffold, defined as neoproteoglycans (neoPGs). The use of a reactive fluorogenic linker enabled real-time monitoring of the conjugation reaction efficiency and tuning of the neoPG valency. Immobilization of the reagents on a 96-well array platform allowed for efficient probing of ligand binding and enzyme substrate specificity, including growth factors and the human sulfatase 1. The neoPGs can also be used directly as soluble probes to evaluate GAG-dependent growth factor signaling in cells.Graphical Abstract
Notch signaling in germ line stem cells controls reproductive aging in C. elegans
Authors: Kocsisova Zuzana , Bagatelas Elena D. , Santiago-Borges Jesus , Lei Hanyue Cecilia , Egan Brian M. , Mosley Matthew C. , Schneider Daniel L. , Schedl Tim , Kornfeld Kerry 
Published: March 2022

AbstractReproductive aging in females often occurs early in life, resulting in a substantial post-reproductive lifespan. Despite the medical importance of age-related infertility, relatively little is known about mechanisms that control this age-related decline. C. elegans is a leading system for aging biology due to its short lifespan and powerful experimental tools, and detailed descriptions of molecular and cellular changes in the gonad during reproductive aging were recently reported. Here we show that reproductive aging occurs early in life in multiple species in the genus Caenorhabditis, indicating this is a feature of both female/male and hermaphrodite/male species. In mutants previously established to display delayed reproductive aging (daf-2, eat-2, phm-2), we observed correlations between changes in the distal germline and changes in egg-laying, consistent with the model that distal germline changes are a cause of reproductive aging. By screening for additional mutants that delay reproductive aging, we identified an allele of che-3 with impaired sensory perception that displayed increased progeny production in mid-life, a pattern of reproductive aging distinct from previous mutants. To directly test the role of Notch signaling in the distal germline, we analyzed the effect of ectopic expression of the Notch effector gene SYGL-1. Ectopic expression of SYGL-1 was sufficient to delay reproductive aging, suggesting that an age-related decline in Notch signaling in the distal germline is a root cause of reproductive aging.
A dual-target herbicidal inhibitor of lysine biosynthesis
Authors: Mackie Emily R. R. , Barrow Andrew S. , Christoff Rebecca M. , Abbott Belinda M. , Gendall Anthony R. , Soares da Costa Tatiana P. 
Published: March 2022

ABSTRACTHerbicides with novel modes of action are urgently needed to safeguard global agricultural industries against the damaging effects of herbicide-resistant weeds. We recently developed the first herbicidal inhibitors of lysine biosynthesis, which provided proof-of-concept for a promising novel herbicide target (Soares da Costa et al., 2021). In this study, we expanded upon our understanding of the mode of action of herbicidal lysine biosynthesis inhibitors. We previously postulated that these inhibitors may act as proherbicides (Soares da Costa et al., 2021). Here we show this is not the case. We report an additional mode of action of these inhibitors, through their inhibition of a second lysine biosynthesis enzyme, and investigate the molecular determinants of inhibition. Furthermore, we extend our herbicidal activity analyses to include a weed species of global significance.
Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth
Authors: Chure Griffin , Banks Rachel A. , Flamholz Avi I. , Sarai Nicholas S. , Kamb Mason , Lopez-Gomez Ignacio , Bar-On Yinon , Milo Ron , Phillips Rob 
Published: March 2022

SummaryThe Human Impacts Database (www.anthroponumbers.org) is a curated searchable resource housing quantitative data relating to the diverse anthropogenic impacts on our planet, with topics ranging from sea level rise, to livestock populations, greenhouse gas emissions, fertilizer use, and beyond. Each entry in the database relates a quantitative value (or a time-series of values) along with clear referencing of the primary source, the method of measurement or estimation, an assessment of uncertainty, links to the underlying data, as well as a permanent identifier called an Human Impacts ID (“HuID”). While there are other databases that house some of these values, they are typically focused on a single topic area like energy usage or greenhouse gas emissions. The Human Impacts Database provides centralized access to quantitative information about the myriad ways in which humans impact the Earth, giving links to more specialized databases for interested readers. Here, we outline the structure of the database and describe our curation procedures. Finally, we use this database to generate a graphical summary of the current state of human impacts on the Earth, illustrating both their numerical values and their dense interconnections.The Bigger PictureOver the last 10,000 years, human activities have transformed the Earth through farming, forestry, mining and industry. The complex results of these activities are now observed and quantified as “human impacts” on Earth’s atmosphere, oceans, biosphere and geochemistry. While myriad studies have explored facets of human impacts on the planet, they are necessarily technical and often tightly-focused. Thus, finding reliable quantitative information requires a significant investment of time to assess each quantity, its methods of determination, and associated uncertainty. We present the Human Impacts Database (www.anthroponumbers.org), which houses a diverse array of such quantities. We review a subset of these values and how they help build intuition for understanding the Earth-human system. While collation alone does not tell us how to best ameliorate human impacts, we contend that any future plans should be made in light of a quantitative understanding of the interconnected ways in which humans impact the planet.
Ancestry-specific maps of GRCh38 linkage disequilibrium blocks for human genome research
Authors: MacDonald James W. , Harrison Tabitha A. , Bammler Theo K. , Mancuso Nicholas , Lindström Sara 
Published: March 2022

AbstractA map of approximately independent linkage disequilibrium (LD) blocks has many uses in statistical genetics. Current publicly available LD block maps are based on sparse recombination maps and are only available for GRCh37 (hg19) and prior genome assemblies. We generated LD blocks in GRCh38 coordinates for African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) ancestry populations. These new maps consist of 1,143 (EAS) - 1,604 (AFR) independent LD blocks across the 22 autosomal chromosomes and can be accessed athttps://github.com/jmacdon/LDblocks_GRCh38.