Environmental and Occupational Health Sciences Institute
Rutgers University Community RepositoryNot a member yet
58345 research outputs found
Sort by
Awareness and perception of the genetic counseling profession in a diverse undergraduate population – before and after
No full textThe field of genetic counseling, which involves communicating complex genetic information and providing psychosocial support to individuals and families, has struggled with issues of diversity, equity, and inclusion, notably among underrepresented minority students over the past two decades. To enhance diversity in genetic counseling, programs must better understand methods for educating, engaging, and attracting students from underrepresented backgrounds. This study aims to evaluate the efficacy of such outreach initiatives and gather feedback from underrepresented undergraduate students of diverse racial/ethnic backgrounds at Rutgers University in the United States. By eliciting feedback and assessing the impact of a presentation in classes with diverse student populations, the study seeks to refine recruitment strategies and delve into factors contributing to the lack of diversity. The study involves a pre-survey, educational outreach via a PowerPoint presentation, and a post-survey distributed to 563 non-genetic major undergraduate students at Rutgers. Results revealed prevalent misconceptions among students regarding genetic counseling, including its scope and accessibility, persisting even after the presentation. Most students were unaware of the psychosocial counseling aspect of the profession beforehand. Primary barriers cited by students considering genetic counseling were the rigorous admissions process and program costs. However, feedback on the presentation was largely positive, with students finding it informative and engaging. To mitigate these barriers, additional outreach events emphasizing genetic counseling as a potential career option, along with discussions on financial aid opportunities and application resources, are recommended. In addition, highlighting the interdisciplinary nature of the field and incorporating personal narratives for speakers may further enhance outreach effectiveness.M.S.Includes bibliographical reference
Mapping desire: queer space in New Brunswick
No full textQueer history has been ignored or hidden in spaces due to bias, discrimination, and even ignorance. To make hidden queer histories visible, this paper focuses on the local queer history of New Brunswick, New Jersey. This work collects, analyzes, and maps out queer spaces in New Brunswick and is guided by queer and post-structuralist thinking. Queer theory also provided inspiration for the aesthetics and representation used in the renderings. Additionally, the paper engages with the creation of small communities in the 1950s-1960s to try to understand how queer people were thought of by general heteronormative society. Then, this project moves through ephemera of the late 20th century that is available in the Rutgers University archives. To link the past to the present, modern stories from queer individuals who live in New Brunswick are presented through anonymous cognitive maps. The concluding series of queer walking tour maps of the city synthesizes queer stories from these three time periods and sources. The walking tour includes significant places to the queer community, representative of both positive and negative emotions and experiences. This map makes visible the hidden queer history of New Brunswick in an accessible format and allows people to understand the ways that queer expression has changed throughout time in New Brunswick.M.L.A.Includes bibliographical reference
Phenology, chilling requirements, and disease resistance in hybrid hazelnut
No full textHazelnut (Corylus spp.) is a major worldwide tree nut crop with production centered in regions with Mediterranean climates. European Hazelnut (Corylus avellana) is the main species for commercial production due to its favorable nut characteristics. Despite rising demand, expansion to new growing regions is challenged by factors including susceptibility to the fungal pathogen Anisogramma anomala and cold tolerance of C. avellana germplasm. Anisogramma anomala is the causal organism of the disease eastern filbert blight (EFB) and is endemic to the eastern United States. It is harbored on the wild American Hazelnut (C. americana), causing few disease symptoms, but is devastating to nearly all C. avellana trees. While EFB can be controlled with fungicides, genetic resistance is the preferred method for long term disease management to keep crop inputs low. In recent years, the breakdown of single gene sources of EFB resistance have demonstrated the need for durable, horizontal resistance such as found in C. americana. In addition to disease resistance, C. americana germplasm contains other favorable traits including cold tolerance and later flowering/budbreak time, both of which are beneficial to the expansion of hazelnut into new colder growing regions. Like other temperate fruit and nut crops, hazelnuts rely on the accumulation of chilling to maintain dormancy followed by warm temperatures for flowering and budbreak in the spring. A major goal of this work was to quantify both chilling and heating requirements of hazelnuts to better predict their responses in new growing regions and longer-term responses in regard to climate change. Additionally, three mapping populations were phenotyped for time of flowering and budbreak and a QTL analysis was performed for these traits. Lastly, 62 C. americana seedlots, 22 F1 hybrid (C. americana x C. avellana) progenies, 38 clonal F1 selections, and 26 F2 progenies were evaluated for resistance/tolerance to EFB. Chilling requirements in C. avellana, C. americana, and interspecific hybrids ranged from 9.3 to 30.7 CP for catkins, 10.5 to 44.0 CP for female flowers, and 28.5 to 51.0 CP for vegetative buds. Growing degree hour requirements ranged from 6,240 to 11,140 GDH for catkins, 3,644 to 8,336 GDH for female flowers, and 5,447 to 13,629 GDH for vegetative buds. Analysis suggested that bloom date may be 5 to 28 days earlier with impending climate change, suggesting breeding for higher GDH requirements may be a solution to avoid bloom during cold temperatures. 24 QTL’s for phenology traits were found between the three mapping populations, including five for date of vegetative budbreak, eight for date of female flowering, six for date of pollen shed, and five for heterodichogamy. A major QTL on linkage group 2 was associated with all four phenology traits. The first QTLs for phenology in C. americana were discovered on linkage groups 2, 3, and 11. C. americana demonstrated durable resistance, with seedlots averaging an EFB rating of 0.31 after ten years of disease exposure. F1 progenies observed during the same period were much more variable, with EFB progeny means ranging from 1.95 to 4.98 and averaging 3.98. F1 breeding selection EFB genotype means ranged from 0.33 to 5.00, representing percent diseased wood of 0.04% to 40.92%. F2 progenies demonstrated transgressive segregation, with progeny means ranging from 0.67 to 4.92 and averaging 2.85. Narrow sense heritability of EFB resistance was estimated at 0.64. In summary, this body of work demonstrates that integration of C. americana germplasm into the breeding program could be beneficial, particularly when dealing with the high disease pressure and colder climate of the eastern United States and offers insight into expansion of hazelnut growing regions also facing these challenges.Ph.D.Includes bibliographical reference
Scaling stateful packet processing applications across multiple cores using DPDK
No full textThe rapidly increasing network speeds and heavy computational demands from applicationsare pushing the software network processing infrastructure to its limits. While the throughput of NICs continues to increase, the improvement in the single-core performance of CPUs has slowed significantly due to the breakdown of Dennard Scaling. Hence, efficiently scaling fast packet processing applications across multiple cores is paramount. We specifically aim to analyze the scaling of stateful packet processing applications using three different techniques 1. Sharing using locks 2. Sharding using RSS 3. Replication using State-compute replication (SCR). We tested them by building a port-knocking firewall using DPDK and analyzed their performance on a realistic wide-area Internet trace from CAIDA.
Our experiments showed that memory contention with more cores limits the scaling of the lock-based approach. Sharding using RSS also doesn’t scale well due to the uneven distribution of packets across cores, especially with heavier flows, limiting the application’s overall performance. SCR is able to achieve linear scaling across multiple cores and process packets at the line rate of 100 Gbps with just 6 cores. This is due to the overhead of replication being compensated by the performance benefits of evenly distributing packets among multiple cores, thus demonstrating the efficacy and scalability of SCR in DPDK.M.S.Includes bibliographical reference
Beyond Enargeia: enargetic description in the Iliad
No full textThis dissertation explores how the Iliad achieves enargetic qualities in its language, the role that such language plays in the poem, and the effects of such language on the audience or reader. I use an extensive review of enargetic scenes and language in the Iliad alongside discussions of enargeia from ancient commentators and modern scholarship to explore the ability of enargetic description to prompt or even facilitate the audience’s imagined embodiment of scenes within the poem.
Chapter One reviews how ancient commentators’ definitions of enargeia centered around sight and visual terminology, but evolved over time to incorporate more imaginative elements. This chapter also investigates the ongoing importance of sight description in enargetic passages in the Iliad. Chapter Two highlights how descriptions appealing to the proximal senses of hearing, smell, taste, and touch draw the audience into a closer context, generate immediacy, and help focalize scenes through individual characters or small groups. Chapter Three discusses how the intimate focalization provided by enargetic description gives insight into non-physical elements of a scene, such as emotional characterization or the distorted perception of time, and how these non-physical elements intersect with sensory experience. Chapter Four uses Alice Oswald’s poem Memorial as a case study for how the enargetic elements identfied in the dissertation are applied and adpated to her “version” of the Iliad.Ph.D.Includes bibliographical reference
Advanced early fire detection in aircraft cargo with MACD and passive UHF RFID temperature sensing while maintaining false alarm resistance
No full textThis study introduces a novel approach to enhance fire protection in aircraft cargo compartments, motivated by the urgency to address catastrophic in-flight fires recorded between 2006 and 2011. The method uses ultra-high frequency (UHF) radio frequency identification (RFID) temperature sensing tags and advanced algorithmic analysis to enhance fire detection capabilities within unit load devices (ULDs). This approach significantly reduces detection times while minimizing false alarms.
The first objective was to create an economical, battery-free fire detection system with UHF RFID temperature sensing tags installed within ULDs. This positions the temperature sensing tags closer to potential fire sources than traditional cargo compartment ceiling-mounted smoke detectors. Wireless temperature sensing tags allow the ULDs to move in and out of aircraft. Passive sensors address the challenges of battery-powered systems, such as battery changes and thermal runaway risks.
The second objective sought to enhance the RFID-based system with near real-time temperature monitoring capabilities within ULDs. The system provides accurate temperature trend analysis by incorporating a moving average convergence divergence (MACD) algorithm adapted from financial markets. This significant advancement improves fire detection times and supports communication of conditions within ULDs to flight crews, enabling quicker response actions.
The third objective aimed to reduce false alarms through an algorithm capable of identifying significant temperature differences between separate ULDs. To achieve this, RFID temperature sensors were installed across all ULDs for continuous environmental monitoring. Under normal conditions, only minimal temperature variance is expected among ULDs. However, if the system detects a notable temperature differential between any two ULDs, it issues an alert. This method enhances the accuracy of fire detection while significantly reducing the likelihood of false alarms.
Experimental results reveal a linear correlation between heat input and the algorithm’s response. This correlation is crucial for near real-time monitoring of varying fire conditions within ULDs. Additionally, the RFID system outperformed traditional external smoke detectors by reducing smoldering fire detection times to an average of 11.7 minutes. For specific 12.08 Wh lithium-ion fire configurations, the RFID system detected them in 5.4 minutes on average, whereas traditional external smoke detectors failed to detect them at all.Ph.D.Includes bibliographical reference
Numerical simulation of the inertial trap impactor under the influence of evaporation
No full textThe global SARS-CoV-2 pandemic necessitated the development of accurate and affordable rapid-testing protocols. These tests generally detect the antigens present in the nose and throat collected by swabbing the target area. While effective for widespread use, a novel approach to generating a testable sample is proposed wherein an inertial trap impactor is used to remove and trap respired aerosols from the user’s breath onto a biosensor as they blow through the device. The goal of this technology is to offer an easier-to-use alternative to nasal and throat swabbing. This thesis aims to develop an understanding of particle trajectories moving through an inertial trap impactor subject to the effects of evaporation, in order to facilitate design and testing.
Axisymmetric pressure-driven flow fields generated by COMSOL were imported to Matlab, and particle motion was numerically simulated to predict capture efficiency in an analogous experimental context. The finite difference method was used to solve the equations of particle motion in the radial and axial directions, with evaporation occurring at every time-step. The capture efficiency results were compared to those of the flat plate impactor, and were found to be more efficient at a given Reynolds number. The effects of evaporation on capture efficiency were also considered. A cellular model was used to calculate the rate of evaporation of particles within a cloud moving through an inertial trap impactor.
Evaporation was calculated assuming a cloud of droplets with a constant, specified, average inter-droplet distance was moving through the impactor. The effect of evaporation is to reduce a particle’s size, making it more likely to follow more closely the streamlines in the flow and leave the impactor without being captured. The worst case scenario tested in this study corresponding to a single droplet starting in 0% relative humidity air resulted in a 21 times diameter increase required for 50% capture efficiency compared to the non-evaporative case. Furthermore, if the analyte in the droplet is subject to evaporation, the total mass lost can be over 20% within the range of conditions tested.
Future work includes the expansion of the range of flow Reynolds numbers simulated, as well as a parametric study on the geometric configuration of the trap impactor. This should be done with the aim to fully characterize the performance of the inertial trap impactor both with and without the consideration of evaporative effects, such that it may inform the design of future diagnostic devices.M.S.Includes bibliographical reference
Limits and possibilities of restorative conferences in schools: an exploration of conference participant characteristics and perceptions
No full textRooted in relational philosophies, restorative practices (RP) in schools are initiatives that seek to provide alternatives to exclusionary discipline. Restorative conferences (RC), in particular, aim to repair harm and reintegrate youth following a conflict. Despite abundant theorizing about conference benefits and hypothesized mechanisms of change, there is not enough evidence to support these claims. This study addresses knowledge gaps about RC acceptability, student perspectives on successful conference characteristics, and the socio-demographics of RC participants. Furthermore, this study examined students (e.g., conference participants vs. suspended students) to understand the degree to which RCs are linked to positive correlates of school climate and to explore the potential of conferences to serve as protective mechanisms. This mixed-methods study drew on survey data from 1,259 students from 9 schools in a large U.S. Northeastern school district serving students from low-income neighborhoods in 2018-2019. Students were categorized into four groups based on whether they experienced (1) suspension without RC participation, (2) RC participation without suspension, (3) both RC participation and suspension, and (4) neither RC participation nor suspension. Aligned with study hypotheses, there were no differences between non-disciplined students and RC participants’ perceptions of adult and peer support, fair treatment across race/ethnicity, and self-reported social-emotional skills. This suggests that RCs may encompass elements of a non-stigmatizing, harm-reduction model, in which students contending with less serious conflict remain connected to adults and perceive fair treatment similarly to their non-disciplined counterparts. Yet, non-suspended RC participants were only slightly higher than suspended students’ perceived adult support and fairness, trending toward a significant difference. Notably, the groups did not differ on perceived peer support or self-reported social-emotional competencies. Finally, suspended students with RCs, relative to suspended students without RCs, did not report higher positive perceptions of school climate and social-emotional competencies. Thus, these findings suggest that RCs were not associated with a compensatory or sufficiently reparative process for students experiencing the adversity of exclusionary discipline. In a similar vein, although most students’ qualitative responses about RCs were positive, a substantive group held mixed perceptions, indicating that students see both benefits in conferences and room for improvement.Psy.D.Includes bibliographical reference
Evaluating noise in protetin degradation
No full textGene expression is a stochastic process that leads to variability in mRNA and protein abundances even within an isogenic population of cells grown in the same environment. This variation, often called gene-expression noise, has typically been attributed to transcriptional and translational processes while ignoring the contributions of protein decay variability across cells. Here, we estimate the single-cell protein decay rates of two degron GFPs in Saccharomyces cerevisiae using time-lapse microscopy. We find substantial cell- to-cell variability in the decay rates of the degron GFPs. We evaluate cellular features that explain the variability in the proteasomal decay and find that the amount of 20S catalytic beta subunit of the proteasome marginally explains the observed variability in the degron GFP half-lives. We propose alternate hypotheses to explain the observed variability in the decay of the two degron GFPs. Overall, our study highlights the importance of studying the kinetics of the decay process at single-cell resolution and that decay rates vary at the single- cell level, and that the decay process is stochastic. A complex model of decay dynamics must be included when modeling stochastic gene expression to estimate gene expression noise.Ph.D.Includes bibliographical reference
Computational study of dietary phytochemicals in disease prevention
No full textChapter 1 provides the background for my research. It discusses the general idea of omics data and its applications in biomedical research. Specifically, how and why we collected and analyzed omics data while studying benefits of dietary phytochemicals tested in preclinical setting. The effects produced by these compounds in vitro and in vivo were associated with specific changes at the molecular level. The chapter describes several key technologies employed in our studies such as quantitative polymerase chain reaction (qPCR), microarrays and Next Generation Sequencing (NGS). The chapter also summarizes computational methods associated with these technologies.
Chapter 2 contains the results from our published study of transcriptomic changes produced by SETD7 knockdown (KD) and PEITC dietary phytochemical treatment in prostate cancer cells. Microarrays were used to analyze the cells’ transcriptomes. We identified 651 differentially expressed genes. Specifically, we found that in SETD7 KD cells a tumor suppressor gene RARRES3 that codes for the retinoic acid receptor responder protein 3 and an antioxidant gene SOD2 that codes for superoxidative dismutase 2 enzyme were up-regulated 28.06-fold and 5.66-fold, respectively. The KD also significantly affected several canonical pathways such as Death Receptor Signaling, TNFR2 Signaling and Acute Phase Response Signaling pathways. At the same time, PEITC downregulated TIMP1, TNKS, HLA-DRB1, GNAI2, and H6PD genes by more than 2.3-fold, and upregulated RBBP4, CNOT7, EXT2, PTK2, PHB, and RAB11B genes by at least 2.3-fold in the wild type (WT) cells compared to the DMSO-treated (control) SETD7 KD cells. Key results from the microarray analyses were validated by qPCR confirming that PCDHB13, CD24, SDC4, GADD45B, SACS, RAB31, and GH2 were upregulated in the KD versus the WT group but decreased in the KD PEITC versus KD group. Additionally, ID1 and LXN were downregulated in the KD versus the WT group but upregulated in the KD PEITC versus KD group. qPCR also confirmed that RRTM1, FCRL6, THSD7A, APOM, ARMC12, TKTL1, and ZFP235 expressions increased in PEITC-treated WT cells, whereas SETD7 KD prevented this induction. TPM3, OR9A2, DCAF4L1, CBLN2, and TAS2r19 were all downregulated in the PEITC-treated WT cells but SETD7 KD prevented this suppression.
Chapter 3 is a study of DNA methylome and transcriptome alterations in high glucose (HG) induced diabetic nephropathy in the mouse kidney mesangial cells and the protective effect of Tanshinone IIA (TIIA) treatment. After a 5-day HG treatment, RNA and DNA were extracted from the cells, sequenced and analyzed. Previously, we observed at least 2-fold increase of intracellular ROS damage in HG compared to the control while TIIA-treated cells were protected from the damage. We identified 213 differentially expressed genes with log2-fold changes greater than 0.3. 124 genes were downregulated in the HG-treated cells but not in the HG+TIIA. At the same time, 89 genes were downregulated by HG treatment, but the trend was reversed by TIIA treatment. Next, we examined CpG methylation profiles of the identified genes. Our main hypothesis was that hypermethylation of CpG clusters in the gene promoter region in DNA should lead to decreased amount of RNA for the same genes. Conversely, hypomethylated promoters may result in higher levels of the gene expressions although other factors can prevent the transcription, hence, we expected this association to be less obvious in the data. We identified several candidate genes and were able to validate that FGL2 and NMU genes’ promoter regions became hypermethylated after HG treatment, but TIIA treatment prevented hypermethylation. The opposite trend was found and validated in GULO and KCNIP2 as HG treatment resulted in demethylation of promoters’ CpGs while TIIA-treated cells did not exhibit it.
Chapter 4 is a study of triterpenoid corosolic acid (CA) modulating global CpG methylation and transcriptome of tumor promotor 12-O-tetradecanoyl- phorbol-13-acetate (TPA) induced mouse epidermal cells. JB6 P+ cells were challenged with TPA and treated with CA for 5 days. DNA and RNA were isolated and sequenced. Genes differentially expressed in the positive control (TPA only) but not in the treatment (TPA+CA) were identified, and their promoter regions analyzed for differential methylation. Out of these, genes for which promoters’ CpG methylation profiles were associated with RNA expressions were further selected for validation using qPCR. Genes such Prolactin-2C2 (Prl2c2) growth and angiogenesis factor, Sprr2h (small proline-rich protein 2) known to be regulated by IL6/STAT3 signaling, Mrc1 (Macrophage mannose receptor1), Dkk2 (Dickkopf-related protein 2) which is WNT signaling pathway inhibitor, NOS2 (Nitric oxide synthase 2) and CYP27B1 (cytochrome P450 family 27 subfamily B member1) were found to be differentially modulated in TPA+CA treatment as compared to TPA only. Smad-3 (signal transducers for transforming growth factor beta (TGF-B) superfamily), Tasp1 gene (endopeptidase which needs for the maintenance of HOX genes), Uri1 (prefoldin like chaperone protein), and Nsg2 (Neuronal vesicle trafficking-associated protein 2) were hypermethylated in TPA treatment while hypomethylated in TPA+CA. Madd (MAP kinase activating death domain), Dusp22 (Dual specificity protein phosphatase 22), and Rassf (tumor suppressor gene family, Ras-association domain family) genes were hypomethylated in TPA but hypermethylated in TPA+CA. Major canonical pathways affected by the treatments included cell cycle regulatory, cancer and cell differentiation, apoptosis, signaling kinases associated pathways such as p53 signaling, Erk signaling, and TGF beta signaling pathway.
Chapter 5 explores epigenomic and transcriptomic of mouse kidney mesangial cells challenged with high glucose (HG) and treated with carotenoid fucoxanthin (FX). We identified several differentially expressed genes and examined the association of RNA expression levels with methylation changes in the promoter regions of those genes. Specifically, we detected that KCNIP2, MAK, CNN1, ARHGDIB and TMEFF1 where downregulated while having one or more hypermethylated CpG clusters. Top canonical pathways affected by FX treatment were multiple signaling pathways/kinases; Toll-like receptor 7/8 pathways and a Hedgehog signaling pathway. CYP2E1signaling, which is thought to activate protoxins, the adenylate cyclase inhibitory pathway, the Hyaluronan metabolism pathway, and the PKA mediated phosphorylation of CREB protein pathway were upregulated by HG and attenuated by FX. Protein kinase A signaling which is involved in metabolism, cytoskeleton dynamics, and regulation of gene expression was downregulated by HG and FX accentuated its expression.
Chapter 6 is a study of mouse gut microbiomes. In a series of three experiments, we explored the effects of Nrf2 gene using a knock-out mouse model, gut inflammation induced by DSS, and PEITC and cranberry enriched diets. Our results indicated that Nrf2 KO was significantly associated with higher diversity and richness of the microbial communities compared to WT. Inflammation negatively affected these communities but PEITC and cranberry diets had protective effect. Firmicutes to Bacteroidetes ratio (F/B), an indirect indicator of inflammatory processes in the guts, confirmed the protective effect of these dietary supplements. We further examined microbiome profile differences between the treatment groups and identified several bacterial phyla, classes, families and OTUs with significantly differentiated relative abundance in the samples. Additionally, we examined metabolic profiles of the microbiomes. As expected, the dietary supplements increased production of many microbial metabolites which, in turn, moved the animal guts condition toward homeostasis.
Finally, in Chapter 7 I provided a conclusion for my research and discussed future prospective including improved study designs and more advanced computational techniques that would further advance our understanding of the effects of dietary phytochemicals on human health.Ph.D.Includes bibliographical reference