Vanguard STEM

#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)

We’re continuing with our monthly roundup of 8 recent peer-reviewed journal articles about STEM-related research, STEM equity or cultural studies in STEM. You can find more information about our year-long #VSGetsLit Book (and Article!) Club here. Come back every month for a new list of peer-reviewed articles and data-driven reports.

#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
You can find our VanguardSTEM cover article here:

In January, the #VanguardSTEM team released our first peer-reviewed article (which you can find here) and we’re now the journal cover article(!). We were so excited for everyone to read (and CITE!) it, that we thought we’d extend that same sentiment to the many other scholarly works that BI[W+NBP]OC in STEM are producing. To that end, we introduced our year-long #VSGetsLit Book & Journal Club. This month we’re back with some publications we found across the innanets, that we thought you might enjoy that relate to basic STEM research as well as STEM equity and cultural studies. We will also add at least 1 previously published and seminal works from the literature to round out the bunch.

Editor’s Note: This is certainly not an exhaustive list and we are not affiliated with the publication’s authors or responsible for the content, journal choice or accessibility of any article below, unless specifically indicated. We simply want to #AmplifyBlackSTEM and #AmplifyBIPOCinSTEM by sharing articles that engage or demonstrate concepts similar to the VanguardSTEM hyperspace and an intersectional scientific methodology that we theorized in our paper. If you have written a recent paper and want us to highlight it, tag us (@VanguardSTEM) on twitter or instagram with #VSGetsLit and/or email us a pdf copy of it.

Here are 8 peer-reviewed articles by and for Black, Indigenous, Women & Non-binary People of Color in STEM.

1. Eccentric Binary Neutron Star Search Prospects for Cosmic Explorer

Find their article here.

#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
FIG. 6. A cumulative histogram that shows the fraction of points where the fitting factor is less than the value on the x-axis for each template bank. Using the eccentric template bank, a majority of the samples are at a fitting factor & 95%. For our eccentricity range, the eccentric template banks appear to do a better job at detecting eccentric systems than the non-eccentric template banks. (Courtesy Lenon, Brown & Nitz 2021)

Authors: Amber K. Lenon, Duncan A. Brown, Alexander H. Nitz

Abstract: “We determine the ability of Cosmic Explorer, a proposed third-generation gravitational-wave observatory, to detect eccentric binary neutron stars and to measure their eccentricity. We find that for a matched-filter search, template banks constructed using binaries in quasi-circular orbits are effectual for eccentric neutron star binaries with e_7≤0.004 (e_7≤0.003) for CE1 (CE2), where e_7 is the binary’s eccentricity at a gravitational-wave frequency of 7~Hz. We show that stochastic template placement can be used to construct a matched-filter search for binaries with larger eccentricities and construct an effectual template bank for binaries with e_7≤0.05. We show that the computational cost of both the search for binaries in quasi-circular orbits and eccentric orbits is not significantly larger for Cosmic Explorer than for Advanced LIGO and is accessible with present-day computational resources. We investigate Cosmic Explorer’s ability to distinguish between circular and eccentric binaries. We estimate that for a binary with a signal-to-noise ratio of 8 (800), Cosmic Explorer can distinguish between a circular binary and a binary with eccentricity e_7≳10−2 (10−3) at 90\% confidence.”

2. Journey to the center of GW170817: Bayesian parameter estimation of outflows from binary neutron

Find their dissertation here.

#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
Figure 5.1: Sample lightcurves generated by our afterglow model, using using the following emcee parameter proposals: log(e) = −1.45, log(B) = −2.28, pindex = 2.13, log(nISM = −3.23, log(Ej ) = 49.58, log(Ec) = 47.90, θj = 1.66, θc = 4.25, log(Γ0) = 3.97, θobs = 24.41. This combination resulted in a log-likelihood of -38.82, indicating a good fit. The first five lightcurves are radio bands, followed by optical (R-band) and X-ray. The scattered points are observational data (converted from mJy). The colors of the observational data points correspond to same frequencies in the model data. (Courtesy Rodriguez 2021)
#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
Figure 5.3: Preliminary posterior distributions obtained from our outflow model by applying constraints from a subset of structured jet parameters obtained from the afterglow fits in Table 5.1. The histograms in the diagonal of the corner plots show the marginalized posteriors and the inner triangle shows the posterior probabilities. The dashed lines indicate the 16th , 50th, and 84th quantiles respectively. (Courtesy Rodrigez 2021).

Author: Isabel J. Rodriguez

Abstract: “The discovery of GW170817 provided the first empirical evidence that merging binary neutron star systems are both progenitors of short gamma-ray bursts, as well as the primary sites of the nucleosynthetic rapid-neutron capture process. Initially detected as gravitational wave (GW) and gamma-ray burst (GRB) triggers, GW170817 was well-localized and follow-up observations detected a kilonova along with the GRB afterglow. Gamma-ray burst afterglows encode information about jet geometry and the environments in which the relativistic jets propagated. However, the information we can garner is limited to regions that are transparent to radiation — meaning it cannot directly give us information about the central engine, the properties of the jet at injection, or tell us how that jet acquires its structure. By using Bayesian parameter estimation analysis to connect astrophysical data with numerical models, we can begin to constrain the properties of these unobservable regions and improve our understandings of short GRBs and neutron star matter. In this work, we performed two separate analyses using emcee, a Python implementation of the Markov Chain Monte Carlo sampling method. We first constrained jet, environment, and observer parameters of a GRB afterglow resulting from an off-axis structured jet. We then used a subset of those results as data in our second analysis to constrain properties of the central engine, neutron star ejecta, and the jet at injection using an outflow model that simulates baryon-loaded wind and jet interactions. In total we were able to constrain 17 parameters, the largest parameter space so far explored using structured jet outflow and afterglow models. We anticipate that with future joint GW-GRB observations of binary neutron star merger events, similar techniques can be used to further probe the nature of neutron star matter, and by extension a neutron star’s equation of state.”

3. Multiwavelength Observations of the RV Tauri Variable System U Monocerotis: Long-term Variability Phenomena That Can Be Explained by Binary Interactions with a Circumbinary Disk

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Authors: Laura D. Vega, Keivan G. Stassun, Rodolfo Montez Jr., Tomasz Kamiński, Laurence Sabin, Eric M. Schlegel, Wouter H. T. Vlemmings, Joel H. Kastner, Sofia Ramstedt, and Patricia T. Boyd

Abstract: “We present an X-ray through submillimeter observations of the classical RV Tauri (RVb-type) variable U Mon, a post-asymptotic giant branch (AGB) binary with a circumbinary disk (CBD). Our SMA observations indicate a CBD diameter of < 550 au. Our XMM-Newton observations make U Mon the first RV Tauri variable detected in X-rays. The X-ray emission is characteristic of a hot plasma (~10 MK), with LX =5 × 1030 erg s−1, and we consider its possible origin from U Mon, its companion, and/or binary system interactions. Combining DASCH and AAVSO data, we extend the time-series photometric baseline back to the late 1880s and find evidence that U Mon has secular changes that appear to recur on a timescale of ~60 yr, possibly caused by a feature in the CBD. From literature radial velocities we find that the binary companion is a ~2 M⊙ A-type main-sequence star. The orientation of the binary’s orbit lies along our line of sight (ω = 95°), such that apastron corresponds to photometric RVb minima, consistent with the post-AGB star becoming obscured by the near side of the CBD. In addition, we find the size of the inner-CBD hole (~4.5–9 au) to be comparable to the binary separation, implying that one or both stars may interact with the CBD at apastron. The obscuration of the post-AGB star implicates the companion as the likely source of the enhanced Hα observed at RVb minima and of the X-ray emission that may arise from accreted material.”

4. BIR repeat-containing ubiquitin conjugating enzyme (BRUCE) regulation of β-catenin signaling in the progression of drug-induced hepatic fibrosis and carcinogenesis

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#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
Figure 6 BRUCE-dependent regulation of β-catenin links to protein kinase activity. A: Whole cell lysates of HepG2 cells transfected with either an siCtrl or siBRUCE were blotted for BRUCE, phospho- and total-β-catenin, as well as a tubulin control; B: Lysates described in (A) were blotted for phospho-protein kinase A (PKA) substrates to measure PKA activity, as well as a glyceraldehyde-3-phosphate dehydrogenase control; C: Western blot analysis of mouse liver tissue lysates from control and liver-specific BRUCE knockout (LKO) exposed to diethylnitrosamine (DEN) for phospho-PKA substrates showing an increase in PKA activity in LKO livers at the time of tumor onset (8 mo); D: Immunofluorescence staining showing colocalization of BRUCE (red) and PKA (green) in endosomes (arrows) in normal human THLE2 hepatocyte line with cell nucleus counterstained with DAPI. The cellular areas outlined in dashed squares are enlarged and shown below; scale bar 20 μm; E: A working model showing a new BRUCE-PKA-β-catenin signaling axis involved in the regulation of fibrosis and HCC. BRUCE regulates β-catenin activation by inhibiting PKA-dependent phosphorylation-activation of β-catenin for hepatic proliferation and carcinogenesis. Mechanistically, BRUCE interacts with PKA in the hepatocyte cytoplasm to restrain PKA activity. When this interaction is disrupted by KO of BRUCE in the mouse liver, or by KD of BRUCE expression in liver cancer cell line, the repression of PKA is derepressed and PKA-dependent phosphorylation-activation of β-catenin at Ser-675 occurs which results in hepatic proliferation. Meanwhile hepatocytes undergo apoptosis induced by DEN-DNA damage and these apoptotic hepatocytes release damage associated molecular patterns to activate hepatic stellate cells. The BRUCE-PKA-β-catenin signaling axis, together with DEN induced DNA damage, hepatic cell death, and oxidative stress, result in an early onset of fibrosis and accelerated HCC. DEN: Diethylnitrosamine; LKO: Liver-specific knockout; BRUCE: BIR repeat-containing ubiquitin conjugating enzyme; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase; PKA: Protein kinase A; DAPI: 4′,6-diamidino-2-phenylindole; HCC: Hepatocellular carcinoma; DAMPs: Damage associated molecular patterns; CTRL: Control. (Courtesy Vilfranc et al. 2021)

Authors: Vilfranc CL, Che LX, Patra KC, Niu L, Olowokure O, Wang J, Shah SA, Du CY.

Abstract: “BIR repeat-containing ubiquitin conjugating enzyme (BRUCE) is a liver tumor suppressor, which is downregulated in a large number of patients with liver diseases. BRUCE facilitates DNA damage repair to protect the mouse liver against the hepatocarcinogen diethylnitrosamine (DEN)-dependent acute liver injury and carcinogenesis. While there exists an established pathologic connection between fibrosis and hepatocellular carcinoma (HCC), DEN exposure alone does not induce robust hepatic fibrosis. Further studies are warranted to identify new suppressive mechanisms contributing to DEN-induced fibrosis and HCC. To investigate the suppressive mechanisms of BRUCE in hepatic fibrosis and HCC development. Male C57/BL6/J control mice [loxp/Loxp; albumin-cre (Alb-cre)-] and BRUCE Alb-Cre KO mice (loxp/Loxp; Alb-Cre+) were injected with a single dose of DEN at postnatal day 15 and sacrificed at different time points to examine liver disease progression. By using a liver-specific BRUCE knockout (LKO) mouse model, we found that BRUCE deficiency, in conjunction with DEN exposure, induced hepatic fibrosis in both premalignant as well as malignant stages, thus recapitulating the chronic fibrosis background often observed in HCC patients. Activated in fibrosis and HCC, β-catenin activity depends on its stabilization and subsequent translocation to the nucleus. Interestingly, we observed that livers from BRUCE KO mice demonstrated an increased nuclear accumulation and elevated activity of β-catenin in the three stages of carcinogenesis: Pre-malignancy, tumor initiation, and HCC. This suggests that BRUCE negatively regulates β-catenin activity during liver disease progression. β-catenin can be activated by phosphorylation by protein kinases, such as protein kinase A (PKA), which phosphorylates it at Ser-675 (pSer-675-β-catenin). Mechanistically, BRUCE and PKA were colocalized in the cytoplasm of hepatocytes where PKA activity is maintained at the basal level. However, in BRUCE deficient mouse livers or a human liver cancer cell line, both PKA activity and pSer-675-β-catenin levels were observed to be elevated. Our data support a “BRUCE-PKA-β-catenin” signaling axis in the mouse liver. The BRUCE interaction with PKA in hepatocytes suppresses PKA-dependent phosphorylation and activation of β-catenin. This study implicates BRUCE as a novel negative regulator of both PKA and β-catenin in chronic liver disease progression. Furthermore, BRUCE-liver specific KO mice serve as a promising model for understanding hepatic fibrosis and HCC in patients with aberrant activation of PKA and β-catenin.”

5. Evolution of Phototransduction Genes in Lepidoptera

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#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)
Immunohistochemistry of a butterfly retinochrome, unclassified opsin (UnRh). UnRh is expressed in several kinds of cells found in the distal retina but not in photoreceptor cells. (A) Drawing of a butterfly ommatidium showing the cornea ©, crystalline cone (cc), rhabdom (r), photoreceptor cells (R1–9), primary pigment cells (ppc), secondary pigment cells (spc), and basement membrane (bm) based on Kolb (1985). Red represents areas where UnRh expression is detected, dark red indicates where the cell presumably narrows and staining is not as bright. A drawing of a cross section shows cells R1–8, blue cells represent LWRh staining and red circles represent UnRh staining. (B) Brightfield image of a longitudinal section of a Heliconius melpomene eye showing the anatomy of each ommatidium and an intact cornea. © Fluorescent image of the same section stained for opsins using rabbit anti-LWRh (blue) and guinea pig anti-UnRh (red) antibodies. (D) Transverse section stained for opsins LWRh (blue) and UnRh (red). (Courtesy: Macias-Muñoz et al. 2021)

Authors: Aide Macias-Muñoz, Aline G Rangel Olguin, Adriana D Briscoe

Abstract: “Vision is underpinned by phototransduction, a signaling cascade that converts light energy into an electrical signal. Among insects, phototransduction is best understood in Drosophila melanogaster. Comparison of D. melanogaster against three insect species found several phototransduction gene gains and losses, however, lepidopterans were not examined. Diurnal butterflies and nocturnal moths occupy different light environments and have distinct eye morphologies, which might impact the expression of their phototransduction genes. Here we investigated: 1) how phototransduction genes vary in gene gain or loss between D. melanogaster and Lepidoptera, and 2) variations in phototransduction genes between moths and butterflies. To test our prediction of phototransduction differences due to distinct visual ecologies, we used insect reference genomes, phylogenetics, and moth and butterfly head RNA-Seq and transcriptome data. As expected, most phototransduction genes were conserved between D. melanogaster and Lepidoptera, with some exceptions. Notably, we found two lepidopteran opsins lacking a D. melanogaster ortholog. Using antibodies we found that one of these opsins, a candidate retinochrome, which we refer to as unclassified opsin (UnRh), is expressed in the crystalline cone cells and the pigment cells of the butterfly, Heliconius melpomene. Our results also show that butterflies express similar amounts of trp and trpl channel mRNAs, whereas moths express ∼50× less trp, a potential adaptation to darkness. Our findings suggest that while many single-copy D. melanogaster phototransduction genes are conserved in lepidopterans, phototransduction gene expression differences exist between moths and butterflies that may be linked to their visual light environment.”

6. The Pieces of Me: The Double Bind of Race and Gender in Engineering

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Authors: Kelly Cross,
Ruby Mendenhall, Kathryn Clancy, Princess Imoukhuede, Jennifer Amos

Abstract: “Women of color (WOC) continue to be underrepresented and underserved in engineering. Current engineering education literature rarely explores the role of the double bind of race and gender in the experiences of WOC. These “hidden figures” are pushed to the margins of engineering based on deeply held negative racial and gender stereotypes. The purpose of this study was to investigate the impact of the intersections of race and gender or the “double bind” on the engineering education of undergraduate female students of color. A quantitative survey measured the engineering identity, ethnic identity, womanist identity, frequency of racial microaggressions, and self-reported mental health (e.g., stress, anxiety, and depression) of female students of color. We found a positive relationship between ethnic identity and engineering identity, as well as relationships between ethnic and womanist identities and self-reported mental health measures. WOC reported high scores on the commitment subscale of the ethnic identity scale, indicating a strong sense of belonging, attachment, and a personal investment in an ethnic group, in addition to frequent racial microaggressions. Taken together, WOC who have strong ethnic and womanist identities are susceptible to negative stereotype social cues, but have some protection from the greater, often race-based stressors they experience in engineering. Depression correlated to the frequency of experiencing racial microaggressions. Our results suggest that engineering must do more to improve racial climate, reduce gender and racial microaggressions, and create inclusive educational spaces to ensure the full participation of these students.”

7. The Effects of Microaggressions on Depression in Young Adults of Color: Investigating the Impact of Traumatic Event Exposures and Trauma Reactions

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Authors: Evan E. Auguste, Keith R. Cruise, Maria C. Jimenez

Abstract: “Microaggressions are a common way that individuals experience racism in the United States. The current study examined the extent to which microaggressions contribute to mental health difficulties, namely trauma reactions and depression, after controlling for other traumatic event exposures. We sought to address gaps in the literature by quantitatively assessing the associations among microaggressions, posttraumatic stress symptoms, and depression symptoms. Participants were 140 young adults of color (68.8% female) who were recruited online. Linear regression analyses evidenced that microaggressions were uniquely associated with depression symptoms, B = 0.27, after controlling for lifetime traumatic event exposures, with this association partially mediated by trauma reactions, B = 0.49. These results suggest that microaggressions are a clinically relevant factor in understanding mental health problems reported by Black, Indigenous, and People of Color in the United States and warrant analysis, assessment, and intervention through a trauma lens.”

8. Antagonistic and mutualistic interactions alter seed dispersal of understory plants at forest edges

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Authors: Wyatt J. Parker, Carmela M. Buono, Kirsten M. Prior

Abstract: “Seed dispersal by ants is an important interaction in North American eastern deciduous forests, where 30–40% of understory plants are myrmecochores, with seeds that possess lipid‐rich appendages (elaiosomes) that attract seed‐dispersing ants. Contemporary forests are fragmented and have regenerated from being previously cleared (secondary forests). In secondary forests, and especially along edges, myrmecochores are a depauperate component of forests. Here, we assess if seed dispersal of myrmecochores by ants, particularly the keystone disperser, Aphaenogaster sp., is intact in forest interiors compared to edges. In three North American northeastern deciduous forests, we compared myrmecochore cover and richness, seed dispersal by ants, and the abundance and richness of ants and other forest floor invertebrates between interiors and edges. We also conducted a seed removal experiment, excluding either ants, rodents (seed predators), or ants and rodents, to test their effects on seed dispersal between interiors and edges. We found differences in the composition of understory plants between interiors and edges, with edges lacking myrmecochores. We also found that seed dispersal by ants was lower in two of the three edges and corresponded to Aphaenogaster sp. abundance. Antagonistic interactions with an invasive slug that is an elaiosome robber, Arion subfuscus, was more apparent than damage by rodents in the experiment, negatively affected dispersal by ants more at edges than in interiors. Here we show that changes in mutualistic and antagonistic interactions affect seed dispersal at forest edges and that not all forest edges are the same, with some more intact than others. Understanding how seed dispersal is impacted in contemporary forests is important towards the goal of conserving and restoring depauperate forest understory communities.”

Our bonus read this month focuses on building and maintaining anti-racist labs. Don’t miss this gem!

9. Ten simple rules for building an antiracist lab

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#VSGetsLit: Eight March Journal Club Finds (+ 1 Bonus!)

Authors: V. Bala Chaudhary, Asmeret Asefaw Berhe

Abstract: “Demographics of the science, technology, engineering, and mathematics (STEM) workforce and student body in the US and Europe continue to show severe underrepresentation of Black, Indigenous, and people of color (BIPOC). Among the documented causes of the persistent lack of diversity in STEM are bias, discrimination, and harassment of members of underrepresented minority groups (URMs). These issues persist due to continued marginalization, power imbalances, and lack of adequate policies against misconduct in academic and other scientific institutions. All scientists can play important roles in reversing this trend by shifting the culture of academic workplaces to intentionally implement equitable and inclusive policies, set norms for acceptable workplace conduct, and provide opportunities for mentorship and networking. As scientists are increasingly acknowledging the lack of racial and ethnic diversity in science, there is a need for clear direction on how to take antiracist action. Here we present 10 rules to help labs develop antiracists policies and action in an effort to promote racial and ethnic diversity, equity, and inclusion in science.”

This article was originally published on April 6, 2021 on as part of our #VSGetsLit series.

If you enjoy our original content, consider donating to our parent not-for-profit, The SeRCH Foundation, Inc., to help support this work.

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