bluuebunny/crossref_metadata_2025_split huggingface dataset:
pSmad 3D Localization in Zebrafish Embryos
Authors: Ku Madeline , Wang Xu , Umulis David 
Published: December 2020

Background and Hypothesis
During embryonic development, individual cell fate is determined by morphogen gradient surrounding a particular cell. In particular, the positional information regarding dorsal-ventral pole is determined by the BMP concentration gradient and the anterior-posterior positional information is determined by Nodal concentration gradient. pSmad is a downstream product of BMP signaling that plays a role in the feedback regulation of BMP. Previously, we had taken confocal images of the immunohistochemistry labeled pSmad embryos on its side view (yolk sac facing the side, where ventral and dorsal pole is visible) to understand the localization of pSmad and its role in BMP signaling. However, signals diminished in the deeper part of the embryos making it harder to distinguish signals from the background noise. In this experiment, we decided to use wavelet segmentation method for image processing that will help us pick up the signals better and to reconstruct the embryos from 3 different views. We hypothesized by adding these 2 procedures, it will give us a more accurate localization of pSmad signaling in zebrafish embryos.
Experimental Design or Project Methods
We first used immunohistochemistry to label pSmad in 3 8 hours post fertilization zebrafish embryos. We then used Zeiss DM800 confocal to image the immunohistochemistry labeled pSmad embryos in 3 different views (pole – yolk facing towards camera, ventral, and side). These images are processed through wavelet segmentation method using Matlab, then reconstruct the half embryo from the 3 views rotation. We will then compare the result we obtained compare to the raw files and results we obtained from previous experiments.
Results
Thus far, we had obtained 3 views on 3 different embryos and complete the wavelet segmentation processing. We had yet to merge the 3 views to reconstruct the embryos and compare to previous results.
Conclusion and Potential Impact
This study will establish a more accurate localization studying method on immunohistochemistry labeled zebrafish embryos that is not limited to pSmad signaling. It can be used to build mathematical model of BMP feedback regulation signaling.
Efficacy of Mutant HPV-16 E6 Proteins in p53 Degradation
Authors: Lange Charles , Rietz Anne , Androphy Elliot 
Published: December 2020

Background and Objective:
High-risk human papilloma viruses (HPV) are the causative agent in the majority of anal, cervical, vaginal, vulvar, penile, and oropharyngeal cancers with an annual incidence of 630,000 cases world-wide. These viruses initially cause dysplasia that subsequently increases neoplasia risk. HPV’s encode eight major viral proteins with the E6 protein being crucial for replication. E6 binding to ubiquitin ligase E6AP initiates polyubiquitination of p53, targeting the protein for proteasomal degradation. We are taking a novel approach to inhibit HPV16+ dysplasia and cancers by designing inhibitors targeting specific amino acids of 16E6, which reside in the E6-E6AP binding pocket, thereby preventing p53 degradation. To affirm interaction with the targeted side chain, we generated E6 point mutations that serve as specificity controls. These mutations are designed to disrupt interaction with the compound. To ensure their suitability for our studies, we are herein characterizing their capacity to bind E6AP and bind and degrade p53.

Methods:
E6 mutants were generated by site-directed mutagenesis and analyzed by sequencing. H1299 cells were transfected with GFP, wild-type (WT) E6, or mutant HPV-16 E6 plasmids +/- WT p53 plasmid. After 48 hours, cells are lysed and 16E6 was immunoprecipitated. Proteins bound to 16 E6 were separated by SDS-PAGE and subjected to western blot. Binding to E6AP and p53 was analyzed and presence of 16E6 was confirmed by immunoblotting. To test for p53 degradation, H1299 cells were transfected with firefly luciferase (Fluc) (transfection control) and p53-luciferase along with WT E6, mutant E6 proteins, or empty LXSN plasmid. After 24 hours p53-luciferase was measured with Dual-Glo Luciferase Assay.

Results:
To be determined

Conclusion:
To be determined
Possible Neuroinflammatory Mechanisms Which May Lead to Long-Term Neurological Disorders in COVID-19 Patients
Authors: Lange Michael , Shi Riyi 
Published: December 2020

This review aims to provide insight into the possible long-term neurological complications that COVID-19 patients may experience after the resolution of intense acute inflammation characterized as “cytokine storm.” Neurological symptoms such as fatigue, headache, dizziness, nausea, confusion, dyspnea, anorexia, malaise, myalgia, ataxia, seizure, hypogeusia, and hyposmia are commonly seen in these patients. COVID-19 related encephalitis is also seen sporadically. However, some researchers believe neuroinflammation is more common than what is reported. Neurological abnormalities that are linked to neuroinflammation are of particular concern because neuroinflammation is hypothesized to cause neurological diseases such as Alzheimer’s Disease, Parkinson’s Disease, and Schizophrenia. Many potential routes can lead to inflammation in the nervous system and elicit neuron cell death in COVID-19 patients. These include the potential neurotropic pathway of the novel coronavirus, CNS parenchymal infectability, thrombotic ischemic stroke, cytokine storm, and blood-brain barrier breakdown. Past pandemics of similar neurotropic viruses could also offer insights regarding the long-term neurological effects of COVID-19. In support of our hypothesis, the Spanish Flu pandemic of 1918-1919 saw an increased incidence of neurodegenerative disease, Parkinson’s disease, and schizophrenia. We do not know exactly what the future will hold for COVID-19 however, it is of paramount importance to attempt to anticipate and prepare for the possible chronic neurological sequelae and mitigate or prevent their effects.
Therapeutic targeting of hypoxia and hypoxia inducible factor 1 with acriflavine in experimental esophageal adenocarcinoma
Authors: Lankford Christian , Hassan Sazzad , Von Holzen Urs 
Published: December 2020

Background: Hypoxia or insufficient tissue oxygenation contributes to cancer aggressiveness and poor clinical prognosis. Typically, cancer cell lines are used in two-dimensional (2D) cultures for screening of anticancer agents, and they do not represent the hypoxic tumor microenvironment. In this study, we established a novel three dimensional (3D) spheroid co-culture model of esophageal adenocarcinoma (EAC). We then observed treatment response of chemo and hypoxia-targeting therapies in 2D, 3D and in vivo models of experimental EAC. Methods: EAC 3D spheroids were generated from co-culturing human EAC and fibroblast cell lines. NanoCulture® plates and dishes were used for 3D spheroid cultures. Hypoxic status was detected by adding hypoxia probe LOX-1 and fluorescent microscopy. Paclitaxel (PT), carboplatin (CP) and nanoparticle albumin-bound paclitaxel (NPT) were used as chemotherapeutic agents, whereas acriflavine was used as hypoxia-targeting agent. In vitro cell growth was detected by WST-1 assay, in vivo tumor growth was detected by measuring subcutaneous xenografts, apoptosis was detected by cleaved caspase 3/PARP expressions, and hypoxia-targeting was detected by HIF-1α expression. Results: 3D culture was more resistant to antiproliferative effect of chemotherapeutic agents PT, CP, NPT over 2D monolayer culture. Contrary to that, hypoxia-targeting agent acriflavine showed stronger antiproliferative effects in 3D culture than in 2D culture. We observed strong expression of hypoxia inducible factor-1α (HIF-1α) in 3D culture with no expression of HIF-1α in 2D culture, and acriflavine treatment completely abolished the HIF-1α expression in 3D culture. We also observed hypoxia inside the 3D culture spheroids, but not in cells grown in 2D culture. In addition, acriflavine showed significant in vivo antitumor efficacy both as monotherapy and in combination with NPT. Conclusion: Thus 3D cultures may be better than 2D cultures in simulating the important in vivo tumor characteristic of hypoxia, and HIF-targeting therapy acriflavine could be a novel treatment strategy for EAC.
Promoting Community-based Engagement with Pregnant and Postpartum Women with Substance Use Disorder via Human-centered Design
Authors: Liu Scott , Cockrum Brandon , Moore Courtney , Claxton Gina , Parks Lisa , Wiehe Sarah , Chambers Joanna , Denne Scott , Litzelman Debra 
Published: December 2020

Background:
Pregnant women with substance use disorder (SUD) are a vulnerable population that often contends with stigma, socioeconomic inequity, and mental health issues. The Community-based Addiction Reduction (CARE) Program connects pregnant and postpartum women with SUD in Central Indiana with addiction recovery coaches (ARCs) and attachment theory therapists, who provide linkage to community resources and mental health support. However, recruitment and retention of participants continue to be challenging.

The goals of this research are to identify barriers and facilitators to recruitment/retention and to translate findings into patient engagement materials.

Methods:
ARCs are women with family or personal experience with SUD, and serve as proxies for patient perspectives. Qualitative data from nine semi-structured interviews conducted with ARCs and their supervisors were clustered thematically to identify barriers and facilitators to recruitment/retention. Rapid prototyping, a methodology within human-centered design (HCD), was then employed to iteratively develop deliverables, incorporating several rounds of critique from ARCs, weekly case conferences, and discussions with clinician-investigators and designers.

Results:
Facilitators to recruitment/retention included: (1) ability to personally relate to ARCs and (2) ARC advocacy when navigating community and health system resources. Barriers to recruitment/retention included: (1) distrust (associated with participants’ histories of adverse childhood events and other trauma); (2) overwhelming number of interactions with various agencies (DCS, clinics, counseling, etc.); (3) fluctuating phone access, (4) intensive enrollment process, and (5) overall program visibility.

The following deliverables were designed: (1) introduction videos of ARCs (2) brief videos of patient advocacy stories told by ARCs, (3) personalized cards paired with existing gift card incentives, and (4) journal for self-reflection and self-motivation.

Potential Impact:
Qualitative findings underscore the importance of patient-centeredness in engagement with CARE participants, who are often overwhelmed and wary of others. HCD approaches within multidisciplinary teams can be leveraged to enhance program uptake and delivery within underserved populations.
Cell-Scale Modeling to Probe Mechanobiology during Early Cortical Development
Authors: Lonnberg Adam , Garcia Kara 
Published: December 2020

Background/Objective: During early cerebral cortex development, neurons form from proliferative glial cells near the ventricular (apical) surface, then migrate along radial glial scaffolds to the cortical surface. In species with wrinkled brains, the presence of basal radial glial cells (bRGCs), radial glial cells which have detached from the ventricular surface, is correlated to the process of gyrification. While mechanical forces are also involved in gyrus creation, the link between the mechanical and biological aspects of this process remains unelucidated. In this study, we hypothesized that radial tension may lead to the production of gyri via the intermediary creation of bRGCs.
Methods: To test this hypothesis, the cell-level modeling software CX3D was used to simulate a system in which radial tension acts on radial glial cells (RGCs), facilitating the semi-stochastic production of bRGCs during the process of neocortex development. The outcome of this model was contrasted with a control case in which bRGCs were not allowed to form, and the two models were compared based upon the presence of neurons on the basal surface.
Results: The production of bRGCs via tension corresponded to a significant increase in the presence of neurons on the pial surface, even if the total number of glial cells—and thus total number of neurons generated—remained constant. Additionally, the likelihood of neurons moving more basally was found to be significantly greater in the presence of bRGCs.
Conclusion and Potential Impact: These results were interpreted to be indications of early gyrus formation. Thus, this study showed that bRGCs—and, ultimately, gyri—may arise from mechanical tension, indicating a possible link between the biological and mechanical explanations of gyrus formation. By providing an alternative lens through which to understand cortical folding, this may have implications for future lines of inquiry, which may expand our understanding of neuro-pathologies associated with misfolding, such as autism and epilepsy.
Comparing Newborn Outcomes After Prenatal Exposure to Individual Antidepressants
Authors: Marks Claire , Quinney Sara , Haas David 
Published: December 2020

Background: Up to 1 out of 5 women experience depression during their childbearing years, with 20-33% treating with drugs. However, data are limited on individual drugs’ effects on pregnancy outcomes. The objective of this study was to compare associations between individual antidepressants and pregnancy outcomes.

Study Methods: Deidentified demographic, medical and obstetric data from women who received at least one antidepressant (SSRI or SNRI) prescription prior to conception through delivery were obtained from Regenstrief Institute. Drugs were were compared using standard statistics and multivariable regression.

Results: A total of 3801 women took bupropion (n=311), citalopram (n=355), fluoxetine (n=520), sertraline (n=1557), duloxetine (n=112), escitalopram (n=534), venlafaxine (n=105), paroxetine (n=45), desvenlafaxine (n=12), or multiple antidepressants (n=250). Most women were white (86.5%), and had either commercial (50.3%) or government (48.1%) insurance.

Race (p=0.002), hospital (p<0.001), and insurance (p<0.001) were associated with selection of drug. Incidence of diabetes (p<0.001), gestational diabetes (p=0.005), hypertension (p=0.015), and gestational hypertension (p=0.006) varied between drugs, with highest rates in women taking duloxetine. NICU admission (p<0.001), transient tachypnea of newborn (TTN) (p=0.001), and adaptation syndrome (p<0.001) were significantly different between drugs, with duloxetine having highest NICU admission (42.9%) and TTN (20.5%). Paroxetine was associated with higher rates of adaptation syndrome (13.3%).

After controlling for maternal age, race, hospital, and insurance, adaptation syndrome was increased with citalopram OR[95%CI] = 2.358[1.147-4.849], duloxetine 3.180[1.362-7.424], escitalopram 2.832[1.418], paroxetine 3.347[1.138-9.847], and multiple drugs 2.603[1.222-5.545] compared to bupropion. Adding hypertension and diabetes to the model above, increased NICU admission rates were seen with citalopram 1.498[1.036-2.168], fluoxetine 1.565[1.109-2.208], duloxetine 2.568[1.593-4.139], escitalopram 2.045[1.458-2.869], and multiple drugs 2.009[1.362-2.964] compared to bupropion.

Conclusion: Different antidepressants have associations with individual maternal and newborn outcomes. Duloxetine and paroxetine appear to have the strongest associations with NICU admission and adaptation syndromes, respectively. These outcomes require further investigation by exposure trimester.
Steroids for All
Authors: McKinzie Alexandra , Yang Ziyi , Daggy Joanne , Tepper Robert , Quinney Sarah , Rhoads Eli , Haneline Laura , Haas David 
Published: December 2020

Background: Due to difficulties estimating the risk of preterm labor, many women diagnosed with threatened preterm delivery and given antenatal corticosteroids to improve neonatal outcomes do not deliver until term. Our objective was to compare the short-term outcomes of infants born at term to women who received betamethasone (BMZ) for threatened preterm labor to infants who were not exposed to BMZ in utero.

Methods: We performed a retrospective cohort study of infants born at or after 37 weeks’ gestational age (GA) to mothers diagnosed with threatened preterm labor during pregnancy. Controlling for covariates, the primary neonatal outcomes of interest, including transient tachypnea of the newborn (TTN), neonatal intensive care unit (NICU) admission, and birthweight, were evaluated for their association with BMZ exposure.

Results: Of 5330 women, 1459 (27.5%) women received BMZ at a mean GA of 32.2±3.3 weeks. The mean age of women was 27±5.9 years-old and the mean GA at delivery was 38.9±1.1 weeks. Women receiving BMZ had higher rates of maternal comorbidities (P<0.001 for diabetes, asthma, and hypertensive disorder) and were more likely to self-identify as white (P=0.022). BMZ-exposed neonates had lower birth weights and increased rates of oxygen usage, TTN, hyperbilirubinemia, hypoglycemia, and NICU admission rates (all P-values <0.05).
Controlling for maternal characteristics and GA at delivery, BMZ exposure was not significantly associated with diagnosis of TTN [OR 1.09 (95% CI 0.80-1.50)], though it was associated with more NICU admissions [1.49 (1.19-1.86)] and lower birthweight by 91.5 (-122.3 to -60.6) grams.

Conclusions: Compared to women evaluated for preterm labor that did not receive BMZ, women receiving BMZ had infants with higher rates of NICU admission and lower birthweights, though the rate of TTN diagnosis was similar between the two groups. While the benefits of BMZ to infants born preterm are clear, there may be negative impacts for infants delivered at term.
Using Late Supplemental Oxygen to Prevent Retinopathy of Prematurity Progression In Premature Infants: a Retrospective Study
Authors: Minturn Robert , Koch Mary Beth , Anderson Emily , Lim Kua Kok , Haider Kathryn 
Published: December 2020

Background/Objective:
Retinopathy of Prematurity (ROP) is a leading causes of childhood blindness. It affects 15,000 surviving US preterm infants annually, with 1,400 infants developing severe ROP and 500 infants developing legal blindness. The pathogenesis of ROP involves 2 phases: During phase 1, the immature retinal vascularization is obliterated due to hyperoxia. During phase 2 (>4 weeks postnatally), abnormal neovascularization occurs due to hypoxia, sometimes requiring surgical intervention. We retrospectively evaluated the impact of late supplemental oxygen (>4 weeks postnatally) on ROP progression in infants born <28 weeks.
Methods:
Preterm infants <28 weeks with >stage 2 ROP admitted to the Riley Hospital for Children Neonatal Intensive Care Unit (NICU) from 7/2017- 12/2019 were included. Nine patients treated with supplemental oxygen therapy were compared to a control cohort managed by a standard protocol after the diagnosis of stage 2 ROP. The primary outcome was the need for surgical intervention with either laser or bevacizumab treatment. Continuous data was analyzed using unpaired t-test, and categorical data was analyzed using fishers exact test.
Results:
There was no statistical difference in regard to clinical variables contributing to risk of severe ROP (sex, race, birthweight necrotizing enterocolitis, bronchopulmonary dysplasia or length of stay) between the two study cohorts. There was a statistically significant decrease in need for treatments (laser or bevacizumab) in patients receiving supplemental oxygen (control: 35/83 patients treated, late O2: 0/9 patients treated, p=0.012).
Conclusion and Implications:
Supplemental oxygen therapy seems to have a protective effect on the development of treatable ROP (type I). Limiting surgical intervention (laser or bevacizumab) would directly benefit the babies by decreasing the need for sedation and any inherent risks of surgery. This initial data suggests the need for future studies with a higher sample size to validate the efficacy of late supplemental O2 in ROP.

Study Group

Control

Number (Mean)

% (SD)

Number (Mean)

% (SD)

p-value

Population (N)

9

-

83

-

Sex

Male

2

22.2%

35

42.2%

N.S.

Female

7

77.8%

48

57.8%

N.S.

Race

Caucasian

5

55.6%

44

53.0%

N.S.

Non-Caucasian

4

44.4%

39

47.0%

N.S.

Birthweight (grams)

698

145.26

721

197.09

N.S.

Gestational Age (Weeks)

24.94

1.19

25.32

1.72

N.S.

Length of Stay (Days)

129.22

27.13

148.58

67.97

N.S.

Necrotizing Enterocolitis

Yes

3

33.3%

21

25.3%

N.S.

No

6

66.7%

62

74.7%

N.S.

Sepsis

Yes

6

66.7%

41

49.4%

N.S.

No

3

33.3%

42

50.6%

N.S.

Bronchopulmonary Dysplasia

Yes

9

100.0%

80

96.4%

N.S.

No

0

0.0%

2

2.4%

N.S.

Need for Additional Treatment (Inpatient)

Yes

0

0.0%

35

42.2%

N.S.

No

9

100.0%

48

57.8%

N.S.

Need for Additional Treatment (Outpatient)

Yes

0

0.0%

35

42.2%

0.012

No

9

100.0%

48

57.8%
Mechanisms of ischemic skeletal muscle regeneration mediated by mechanically constrained human allogeneic mesenchymal stromal cells
Authors: O'Connor Alex , Miller Steven , Loke Michael , Gil Chang-Hyun , Leckie Katherin , Doiron Theresa , King Justin , Moldovan Leni , Murphy Michael 
Published: December 2020

Background and Hypothesis: Critical limb threatening ischemia (CLTI) is the end stage of peripheral arterial disease (PAD). CLTI presents a significant risk for lower extremity amputation, especially in diabetic patients with poor options for revascularization. Additionally, using a novel diabetic mouse model of CLTI, we have shown that IM injection of 3D cultured MSCs (spheroids) is more effective in promoting skeletal muscle regeneration of ischemic muscle than monolayer cultured MSC. We hypothesize that this result is due to the mechanical constrained nature of the MSC in spheroid form, which has been shown to alter the cellular phenotype. Alginate encapsulated cells are another form of mechanical confinement, and have additional benefits including resistance to immunological attack, making them a practical therapy for treatment of CLTI patients.

Project Methods: In this work, cells were encapsulated in 2% alginate using a centrifugation method. Media from these cells along with others were analyzed for IL-10 and IL-33 using ELISA. Mouse tissue samples were stained with WGA-555 antibody and analyzed using a scanning microscope. Effects on tissue perfusion were measured with Laser Doppler Perfusion Imaging. At the time of this abstract, the media from encapsulated and naked MSCs is being used to culture myoblasts, looking at cell growth.

Results: ELISA results did not show significant increases in IL-10 or IL-33 for encapsulated vs. non-encapsulated cells. LDPI has shown an increased perfusion rate for hindlimbs treated with encapsulated MSCs vs naked MSCs. Muscle fiber analysis is ongoing, but initial data appears promising.

Conclusion and Potential Impact: This experiment provides a starting point for improving and expanding cell therapy for critical limb ischemia, potentially resulting in better outcomes for diabetic patients and preventing lower limb amputations. The encapsulation process also has value in other types of cell therapy, as it could protect cells from host defenses and increase dwell time.