bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel tools for investigations of cytoskeletal re‐arrangement during alveolar epithelial‐mesenchymal transition
Authors: Ehrhardt Carsten , Medina Carlos , Davies Anthony Mitchell , Buckley Stephen Timothy 
Published: June 2021

Inherent in epithelial‐mesenchymal transition (EMT) is the establishment of an elongated cell morphology and formation of stress fibres. The influence of these cellular alterations on the biomechanics of lung parenchyma remains unclear. Alveolar A549 cells, after exposure to TGF‐β1, were studied using atomic force microscopy (AFM) and high content analysis (HCA) imaging.A549 cells were grown with or without TGF‐β1 in the presence or absence of a collagen I substrate for 72 h. Using AFM, the Young′s modulus of living cells was measured in contact mode. Surface membrane features were assessed on fixed cells using intermittent contact mode. In parallel, morphological and fluorescence staining intensity/distribution parameters were evaluated using a HCA imaging system.TGF‐β1 resulted in a greater than two‐fold increase in cell stiffness. This effect was augmented in the presence of collagen I. TGF‐β1‐treated cells also exhibiting a rougher surface profile with notable protrusions. In accordance with these findings, concurrent quantitative examination of the morphological attributes of stimulated cells using HCA, revealed dramatic alterations in cell shape, F‐actin content and distribution.These data indicate a strong correlation between the cytoskeletal‐associated cellular architecture and the mechanical dynamics of alveolar epithelial cells undergoing EMT.
A new foramen on ala of sacrum
Authors: Singh Rajani 
Published: June 2021

A new foramen on posterior part of ala of sacrum was found during routine osteology class of MBBS students in the Department of Anatomy, CSM Medical University Lucknow, UP, India.Almost no literature is available on this virgin foramen therefore, theory of this variant and clinical significance need to be conceptualised. So objective of this study has been set to add new model of anatomical theory and to develop clinical implication of this foramen.Therefore, sixty six sacra were examined and analysed for incidence, position, shape and size of foramen Rajani (as named). Foramen is located at 8mm from sacral canal, 20mm from posterior tip of ala of sacrum and 5mm from posterior border of body of first sacral vertebra with incidence of 1.5%. It is oval shaped having its horizontal and vertical dimensions as 6 mm, 4mm. It communicates with the sacral foramina and sacral canal.The structures, common iliac, or iliolumber artery or lumbosacral trunk is likely to pass through the foramen Rajani. These structures may be damaged during pedicle screw fixation or instrumentation by orthopaedic surgeons and neurologists.Author could not avail the financial support from any institution.
A rare variant of the median nerve as a reminder of the patient uniqueness
Authors: Kumka Myroslava 
Published: June 2021

ObjectiveDespite the wealth of data concerning anatomical variation of the median nerve, it remains important to continue describing rare variations as they arise. This study represents a unique variation of the median nerve in the human forearm.Methods32 upper limbs of 16 embalmed cadavers were utilized using anatomical dissections.ResultsThe median nerve in a right forearm of a 61 year old male cadaver followed the pathway seen in the majority of cases except during the course within the epimysium of the deep surface of Flexor Digitorum Superficialis (FDS). About half way down the muscle belly, a substantial branch equal in diameter to the main trunk of the median nerve, branched off the main trunk and perforated the FDS muscle. This variant branch continued distally within the FDS muscle belly, until it reached the distal third of forearm. Then, this aberrant branch reunited with the main trunk of the median nerve as it emerged on the lateral aspect of the distal tendon of FDS (7.4cm distally from the branch point at a level 2.5cm proximal to the pisiform bone).ConclusionThe unique variation described in this study was not found to be described in the literature. It is a reminder of the concept of patient uniqueness and the need for individualization of medical, manual, and surgical treatments offered to patients.
Estimating age from photographs of children's faces
Authors: DeLeon Valerie Burke , Chollet Madeleine B , Monteiro Stephen , Chung Sarita 
Published: June 2021

Reuniting children separated from their families following mass disasters is a primary goal for emergency management teams. We are developing a system to facilitate this process based on automated extraction of information from photos of children collected by emergency personnel. One of our goals has been to determine the best method for estimating age of a child from such a photo, obtained under adverse field conditions where standardized collection protocols cannot be assured.Our sample consisted of 110 children of known ages (2 mos – 16 yrs). Photos of the face were collected in frontal view. We manually collected a set of 17 landmarks using ImageJ. We developed a novel approach to establish scale in each photo based on our expectation that iris size does not vary with age. Right and left sides were averaged to reduce the effect of positioning error. Landmarks were superimposed, and we used multiple regression to test the predictive value of these facial shape variables for the estimation of age.Our results allowed us to predict age +/− 2.5 years (95% CI). Centroid size was the most important variable in predicting age, highlighting the importance of our novel approach to establishing scale. We plan to extend these finding to landmarks that can be automatically extracted from facial photos, allowing a fast and efficient method to limit the number of photos that families must review during the reunification process.Research was funded by HRSA EMSC Targeted Issue 5H34MC105750300.
Population Differences in Glenoid Fossa Dimensions: A 3‐D Geometric Morphometric Study
Authors: Maloney Marvelle Tekola , Pagano Anthony Santino , Marquez Samuel 
Published: June 2021

The postcranial skeleton has long been studied within the context of modern human variation. Populations from cold and warm climates have been shown to exhibit shorter and longer limbs, respectively. This study tests whether the dimensions of the glenoid fossa and overall scapula also vary between populations from temperate and tropical climates. Three‐dimensional landmark coordinate data was collected from a sample of Euroamerican (EA; n=15) and Afroamerican (AA; n=15) scapulae from the division of Anthropology of the American Museum of Natural History in New York. Coordinate data from each individual was optimally scaled and superimposed as part of a Generalized Procrustes Analysis. Surface area of the glenoid fossa and the volume of humeral head accommodated within it were synthesized from interlandmark distances. It was found that the EA possessed significantly (p<0.05) taller (between the superior and inferior scapular angles) and narrower (between the acromioclavicular joint and medial boundary of the spine) scapular shape. However, there was no significant difference in the dimensions of the glenoid fossa. The results suggest that the overall proportions of the scapula share a closer relationship to limb proportion and ancestry than glenoid fossa morphology.Grant Funding Source: SUNY Downstate Medical School
Tracking the Inferior Limit of Human Spinal Cords in Donor Bodies and Live Subjects
Authors: Golubovskaya Yevgeniya , Fisher Yuliya , Pagano Anthony S , Marquez Samuel 
Published: June 2021

The human spinal cord is usually reported in medical texts as ending at the L1‐L2 vertebral levels. However, some individuals exhibit terminations at higher or lower vertebral levels. This study investigates variation in the level of caudal termination of the human spinal cord in a geriatric cadaveric sample (n=22; above 63 years of age at death) and in younger, living individuals (n=10). To determine that vertebral columns examined in donor bodies showed normal curvature, a rod was placed from external occipital protuberance (EOP) to sacral hiatus to determine the vertical line of reference (VLR) and its length. Individuals showing deviation from the VLR (i.e., scoliotic patterns) were noted. Laminectomies were performed on donor bodies to expose the vertebral canal, allowing the assignment of vertebral level to the conus medullaris. A similar protocol was followed on MR images of live subjects. All measures were collected by multiple observers to reduce bias and increase accuracy. Most (63%) of the cadavers exhibited termination at or before the superior border of L2. However, variations were present with termination levels ranging from T11‐L3 vertebrae. The live subjects expressed a similar pattern thus demonstrating that termination level of the spinal cord is independent of age. These results underscore the importance of performing spinal taps at the lowest possible vertebral levels.Grant Funding Source: SUNY Downstate College of Medicine
Assessing Compressive Strengths and Load to Failure Limits among Vertebral Bodies: An Anatomical Study
Authors: Fisher Yuliya , Golubovskaya Yevegeniya , Hayes Westley , Saha Subrata , Marquez Samuel 
Published: June 2021

The strength and compression resistance of vertebral bodies have important clinical implications with regard to susceptibility to impact trauma. This study compares compression resistance limits between the thoracic and lumbar centrums from cadaveric material to evaluate structural strength and fracture risk. The samples were radiographed to ensure healthy specimens with no evident pathologies and to document density properties (e.g., osteoporotic characteristics). Vertebral bodies were mechanically tested in compression, using the Instron 8874 (Norwood, MA) Servohydraulic Test System. Results show thoracic and lumbar strengths ranging from 0.91 N/mm2 to 1.57 N/mm2 and 0.67 N/mm2 to 1.05 N/mm2, respectively. Average maximum load to failure for the thoracic samples was 1011 N and 1620 N for lumbar samples. This study showed that while lower vertebral bodies exhibited higher load to failure values, thoracic centrums demonstrated greater maximum stress during compressive testing. Our preliminary results may shed light on the clinical understanding of compression fractures, common in the elderly, for improved outcomes.Grant Funding Source: SUNY Downstate College of Medicine
The evolution of interoception: a comparison of insular and cingulate cortices in human and non‐human primates
Authors: Bethune Serene A. , Kaufman Jason A. 
Published: June 2021

The insular cortex (IC) and anterior cingulate cortex (ACC) are components of a neural network involved in interoception, or awareness of the body's internal state. Previous research suggests that the cortical representation of interoceptive information in IC and ACC is unique to higher primates, including great apes and humans, and has been expanded and/or lateralized in these species. In this study, we used voxel‐based morphometry to measure the volume of IC and ACC among humans and anthropoid primates with particular interest in asymmetries and allometric deviations. T1‐weighted anatomical scans of anthropoid primate brains were acquired ex vivo using 7‐ and 9.4‐Tesla high‐field imaging systems. T1‐weighted scans of human brains were acquired in vivo using 3‐Tesla clinical imaging systems. Our data indicate that human and bonobo brains both exhibit left‐right asymmetry of the ACC in which the volume of the right ACC is significantly larger than the left. These results are consistent with known lateralization of higher cognitive functions, with the right hemisphere dominating in interoceptive tasks. The lateralization of IC and ACC could represent an important evolutionary adaptation for interoceptive capacities necessary for complex social cognition.This research was supported by an intramural grant from Midwestern University.Grant Funding Source: Midwestern University Intramural Grant
Proteoglycan and ADAMTS expression during fibrogenic remodeling in the liver
Authors: Maurice Sean B , Crick Cody , Kim Wan‐Cheol , Law Christine , Kim Sang‐Eun , Winwood Paul J 
Published: June 2021

Liver fibrosis and end stage cirrhosis are leading causes of morbidity and mortality worldwide. Changes in the structure and composition of the proteoglycan rich extracellular matrix (ECM) are known to play a role in these processes, though these changes are incompletely understood and characterized. An increased understanding of these events may one day allow early recognition and targeted therapy, leading to the reversibility of liver fibrosis as a future clinical outcome.In other tissues, proteoglycans including versican are key components of fibrotic ECM that modulates cellular functions. The ADAMTS enzymes are now known to cleave versican and other proteoglycans in a manner previously ascribed to the MMPs. This work focuses on the role of the hepatic stellate cell in synthesizing a proteoglycan rich fibroproliferative ECM in vitro and in vivo.We have investigated several candidate proteoglycans, including versican, along with several candidate ADAMTS enzymes, in two models of liver fibrosis. Using qPCR and confocal microscopy, we report a more thorough expression profile for these important ECM constituents than has previously been described. These findings underscore the need to better characterize the fibroproliferative liver ECM.Grant Funding Source: Northern Medical Program
TGF‐Beta Permits Invasion of Pre‐Cancerous Keratinocytes in De‐Epidermized Dermis
Authors: Hughes Lindsay Nicole , Vaughan Melville B 
Published: June 2021

Epithelial to mesenchymal transition (EMT) is an important phenotype change in the progression of carcinoma. Immortalized keratinocytes that over‐express the oncogene ras (Ker‐ct‐ras), are known from previous research to undergo EMT in vitro when put in a permissive environment. Our objective was to add Transforming Growth Factor Beta (TGF‐beta) to permit EMT in two known EMT‐inhibiting environments, De‐epidermized Dermis (DED) and liquid basement membrane skin equivalents. To test this hypothesis, Ker‐ct‐ras were plated on top of DED, then cultured in the presence or absence of TGF‐beta. The tissues were fixed at 7, 13, and 20 days for frozen and paraffin sections. Dermal invasion and protein expression changes related to EMT were evaluated, such as loss of e‐cadherin and gain of vimentin. The cells migrated from the epidermis into the dermal layer in a DED environment treated with TGF‐beta. The DED model is appropriate to study EMT and MET but is difficult to obtain and utilize, thus liquid basement membrane skin equivalents will be tested similarly. The responsiveness of Ker‐ct‐ras to environmental changes will be helpful to study gene expression changes related to cancer development.Grant Funding Source: NCRR INBRE P20RR016478
Mouse models for the study of SPO11 splicing isoforms
Authors: Pratto Florencia , Bellani Marina , Camerini‐Otero Rafael Daniel 
Published: June 2021

Meiotic recombination is initiated by the formation of programmed DNA double‐strand breaks (DSB) catalyzed by the SPO11 protein. This protein is widely conserved and homologs have been isolated from mouse and human. There are many alternatively spliced variants of SPO11 and two major forms (α and β) are readily detected in testes.In males, the two major isoforms have distinct expression kinetics. Spo11 β transcripts (including all 13 exons) are found in early stages of prophase I whereas Spo11 α transcripts (exon 2 skipped) are mainly synthesized past pachytene stage. Since breaks are introduced in early prophase, the simplest model suggests that the larger form of SPO11 is the catalytic form that generates the DSB, while the smaller form has an alternative role in late prophase.To address the role of SPO11 α we have generated an isoform specific transgenic mouse by deleting exon 2 in a BAC containing a genomic region that includes the SPO11 locus. We were able to detect overexpression of SPO11 α in a wild type mouse carrying 7 copies of the transgene and found that overepression does not affect meiotic progression.We found that even though SPO11 α is expressed in a Spo11−/−Spo11α+/− transgenic mouse, it fails to rescue the meiotic arrest characteristic of the Spo11 KO mouse. This favors the notion of SPO11 β as the isoform responsible of introducing the breaks.Supported by the Intramural Research Program of the NIDDK, NIH.
The nuclear matrix protein, Matrin 3 is required export of HIV‐1 unspliced/partially spliced RNAs
Authors: Yedavalli Venkat , Jeang Kuan‐Teh 
Published: June 2021

One central aspect of gene regulation and cell functions is post‐transcriptional regulation of transcripts. Post‐transcriptional regulation involves splicing, nucleo‐cytoplasmic export of spliced RNA, stabilization‐degradation, and the translation of transcribed mRNAs. For HIV‐1, complexities exist because a single unspliced RNA must direct the synthesis of viral proteins and also serves as the genomic RNA for progeny virions. Thus unlike cellular RNAs, viral RNAs that are unspliced or partially spliced must be able to exit the nucleus and progress into the cytoplasm. To accomplish this task, HIV‐1 encodes a viral protein Rev which binds to a cis‐RNA element, RRE, which is contained on unspliced and incompletely spliced viral RNA. Rev acts to direct the export of RRE‐containing viral RNAs, and Rev has been shown to interact with cellular proteins CRM1, DDX3, PIMT and others to mediate their export. Here, we report the identification of a nuclear matrix protein, Matrin 3, as a key co‐factor which mediates Rev‐dependent expression. We discuss proposed mechanisms for how Matrin 3 acts to assist Rev function.Research supported by Intramural funds from NIAID, and by the Intramural AIDS Targeted Antiviral Program (IATAP) from the office of the Director, NIH
Hydrogen peroxide regulates splicing by modulating the protein levels of select splice factors
Authors: Sharina Iraida , Zhu Wen , Murad Ferid , Cote Gilbert 
Published: June 2021

In our previous studies we demonstrated the existence of an alternatively spliced soluble guanylyl cyclase (sGC) isoform C‐α1 resistant to oxidative stress‐induced protein degradation. We extended these studies to address if sGC RNA splicing can be regulated by H2O2 exposure in human breast carcinoma MDA468 cells which constitutively express sGC. RT‐PCR demonstrated that treatment with 1 mM H2O2 for 24h induced the C‐α1 sGC transcript level. To identify potential sGC splicing regulators we performed an in silico analysis using ASD search engine from EMBL. Binding sites for SRp20, hnRNP 2AB1, HuR and PTB1 splice regulators were identified proximal to the regulated and canonical splice acceptors within intron 2. Thus, we investigated if the exposure to H2O2 affects the abundance of these predicted splice regulators. Using Western blotting we observed a significant decrease in levels of PTB1 and hnRNP A2/B1, but not HuR or SRp20 proteins. Next we demonstrated that the expression of PTB1 is affected on the protein, not mRNA level. We also found that oxidative stress‐induced degradation of PTB1 is not mediated by Caspase‐3. These data suggest that H2O2, a ubiquitous molecule associated with oxidative stress, modulates the expression of a select subset of splicing factors, which might play an important role in cellular stress response and adaptation.Research is supported by the Welch and JS Dunn Foundations to F.M.
Appropriate interaction of Ecm29 with the proteasome is necessary for proteasome functional integrity and requires the Not4 E3 ligase
Authors: Collart Martine A 
Published: June 2021

In this study we determine that Not4 is important for ubiquitin turnover and affects proteasome integrity, in part through Ecm29, a protein that contributes to the assembly of the proteasome. Deletion of Not4 leads to accumulation of polyubiquitinated proteins, reduced levels of free ubiquitin and synthetic lethality when combined with the deletion of the Doa4 or Ubp6 deubiquitinating enzymes. Consistently, purification of the proteasome in the absence of Not4 reveals functional, salt‐resistant interaction between the proteasome regulatory particle, RP, and the proteasome core particle, CP, and instability of all other forms of RP. Purification of proteasome holoenzyme via RP reveals co‐purification of Ecm29 from wild type cells, but much less from not4 cells. Indeed, in the absence of Not4, Ecm29 interacts less well with the proteasome, gets ubiquitinated and degraded Interestingly, Ecm29 was mostly identified in purified RP‐containing complexes that are inactive, and are not detectable in cells lacking Not4. On the other hand, Ecm29 co‐purifies with the Ccr4‐Not complex and co‐immunoprecipitates with Not4. Our results characterize Ecm29 as a proteasome chaperone whose appropriate interaction with the proteasome requires Not4.This work was supported by the Swiss Natinal Science Foundation.
Benchmarking a fluorescence microplate‐based aggregation assay using subvisible protein particle standards
Authors: Shen Dee , Chan Eric , Dai Lijun , Coleman Jack , Patton Wayne F 
Published: June 2021

Aggregation represents one of the most significant obstacles to protein‐based pharmaceutical development. During drug formulation, aggregation can impact product quality in terms of biological activity and immunogenicity. Improved methods are required to detect and monitor aggregation during manufacturing. We report upon a fluorescence microplate assay employing a novel fluorescent probe specifically devised to detect aggregated proteins and peptides. The probe is nonfluorescent in solution, but becomes brightly fluorescent when bound to the tertiary structure of aggregated proteins. The assay is capable of detecting less than 0.2% aggregated protein in a concentrated antibody formulation, with a linear dynamic range of two‐orders of magnitude. Sub‐visible oligomeric particles are readily detected without a need for sample separation, solvent exchange or dilution. Subvisible protein particle standards were developed to benchmark the fluorescence microplate assay, as well as orthogonal characterization methods, including laser‐based nanoparticle tracking and micro‐flow Imaging. Advantages of the microplate‐based assay include simple implementation with widely available instrumentation, results achievable in 30 minutes or less and robust assay performance. The assay provides a convenient, complementary orthogonal method for cross‐validation of instrument‐intensive techniques.This work was supported by ENZO Life Sciences.