bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Size and Shape of the C4 Segment of the Intracavernous Carotid Artery Intermediate to the Petrolingual Ligament and the Abducens Nerve: Implications for Neurosurgery
Authors: Nestor Nicholas , Hunter Dawn , Ritz Brianna , Zdilla Matthew 
Published: June 2021

Neurosurgical management of the neurovascular structures encompassed within the cavernous sinus may be aided by improved understanding of neurovascular anatomical relationships. Therefore, this study assessed the morphometry of the C4 segment of the intracavernous carotid artery as it relates to the petrolingual ligament and abducens nerve in cadavers. A total of 40 sides were assessed (18 female and 22 male sides). The area of the carotid artery intermediate to the petrolingual ligament and the abducens averaged 17.56±10.86mm2 (Mean±SD). The anterior and posterior distances from the petrolingual ligament to the abducens nerve averaged 3.12±1.72mm and 3.17±1.58mm, respectively. Further, unpaired T‐tests revealed no significant differences between sexes with regard to the area (p = 0.82), anterior distance (p = 0.96), and posterior distance (p=0.94). Further, three morphotypes for the window between the petrolingual ligament and abducencs were identified; namely, quadrilateral (n=30), triangular (n=8), and atretic (n=2). The results of this study will help improve the approach to lesions including C4 aneurysms and local tumors including those of the abducens.Support or Funding InformationFunding: WV Research Challenge Fund [HEPC.dsr.17.06]This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Predictive model of cranial growth in infants with cranial deformation
Authors: Aldridge Kristina , Shock Leslie A , Panchal Sarjukumar , Martin Andrea L , Mukherjee Anish , Chakraborty Sounak , Muzaffar Arshad R 
Published: June 2021

Differences in cranial growth trajectories define morphological variation in both normal and pathological conditions. Predicting divergent trajectories is key to understanding how and when morphological variation is produced. The incidence of cranial deformation in human infants, specifically deformational plagiocephaly and brachycephaly, has increased dramatically with the initiation of the Back to Sleep campaign in the 1990s. Treatment often requires several months of helmet therapy. However, practitioners have no objective means for reliably estimating the necessary duration of therapy. The goal of this study was to develop a model to provide individualized predictions of duration of helmet therapy using cranial growth trajectories.We obtained STARscanner® 3D laser scan images of 541 children seen in clinic for abnormal head shape at their first visit and again at completion of helmet therapy with IRB approval. Measurements obtained from images at both visits included head circumference, cephalic ratio, oblique diameter difference, cranial vault asymmetry index, sex, and age. A Multivariate Random Forest Model was used to fit the model with 200 trees and 441 patients in the training set. A five‐fold cross‐validation was performed to assess accuracy of the model's prediction of cranial measurements with respect to the duration of helmet therapy. Data from the remaining 100 patients were used to validate the resulting model.Our Multivariate Random Forest model predicts accurately cranial growth trajectories during helmet therapy in infants with cranial deformation. The five‐fold cross validation error of our model is more than 22% lower than standard linear models, with average mean squared error of 0.2568. These results demonstrate that necessary duration of helmet therapy can be accurately predicted using our smart machine learning method.Thousands of infants per year are treated for cranial deformation. Using machine learning, we have developed a model that predicts individualized, evidence‐based treatment strategies accurately. The model is incorporated into a web‐based interface that can be used by practitioners in real time. Used in combination with practitioners' expertise, families will be informed about the likely length of treatment and degree of improvement that may be expected for their individual child. Importantly, while the model developed here is specific to infant cranial deformation, the approach is easily translatable to other craniofacial anomalies, as well as to normal patterns of cranial growth.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Airway management and anatomical development of the pediatric aerodigestive tract (ADT): current knowledge and clinical applications
Authors: Curcio Daniella Francon , Barros Mirna Duarte , Liquidato Bianca Maria , Mendes Carlos Jose Lazzarini , Cabral Julia Chaeves , Morad Helena Machado , Laitman Jeffrey T. 
Published: June 2021

Pediatric airway management can be difficult and especially hazardous due to a number of anatomical features of the developing aerodigestive tract (ADT), which is so different from the adult. Such differences have been presented annually since 2013 at EB meetings (Micham and Laitman, 2013; Curcio et al., 2014; Curcio and Laitman, 2015; Meaike et al., 2016; Gupta et al., 2016; Curcio et al., 2017, Curcio and Laitman, 2018). Particularly in regards to clinical applications involved in airway management procedures, our attention has been drawn to bedside tests that have been used to predict difficult intubation and difficult laryngoscopy in infants and young children. In stage 1 of this study we compiled a multi‐field database review of the mostly used bedside tests that predict difficult intubation of infants under 5 months of post‐natal life. We verified that ease of tracheal tube passage depends on the size of the cricoid ‐ the circular or near circular cartilage located at the inferior most portion of the funnel‐shaped infant larynx. We also selected the Laryngoscore (Piazza et al. 2014; 2018; Incandela et al, 2018), the frontal plane to chin distance, and the FPCD/weight ratio (Mansano et al., 2016) to be included in the next stages of this study. Our hypothesis is that it might be possible to adapt and increase the accuracy of such bedside tests and protocols that predict difficult intubation and laryngoscopy in infants and young children. This study is part of a larger project designed by our Brazilian‐US joint research team that seeks to explore possibilities and optimize airway management in elective procedures, critical and emergency care of pediatric patients under 5 months of age.Support or Funding InformationIn conjunction with the Building Bridges initiatives. Funded in part by CNPq ‐ Brazilian National Counsel of Technological Development.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Connexin 43 Function in the Cranial Neural Crest
Authors: Jourdeuil Karyn , Taneyhill Lisa Anne 
Published: June 2021

Connexins are transmembrane proteins that cluster to form intercellular channels called gap junctions, which function to allow direct diffusion of small molecules and ions between adjacent cells. Gap junctions are composed of two connexons (one on each cell which are docked head‐to‐head) consisting of either homomeric or heteromeric connexin proteins. Connexin 43 (Cx43) is one of the predominant components of gap junctions and is expressed in multiple organisms and their tissues. To date, however, very little is known about the role of gap junctions, and specifically Cx43, in the neural crest. Our prior immunohistochemical analyses revealed that Cx43 is expressed in premigratory cranial neural crest cells both prior to and during their epithelial‐to‐mesenchymal transition (EMT), and in migratory neural crest cells. Given the robust expression of Cx43 in premigratory neural crest cells, we sought to elucidate the role of Cx43, and gap junctions in particular, during neural crest cell EMT. To this end, we evaluated the presence of gap junctions in the neural crest and performed molecular and chemical perturbation experiments to alter Cx43 and general gap junction function. Our results reveal that gap junctions form between migratory neural crest cells, demonstrated in the embryo and in explants of premigratory neural crest tissue cultured ex vivo. Live‐imaging of embryos initially possessing Calcein‐AM (a dye that only traverses gap junctions) in a small number of premigratory neural crest cells demonstrates passage of dye to adjacent cells over time. Additionally, depletion of Cx43 from premigratory neural crest cells reveals changes in some neural crest cell molecular markers. In ex vivo explants, Cx43 knockdown in migratory neural crest cells precludes transfer of Calcein‐AM dye, and abrogation of gap junction function through chemical inhibition hinders neural crest cell EMT and/or migration. In future experiments, we will ascertain the effects of Cx43 knockdown and overexpression on neural crest cell EMT and migration in vivo by examining passage of Calcein‐AM dye to assess gap junction function and through immunohistochemistry to evaluate changes in neural crest cells. These data will provide insight into how neural crest cells interact and communicate during EMT and migration to allow for proper embryonic patterning throughout vertebrate development.Support or Funding InformationThe work was supported by grants to L.A.T. (NIH R01DE024217, American Cancer Society RSG‐15‐023‐01‐CSM).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Developmental localization of syntaxin 1 and synaptosomal‐associated protein 25 in rat palate
Authors: Hakami Afaf , Shafei Ahlam , Alhakami Khalid , Hakami Zaki 
Published: June 2021

IntroductionThe palate, which plays an important role in oral cavity function, including the mastication and swallowing of food, obviously differs structurally with feeding habits. Nevertheless, the palate is considered the most common location of both benign and malignant minor salivary gland tumors. Soluble N‐ethylmaleimide‐sensitive fusion protein attachment protein receptor (SNARE) proteins are important in the control of tumorigenesis through the regulation of multiple signaling and transportation pathways. However, the developmental distribution of SNARE proteins on the palatal structures has been scarcely reported. Therefore, this study aimed to investigate SNARE proteins, syntaxin‐1, synaptosomal‐associated protein of 25 kDa (SNAP‐25) during the development of rat palates.Materials and MethodsImmunohistochemistry for protein gene product 9.5 (PGP 9.5), a pan‐neuronal marker, syntaxin‐1 and SNAP‐25 was performed on frozen sections of rat palatal tissues at different stages.ResultsPGP 9.5 immunoreactive fibers (IRF) were present in developing palate. They were observed along the palatal sub‐epithelial layer and the underlying connective tissues in association with developing acini, ducts, blood vessels. Nerve fibers containing syntaxin‐1 and SNAP‐25 showed similar distribution to PGP 9.5 and thick bundles of nerve fibers were observed with smooth muscles and varicoses. With maturation after postnatal day 7 (PN7), thin nerve fibers containing PGP 9.5 and SNAP‐25, but less syntaxin‐1, were detected penetrating into the epithelium, reaching beneath the cornified layer. They ramified out from subepithelial thick bundles into connective tissues until encircling the secretory units observed (PN21). In adults, the number of syntaxin‐1‐IRF was low in comparison with SNAP‐25 and PGP 5 fibers.ConclusionThe findings indicated the importance of SNARE proteins during the maturation of the palatal tissues.Support or Funding InformationNoneThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
G‐Triplex DNA Formation Determined by SPR and Native Agarose Gel Electrophoresis
Authors: Al‐Der Carina C , Smith Sydney E , Tippayasak Krishna , Tuesuwan Bodin , Kerwin Sean M , David Wendi M 
Published: June 2021

G‐quadruplex DNA structures (G4 DNA), such as those found in human telomeres, may play important roles in cellular replication and gene regulation. Dysregulation of processes involving G4 DNA is associated with cancer and some neurodegenerative diseases. G4 DNA, composed of stacked G‐tetrads based on hydrogen bonding between guanine nucleotides, has been characterized by a number of techniques, including the gel electrophoresis and surface plasmon resonance (SPR) methods used in the current study. G‐triplex DNA structures (G3 DNA) are folding intermediates of some quadruplexes, but their role in vivo is less clear. To further characterize G3 DNA we adapted a native agarose gel electrophoresis method for separating small oligonucleotides and also used SPR to probe the extent of folded and unfolded structures. We have previously used SPR to calculate the extent of intramolecular folding in the human telomeric G4 sequence under varying buffer conditions. G3‐forming oligonucleotides from a truncated human telomeric sequence, truncated thrombin binding aptamer sequence, and other similar G‐rich sequences were subjected to the same SPR method. The extent of folding was determined by calculating % hybridization values for a C‐rich complementary duplex binding probe to the immobilized G3‐forming sequence. Under most buffer conditions, hybridization to the truncated thrombin binding aptamer was >50%, in agreement with the lower thermal stability of this G3‐folded structure. Differences in kinetic profiles for the hybridization of the probe in the presence of different cations (Li+, Na+, K+, Ca2+) were apparent. In contrast, almost no hybridization was observed for a G3TG3TG3 sequence under similar buffer conditions. Analysis by native agarose gel electrophoresis indicates the persistence of folded structures for the truncated human telomeric sequence (G3), similar truncated telomeric G‐rich (G3) sequences, and a G4‐forming sequence from c‐MYC, but not for the truncated thrombin binding aptamer sequence.Support or Funding InformationCancer Prevention and Research Institute of TexasThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Sequence and Environmental Effect on the Formation of G‐Triplex DNA
Authors: Bracey Harrison , Baqdounes Yasmin , Navapan Nattinee , Tuesuwan Bodin , David Wendi , Kerwin Sean 
Published: June 2021

It has recently been shown that certain G‐quadruplex DNA (G4) structures fold via a “G‐triplex” intermediate, and that the corresponding truncated G‐quadruplex‐forming oligonucleotides also adopt G‐triplex structures. However, it is not clear how general G‐triplex formation is, or how sequence and buffer conditions affect G‐triplex formation. Our approach to investigate G‐triplex formation by a series of truncated G4‐DNA sequences used CD spectroscopy, UV thermal‐difference spectroscopy, CD derived and UV derived melting temperature measurements, and native PAGE gels to characterize the topology and thermal stability of these structures in Li+, Na+, K+, Mg2+ and Ca2+ containing buffers.G‐triplex formation is a general phenomenon for a wide range of truncated G4 DNA sequences. We examined 16 different variants of the G≥2T1–4G≥2T1–4G≥2 sequence as well as truncated versions of the TBA and human telomeric G4 DNA in both forward and reverse permutations. All of these sequences can adopt G‐triplex structures. However, we note that the number of nucleotides in the loop and sequence direction affect G‐triplex topology. Sequences with longer G‐tracks tends to form parallel G‐triplex, as do sequences with fewer loop residues. Permutation of the direction of the truncated G4 DNA sequence also affect G‐triplex folding topology. Environmental effects on topology were also noted, with divalent metal ions (Mg2+ and Ca2+) favoring parallel topologies. Using thermal‐difference spectroscopy, we have identified two families of spectra that correlate to G‐triplexes with a parallel topology. Analysis by native PAGE indicates that some sequences may form multiple G‐triplex topologies under certain environmental conditions.Temperature melts have provided information regarding sequence composition, sequence direction, and environmental conditions on the thermal stability of G‐triplex DNA. Sequences with longer G‐runs form G‐triplex structures that are more thermally stable (GGGG > GGG > GG). Shorter T‐loops form G‐triplex structures that are more thermally stable (TT >TTT > TTTT). Direction of sequence also effects the stability. Environmental conditions such as the presence of different cations have an effect of stability (Ca2+ > K+ > Mg2+ ≥ Na+).The biological relevance of G‐triplex DNA is still not entirely understood. Understanding how sequence effects and environmental conditions affect G‐triplex structure and stability is essential for better studying G‐quadruplex DNA and the biological relevance of G‐triplex DNA.Support or Funding InformationCPRIT HIHR Grant RP160852 and Texas State University.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterizing Basal‐like Triple Negative Breast Cancer using Gene Expression Analysis: A Data Mining Approach
Authors: Alsabi Qamar , Zadeh Amir Hassan , Ramirez Jaime , Nosoudi Nasim 
Published: June 2021

Triple‐negative breast cancer (TNBC) constitutes approximately 20%–25% of all breast cancer cases with poor prognosis. It is unresponsive to targeted hormonal therapies, which limits treatment options to nonselective chemotherapeutic agents. Recently, gene expression analysis has shown promise to characterize triple negative breast cancers (TNBC). Although TNBCs have many basal‐like breast cancer characteristics, the relationship between clinically defined triple‐negative breast cancer and the gene expression profile of basal‐like breast cancer (BLBC) is not fully examined. The purpose of this study is to assemble publicly‐available TNBC gene expression datasets generated on Affymetrix gene chips and define a set of genes, or gene signature, that can classify BLBC and Non‐BLBC subtypes under TNBC type. We compiled over 3,500 breast cancer gene expression profiles from several individual publicly available datasets and extracted Affymetrix gene expression data for 580 TNBC cases. Several popular data mining along with variable reduction and feature selection techniques were applied to the resultant data sets to build predictive models to understand molecular characteristics and mechanisms associated with BLBCs and classify them more accurately according to important features extracted from Microarray data analysis of BLBC and Non‐BLBC cases. Our result can lead to proper identification and diagnosis of BLBCs, which can potentially direct clinical implications by dictating the most effective therapy.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Screening for Novel Regulators of Wingless Signaling
Authors: Marsh‐Armstrong Gwynn Isabel , Kennell Jennifer 
Published: June 2021

The Wingless (Wg) pathway within Drosophila melanogaster is a well characterized intercellular signaling network that has been implicated in tissue specific cellular differentiation. However, the mechanism by which Wg signaling contributes to tissue specific changes in gene expression is still unclear. Previously, the Kennell Lab conducted a series of misexpression screens in order to identify novel regulators of Wg signaling. Wg signaling alters gene expression in various tissues through the action of the transcriptional coactivator Armadillo (Arm). As such, the Kennell lab was able to identify potential regulators of Wg signaling during eye development by measuring whether the alteration of a gene's expression using UAS enhancers had any effect on the development of an Arm‐dependent small‐eye phenotype. Once genes known to cause apoptosis independent of Wg signaling were discarded from the list of genes that caused suppression of the small‐eye phenotype, fifteen promising candidates remained. Of these identified genes, siz and CG5902 were selected for further in vivo characterization. The gene CG5902 has never before been characterized and the gene siz has been implicated in actin cytoskeleton organization and central nervous system development. The gene CG5902 was successfully subcloned into expression vectors and transfected into Kc167 cells in order to test Arm target gene expression using reporter gene assays. Additionally, siz and CG5902 knockdown strains of Drosophila melanogaster are currently being created in order to further characterize the effect of these genes on Arm target gene expression and eye development.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
SV40 virion formation functions as a novel epigenetic switch controlling early and late transcription
Authors: Milavetz Barry , Balakrishnan Lata , Ajeeth‐Kumar Meera 
Published: June 2021

Simian Virus 40 (SV40) is a small double‐strand DNA virus, which exists in the form of chromatin throughout its lifecycle. Because of its chromatin structure, the virus is expected to undergo the typical forms of epigenetic regulation, including differential nucleosome location and histone modifications. In order to characterize the epigenetic changes occurring during the formation of virions from late‐stage SV40 minichromosomes (encapsidation), we have compared the location of nucleosomes containing acetylated or methylated lysines from the histone tails of H3 and H4 present in the chromatin from late‐stage minichromosomes, encapsidation intermediates, and disrupted virions. In late‐stage minichromosomes, we found that nucleosomes carrying histone modifications were primarily found in the SV40 regulatory region within the enhancer and at the early and late transcription start sites. Significantly, the nucleosome containing modified histones within the enhancer would be expected to repress early transcription by overlying regulatory sequences in the SP1 and enhancer regions required for early transcription while still allowing for late transcription. In contrast, in chromatin from virions the nucleosome found in the enhancer has been shifted approximately 70 base‐pairs toward the late region uncovering the regulatory sequences necessary for early transcription and likely repressing late transcription. This encapsidation‐dependent epigenetic switch was associated with the final stages of virion formation.Support or Funding InformationThis work was funded by grants from the National Institutes of Health, AI094441 (to B.M.) and GM098328 (to L.B.) and P20 GM113123 (to Epigenetics Core)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.