cssi/SciSciGPT-SciSciNet huggingface dataset:
Fluidics for a Multi-Analyte Detector Based on Intermolecular Binding Forces

We are developing a novel biosensor—the Bead Array Counter (BARC)—which has the potential to simultaneously detect thousands of analytes. BARC is an adaptation of atomic force microscope (AFM) experiments in which the interaction forces that bind DNA—DNA, antibody-antigen, or ligand-receptor pairs together are measured. Using magnetic microbeads to exert force and numerous magnetoresistive sensors to detect the microbeads, it is possible to perform thousands of such experiments simultaneously. Thus, with BARC, it is possible to detect individual molecular bonds and test their strength. For our preliminary investigation, we are developing BARC as a hybridization assay in which DNA probes are covalently attached to the sensors by inkjet patterning techniques. We are also developing miniature fluidic devices through modeling and testing of prototype designs that will assure the delivery of microliter volumes of fluid and the even dispersion of microbeads at the site of detection. Operational idiosyncrasies of BARC require special considerations in the construction and actuation of the miniaturized pumps and valves, such as non-magnetic components and attention to particulate matter. Other objectives include thermoplastic replication of the fluidic channels, modularity of the fluidic and electronic components, ease of sample delivery and assay preparation, reduction of contamination between assays, and materials compatibility with the assay chemistry.
First record of the family Ringiculidae (Gastropoda) from the Middle Tertiary of Antarctica

A new species of the late Mesozoic–Cenozoic family Ringiculidae (Ringicula (Ringicula) cockburnensis n. sp.) is described from basal glauconitic beds of late Eocene age of Cockburn Island, Antarctica, and is the first reported occurrence of the family Ringiculidae from the continent of Antarctica. Ringicula (R.) cockburnensis n. sp. most closely resembles R. castigata from the middle Oligocene Duntroonian Stage of New Zealand and provides further support for the strong provinciality (Weddellian Province) that existed along the southern margin of the Pacific during the Late Cretaceous and early Tertiary.
Theories of the World System

However appealing the radical pluralist vision of a small-scale, decentralized political system, today large-scale institutions in the world system make the crucial decisions that affect human lives. Protesters can no longer just think globally and act locally but must also consider the impact of transnational institutions on people everywhere. The major powers, along with minor regional powers, now possess nuclear weapons that can destroy millions in a catastrophic war. Investment decisions of multinational corporations determine employment opportunities and economic growth all over the world. Various intergovernmental agencies, such as the United Nations, its specialized agencies, the World Bank, the International Monetary Fund (IMF), and the Organization of Petroleum-Exporting Countries (OPEC), enact policies that shape nearly everyone’s health, education, and economic well-being. Transnational social movements — for example, Amnesty International, Greenpeace International, the International Fellowship of Reconciliation, Disabled People’s International, and Service for Peace and Justice in Latin America — play key roles on the world stage. As these movements interact with individual citizens, national government officials, and heads of international institutions, they struggle to prevent war, settle conflicts peacefully, and lessen the destructive consequences of rapid economic growth.
A Frailty Mixture Model for Estimating Vaccine Efficacy

SUMMARY Vaccines can have heterogeneous effects on the host's immune response. Somevaccinated people may have a strong response and be highly protected against infectious challenge, but others may only denve varying levels of partial protection. We derive a statistical model for estimating vaccine efficacy that expresses the often unmeasured heterogeneous host response and other vaccine effects in terms of estimable parameters. In addition, the-model incorporates the infection process into the base-line hazard rate. The model falls into the general category of frailty models (with point mass at 0) employed in survival analysis. As an example, we estimate the efficacy of a measles vaccine from a measles outbreak in Burundi.
Phase II trial of bevacizumab and pemetrexed for recurrent or persistent epithelial ovarian, fallopian tube, or primary peritoneal cancer.

5013 Background: This phase II clinical trial evaluated the efficacy and safety of the combination of bevacizumab, a VEGF inhibitor, and pemetrexed, a multi-targeted antifolate agent inhibiting thymidylate synthase, for recurrent or persistent epithelial ovarian, fallopian tube (FT) or primary peritoneal (PP) cancer. Methods: Patients with measurable recurrent/persistent epithelial ovarian, FT or PP cancer after at least one prior platinum- and taxane-containing regimen were eligible. Patients might have received < 2 prior cytotoxic chemotherapy regimens but no prior bevacizumab. Pemetrexed 500 mg/m2 IV and bevacizumab 15 mg/kg IV were given every 3 weeks until progression, unacceptable adverse effects, or patient/physician choice. 32 patients were needed to have 90% power to detect the primary endpoint of 6-month PFS ≥ 40% with a two-sided 0.05 significance. Secondary endpoints included toxicity and response by RECIST and CA-125 criteria. Results: Thirty-four patients received a median of 7 treatment cyc...
Grasping and Fixturing as Submodular Coverage Problems

Grasping and fixturing are concerned with immobilizing objects. Most prior work in this area strives to minimize the number of contacts needed. However, for delicate objects or surfaces such as glass or bone (in medical applications), extra contacts can be used to reduce the forces needed at each contact to resist applied wrenches. We focus on the following class of problems. Given a polyhedral object model, set of candidate contacts, and a limit on the sum of applied forces at the contacts or a limit on any individual applied force, compute a set of k contact points that maximize the radius of the ball in wrench space that can be resisted. We present an algorithm, SatGrasp, that is guaranteed to find near-optimal solutions in linear time. At the core of our approach are (i) an alternate formulation of the residual radius objective, and (ii) the insight that the resulting problem is a submodular coverage problem. This allows us to exploit the submodular saturation algorithm, which has recently been derived for applications in sensor placement. Our approach is applicable in situations with or without friction.
Increased Tree-ring Network Density Reveals More Precise Estimations of Sub-regional Hydroclimate Variability and Climate Dynamics in the Midwest, USA

Understanding the historic variability in the hydroclimate provides important information on possible extreme dry or wet periods that in turn inform water management plans. Tree rings have long provided historical context of hydroclimate variability of the U.S. However, the tree-ring network used to create these countrywide gridded reconstructions is sparse in certain locations, such as the Midwest. Here, we increase (n = 20) the spatial resolution of the tree-ring network in southern Indiana and compare a summer (June–August) Palmer Drought Severity Index (PDSI) reconstruction to existing gridded reconstructions of PDSI for this region. We find both droughts and pluvials that were previously unknown that rival the most intense PDSI values during the instrumental period. Additionally, historical drought occurred in Indiana that eclipsed instrumental conditions with regard to severity and duration. During the period 1962–2004 CE, we find that teleconnections of drought conditions through the Atlantic Meridional Overturning Circulation have a strong influence (r = −0.60, p < 0.01) on secondary tree growth in this region for the late spring-early summer season. These findings highlight the importance of continuing to increase the spatial resolution of the tree-ring network used to infer past climate dynamics to capture the sub-regional spatial variability. Increasing the spatial resolution of the tree-ring network for a given region can better identify sub-regional variability, improve the accuracy of regional tree-ring PDSI reconstructions, and provide better information for climatic teleconnections.
The influence of Helicobacter pylori on the ethnic distribution of esophageal eosinophilia.

Background Environmental factors associated with ethnicity may contribute to the occurrence of eosinophilic esophagitis. Our study aimed to investigate the influence of Helicobacter pylori on the ethnic variation of esophageal eosinophilia in a large national sample of patients undergoing esophago-gastro-duodenoscopy. Methods The Miraca Life Sciences Database is an electronic repository of histopathologic patient records. A case-control study evaluated the influence of ethnicity on the occurrence of esophageal eosinophilia and how age, gender, and histologic diagnosis of H. pylori modify this relationship. Results The total study population comprised 596 479 subjects, of whom 25 969 harbored a diagnosis of esophageal eosinophilia. Young age, male sex, and H. pylori infection in declining order exerted the strongest influence on the occurrence of esophageal eosinophilia. In comparison with the population comprising of Caucasians and African-Americans, esophageal eosinophilia was less common among patients of African (OR=0.10, 95% CI=0.01-0.46), Middle Eastern (0.22, 0.15-0.31), East Asian (0.32, 0.26-0.38), Indian (0.28, 0.21-0.37), Hispanic (0.40, 0.37-0.43), or Jewish descent (0.58, 0.51-0.66), but more common among patients of Northern European descent (1.25, 1.07-1.45). With the exception of Northern Europeans, all ethnic subgroups were characterized by a higher prevalence of H. pylori than the comparison group. A low prevalence of H. pylori was significantly associated with a high prevalence of esophageal eosinophilia (R2=0.90, P<.001). Conclusion Esophageal eosinophilia prevalence markedly varies by patient ethnicity. As there is a strong inverse correlation between H. pylori and esophageal eosinophilia, H. pylori infection may be in part responsible for the observed ethnic distribution of esophageal eosinophilia.
Cementless vs Cemented Tibial Fixation in Primary Total Knee Arthroplasty

Abstract Background The ideal fixation for modern tibial components in total knee arthroplasty (TKA) remains controversial with uncertainty on whether cementless implants can yield equivalent outcomes to cemented fixation in early follow-up. Methods A series of 70 consecutive cases with reverse hybrid cementless fixation were matched to 70 cemented cases from 2008 to 2015 based on implant design and patient demographics. Results Cementless TKA demonstrated greater aseptic loosening (7 vs 0, P = .013) and revision surgery (10 vs 0, P = .001) than cemented fixation within 5 years of follow-up, but with no clinically significant differences in outcome scores. Conclusion It remains unclear whether early aseptic loosening in cementless TKA can be reduced with enhanced adjunct fixation and what proportion of early failure justifies the potential lifelong fixation through biologic ingrowth of cementless tibial components.
Self-Assembled Monolayers as Models for Polymeric Interfaces

Surface modification techniques are widely used to tailor a polymer’s interfacial properties such as permeability, wettability, adhesion, and biocompatibility, transforming inexpensive raw materials into highly valuable finished products.1–3 These surface modification processes most commonly involve either wet chemical or vacuum based treatment strategies. Over the past decade, vacuum based methods, which include plasma based processing, 4–8 noble gas sputtering and metallization9 have become the preferred pathway to modification. Compared to wet chemical processes, vacuum based technologies are fast, easily controlled and environmentally benign.10 Despite their technological importance, a molecular level understanding of vacuum based surface modification processes at polymeric interfaces is not well understood. This lack of mechanistic understanding can be ascribed to the complexity of the typical reaction medium coupled with the heterogeneity of polymeric substrates.
Firefighter-Paramedic With Posttraumatic Stress Disorder, Horrific Images, and Depression: A Clinical Case Study:

Despite the existence of evidence-based treatments for posttraumatic stress disorder (PTSD), no identifiable study reported delivery of exposure therapy for a first responder with PTSD, as well as ...
Hybrid Rocket Theory and Design

A hybrid rocket is so named because one of the propellant components is liquid and the other solid. Normally the oxidizer is liquid and the fuel is solid. In a typical design (Fig. 7-1), the oxidizer is sprayed in at the head end of a solid cylindrical fuel grain. It is apparent that once the liquid oxidizer is injected, the combustion process proceeds according to natural law and the geometric constraints designed into the grain and is not subject to external control. It is very important, therefore, to understand the details of the combustion if it is to occur in the manner desired by the designer.
A Solution-Procedure Without Approximations

During the 1890s, at the invitation of George Darwin, Brown prepared a paper for inclusion in the volume of the Transactions of the Cambridge Philosophical Society commemorating the jubilee of Sir George Gabriel Stokes.
Why trust an algorithm? Performance, cognition, and neurophysiology

Abstract OBJECTIVE We measured neurophysiologic responses and task performance while participants solved mazes after choosing whether to adopt an imperfect helper algorithm. BACKGROUND Every day we must decide whether to trust or distrust algorithms. Will an algorithm improve our performance on a task? What if we trust it too much? METHOD Participants had to pay to use the algorithm and were aware that it offered imperfect help. We varied the information about the algorithm to assess the factors that affected adoption while measuring participants’ peripheral neurophysiology. RESULTS We found that information about previous adoption by others had a larger effect on adoption and resulted in lower cognitive load than did information about algorithm accuracy. The neurophysiologic measurement showed that algorithm adoption without any information resulted in low cognitive engagement during the task and impaired task performance. Conversely, algorithm use after information about others’ use improved engagement and performance. CONCLUSION By objectively measuring cognitive load and task performance, we identified how to increase algorithm adoption while sustaining high performance by human operators. APPLICATION Algorithm adoption can be increased by sharing previous use information and performance improved by providing a reason to monitor the algorithm. Precis We collected neurophysiologic data while varying information about an algorithm that assisted participants in solving a timed and incentivized maze and found that information about prior use by others more effectively influenced adoption, reduced cognitive load, and improved performance compared to algorithm accuracy information.
Factors predicting reclassification of variants of unknown significance

Abstract Genetic variants of unknown significance (VUS) are an increasingly common result of genetic testing. VUS present dilemmas for treatment and surveillance. Family history may play a role in VUS reclassification over time. Methods: All genetic tests performed at a tertiary referral center 2006–2015 were evaluated for the presence of VUS. Patients with VUS were evaluated for demographics, clinical characteristics, family history, and gene characteristics. Results: In total, 2291 individuals were tested from 1639 families; 150 VUS were identified. Twenty-eight VUS reclassified, 21 to benign and 7 to pathogenic. Logistic regression demonstrated the number of family members with associated phenotypic disease was a significant predictor of reclassification. Conclusion: The likelihood of VUS reclassification can be predicted by increased positive family history of disease. Most VUS reclassify to benign, but one-fourth reclassify to pathogenic. The actual risk of a VUS should be assessed based on family history and routinely checked for reclassification.
Bioinformatic Analysis of Microbiome Data

In this chapter, we first introduce microbiome study and DNA sequencing. Then we cover some basics of phylogenetics. Next we focus on reviewing 16S rRNA sequencing and shotgun metagenomic sequencing approaches. Finally, we briefly introduce two tools for bioinformatical analysis of 16S rRNA sequencing data.
An Exploratory Look at the Role of Childcare Providers as a Support and Resource for Breastfeeding Mothers

Introduction: The childcare setting remains largely unexplored as a potential barrier to breastfeeding continuation and, therefore, the lack of interventions targeting childcare providers may be a missed opportunity for improved breastfeeding support. This article explores the perceptions of 25 first-time breastfeeding mothers on navigating the critical transition to childcare and the role of childcare providers regarding breastfeeding support. Methods: Mothers were selected if they indicated an intent to breastfeed on a prenatal questionnaire and had enrolled their child in childcare. Semistructured interviews guided by Bronfenbrenner's bioecological model were conducted to capture mothers' experiences. Responses were analyzed utilizing thematic analysis to generate themes rooted in mothers' experiences with childcare and breastfeeding. Results: A thematic analysis resulted in three key themes: Providers are not Critically Evaluated, A Stressful Transition, and Childcare as a Service, not Support. These themes indicated that although mothers intended to continue breastfeeding during and after the transition to childcare, they had not previously given much consideration to the childcare setting beyond that of a service provider. Conclusion: Findings illustrate new considerations to support modern breastfeeding mothers through the transition to work and childcare are needed such as basic and practical education and training to prepare childcare providers to support breastfeeding mothers in the way that best meets their needs, enhanced education for mothers on how to seek and evaluate providers for breastfeeding competence, and policy initiatives focused on fostering engagement between mothers and providers. By taking mothers' perceptions into consideration, researchers, practitioners, and policymakers can offer breastfeeding support that mothers will be receptive to and more likely to engage with, thereby advancing the health of both mothers and infants.
Twofold Pictorial Experience

Richard Wollheim famously argued that figurative pictures depict their scenes, in part, in virtue of their ability to elicit a unique type of visual experience in their viewers, which he called seeing-in. According to Wollheim, experiences of seeing-in are necessarily twofold, that is, they involve two aspects of visual awareness: when a viewer sees a scene in a picture, she is simultaneously aware of certain visible features of the picture surface, the picture’s design, and the scene depicted by the picture. Even though Wollheim’s notion of twofoldness has been very influential, a number of philosophers have put forward powerful arguments against it. In this paper, I defend the claim that some pictorial experiences are twofold in Wollheim’s sense. My argument has two parts. In the first part, I provide a phenomenal contrast argument in favor of twofoldness. In the second part, I respond to what I take to be the most important objections against twofoldness. I believe that both parts together provide strong support for the claim that some pictorial experiences are twofold in Wollheim’s sense.
Microbiomes of stony and soft deep-sea corals share rare core bacteria

Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved “core microbiomes” of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis. Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians. Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts’ phylogeny.
11 – Manganese bioavailability

Publisher Summary Manganese was recognized as an essential dietary nutrient for growth and reproduction in rats and mice in the early 1930s, and its role with regard to the prevention of perosis in chicks was reported five years later. High-concentrate diets based predominantly on cereal grains and soybean meal are likely to be deficient in manganese for all species of poultry, and for finishing sheep and cattle. Solubility in various solutions that mimic physiological conditions has been used to predict the bioavailability of inorganic manganese sources. Disappearance of manganese after 48-hour incubation in nylon bags in the rumen of sheep was studied with two legumes and two grasses cut at 6 or 12 weeks of regrowth. Absorption of manganese in adult animals is on the order of 3 or 4% but can be greater in younger animals. The earliest studies conducted on manganese bioavailability used deficient natural or purified diets that were often supplemented with high levels of calcium and phosphorus, which resulted in poor growth and perosis in young chicks. Few studies have been conducted with radio-labeled manganese to determine the bioavailability of supplemental sources. Factors influencing bioavailability are dietary and animal factors. Manganese bioavailability research is conducted primarily with supplemental forms of the element which have potential use with domestic animals.
Splendid Little Papers from the "Splendid Little WAR": Mapping empire in the soldier newspapers of the Spanish-American War

“Splendid Little Papers” recovers a forgotten moment in the print culture history of U.S. empire by examining a handful of newspapers and periodicals— Bounding Billow, American Soldier, Manila Outpost , and Volunteer —that were founded and written by and for U.S. soldiers in the Philippines and Cuba during the Spanish-American War. Foregrounding their status as periodicals, this essay argues that soldier papers used the formal technologies of print to remap the nation’s relationship with the world and in the process helped their readers see themselves as part of an imagined community of empire.
Utilization of Lean Principles to Redesign Electronic Charting to Reduce Charge and Documentation Errors by Respiratory Therapists

Background: In our health system, respiratory therapists (RTs) bill for services as they document within the electronic medical record (EMR). In the USA, hospitals lose millions of dollars in revenue annually because of documentation errors,1 and this is true in our institution. We aimed to use LEAN processes to review and implement changes to the EMR to reduce RT documentation errors and missed revenue. Methods: We began this initiative with a preliminary data collection phase where we obtained data from our auditing department to comprehend the severity of the situation. We started the Process Improvement and Implementation Phases by identifying stakeholders and holding a lean-focused event (5 days) led by a Continuous Improvement specialist and RT. After the identification of critical barriers and implementing changes during the Modification Phase, we reviewed data to ensure changes were effective. Results: Major barriers included duplicated charting rows, brand-specific labels, the inclusion of too many required fields, and incorrect order of line items for workflow. In total, 123 fields were removed, and 46 were modified during our Modification Phase. When comparing 2018 (before changes) to 2019 (after changes), there were 3,077 and 1,978 RT errors, respectively. The average error per month in 2018 was 256.4 (STD 45.7) and in 2019 was 164.8 (STD 78.4). In Q1 for 2019 there was in increase in total errors that was attributed to technology issues with duplicate charge rows appearing from our changes. Q2, Q3, and Q4 all saw improvement in charge errors in the EMR by 68%, 58%, and 54% (60 % improvement average). See Graph 1 for detailed data. Conclusions: Documentation errors made by clinical staff in revenue generating departments/EMRs directly impact accurate charges. Precise and complete documentation is required to generate a charge for the services RT’s provide. Without it, insurers will deny charges. In our institution we were able to decrease the number of documentation rows significantly while still being in compliance with procedural/legal standards. Additionally, we arranged the order of the EMR flowsheet to match the flow of care provided at the bedside, which made the documentation process more intuitive. These changes resulted in the department decreasing its overall documentation errors by 35.7%, which has the potential of saving the health system close to $2 million in gross billed revenue annually.
Rubella virus-associated chronic inflammation in primary immunodeficiency diseases.

Purpose of the review The aim of this article is to summarize recent data on rubella virus (RuV) vaccine in chronic inflammation focusing on granulomas in individuals with primary immunodeficiencies (PIDs). Recent findings The live attenuated RuV vaccine has been recently associated with cutaneous and visceral granulomas in children with various PIDs. RuV vaccine strain can persist for decades subclinically in currently unknown body site(s) before emerging in granulomas. Histologically, RuV is predominately localized in M2 macrophages in the granuloma centers. Multiple mutations accumulate during persistence resulting in emergence of immunodeficiency-related vaccine-derived rubella viruses (iVDRVs) with altered immunological, replication, and persistence properties. Viral RNA was detected in granuloma biopsies and nasopharyngeal secretions and infectious virus were isolated from the granuloma lesions. The risk of iVDRV transmissibility to contacts needs to be evaluated. Several broad-spectrum antiviral drugs have been tested recently but did not provide significant clinical improvement. Hematopoietic stem cell transplantation remains the only reliable option for curing chronic RuV-associated granulomas in PIDs. Summary Persistence of vaccine-derived RuVs appears to be a crucial factor in a significant proportion of granulomatous disease in PIDs. RuV testing of granulomas in PID individuals might help with case management.
Kurepa trees and spectra of $${\mathcal {L}}_{\omega _1,\omega }$$ L ω 1 , ω -sentences

We use set-theoretic tools to make a model-theoretic contribution. In particular, we construct a single $${\mathcal {L}}_{\omega _1,\omega }$$ -sentence $$\psi $$ that codes Kurepa trees to prove the following statements:
A Weapon and a Tool: Decolonizing Description and Embracing Redescription as Liberatory Archival Praxis

This article uses Indigenous decolonizing methodologies and Critical Race Theory (CRT) as methodological and theoretical frameworks to address colonial and racialized concerns about archival description; to argue against notions of diversity and inclusion in archival descriptive practices; and to make recommendations for decolonizing description and embracing redescription as liberatory archival praxis. First, we argue that extant descriptive practices do not diversify archives. Rather, we find that descriptive work that isolates and scatters aims to erase the identifiable existence of unique Indigenous voices. Next, we argue that while on one hand, the mass digitization of slavery-era records holds both the promise of new historical knowledge and of genealogical reconstruction for descendants of enslaved peoples, on the other hand, this trend belies a growing tendency to reinscribe racist ideologies and codify damaging ideas about how we organize and create new knowledge through harmful descriptive practices. Finally, working specifically against the rhetoric of diversity and inclusion, we challenge the ways archives claim diverse representation by uncritically describing records rooted in generational trauma, hatred, and genocide, and advocate for developing and employing decolonizing and redescriptive practices to support an archival praxis rooted in justice and liberation, rather than more palatable (and less effective) notions of “diversity and inclusion”.
Student Annotations of Published Data as a Collaboration between an Online Laboratory Course and the C. elegans Database, WormBase

Course-based undergraduate research experiences (CUREs) provide the same benefits as individual, mentored faculty research while expanding the availability of research opportunities. One important aspect of CUREs is students' engagement in collaboration. The shift to online learning during the COVID-19 pandemic created an immediate need for meaningful, collaborative experiences in CUREs. We developed a partnership with the Caenorhabditis elegans (C. elegans) database, WormBase, in which students submitted annotations of published manuscripts to the website. Due to the stress on students during this time of crisis, qualitative data were collected in lieu of quantitative pre- and postanalyses. Most students reported on cognitive processes that represent mid-level Bloom's categories. By partnering with WormBase, students gained insight into the scientific community and contributed as community members. We describe possible modifications for future courses, potential expansion of the WormBase collaboration, and future directions for quantitative analysis.
Development of lipid nanoparticles for delivery of siRNA to neural cells

Lipid nanoparticles (LNPs) are a clinically approved platform to deliver siRNA to the liver. We are optimizing this platform to deliver siRNA for the treatment of pain. siRNA against TRPV1 (siTRPV1) was chosen as a proof of concept. siTRPV1-LNPs were formulated using C12-200, an ionizable cationic lipid and helper lipids. Their particle size and surface charge was characterized using dynamic light scattering and siRNA encapsulation efficiency was determined using a Ribogreen assay. A panel of breast cancer cell lines (MCF-7, MDA-MB-231 and BT-549) that express TRPV1 were selected for in vitro screening of LNPs to determine their cytocompatibility and gene knockdown effects using an ATP assay, qPCR and western blotting. The effects of mixing speeds during LNP formulation, slow vs. fast, were compared for determining their effects on %siRNA encapsulation. The values increased from 74.4% at slow mixing to 83.8% at faster mixing speeds. siRNA-LNPs showed a particle diameter of ca. 251 nm compared to 434 nm for empty LNPs. A lower polydispersity index of 0.15 was observed for siRNA-LNPs compared to 0.41 for empty LNPs, suggesting narrower particle size distribution upon siRNA loading. Zeta potential of siRNA-LNPs (+0.15 mV) was slightly lower compared to empty LNPs (+0.41 mV). siRNA-LNPs had a negligible impact on cell viability, which was >95% in all three cell lines and primary rat dorsal root ganglion neurons four hours post-exposure. We are currently optimizing transfection parameters to determine TRPV1 knockdown in primary DRG cultures. LNPs were well-tolerated by TRPV1-expressing cell lines and primary DRG cultures, allowing their further exploration for TRPV1 silencing.
ARE PRETERM SGA AT HIGHER RISK FOR PARENTERAL NUTRITION ASSOCIATED CHOLESTASIS

Background Parenteral nutrition associated cholestasis (PNAC) is one of the most alarming disease of prematurity and SGA infants seem to be more prone to this complication. Objective To assess the role of intrauterine growth retardation on PNAC development. Methods Records of VLBW infants admitted to our NICU during the last 10 years and exposed to parenteral nutrition >14 days were reviewed. PNAC was defined by direct bilirubin >2.0 mg/dl. Clinical data and nutritional intakes were compared between infants who developed CNAP and controls. Results Among 446 selected infants, 55 (12.3%) developed PNAC; these infants had lower BW (850±274 vs 1052±238 g) and lower GA (27.4±2.5 vs 28.7±2.3 wks). The prevalence of SGA infants (30.9 vs 28.6% BW Conclusions Intrauterine growth retardation does not represent a significative risk factor for PNAC whereas our data support the preventive role of early enteral feeding.
GECO: gene expression clustering optimization app for non-linear data visualization of patterns

Due to continued advances in sequencing technology, the limitation in understanding biological systems through an “-omics” lens is no longer the generation of data, but the ability to analyze it. Importantly, much of this rich -omics data is publicly available waiting to be further investigated. Although many code-based pipelines exist, there is a lack of user-friendly and accessible applications that enable rapid analysis or visualization of data. GECO (Gene Expression Clustering Optimization; http://www.theGECOapp.com ) is a minimalistic GUI app that utilizes non-linear reduction techniques to rapidly visualize expression trends in many types of biological data matrices (such as bulk RNA-seq or proteomics). The required input is a data matrix with samples and any type of expression level of genes/protein/other with a unique ID. The output is an interactive t-SNE or UMAP analysis that clusters genes (or proteins/other unique IDs) based on their expression patterns across the multiple samples enabling visualization of expression trends. Customizable settings for dimensionality reduction, data normalization, along with visualization parameters including coloring and filters, ensure adaptability to a variety of user uploaded data. This local and cloud-hosted web browser app enables investigation of any -omic data matrix in a rapid and code-independent manner. With the continued growth of available -omic data, the ability to quickly evaluate a dataset, including specific genes of interest, is more important than ever. GECO is intended to supplement traditional statistical analysis methods and is particularly useful when visualizing clusters of genes with similar trajectories across many samples (ex: multiple cell types, time course, dose response). Users will be empowered to investigate -omic data with a new lens of visualization and analysis that has the potential to uncover genes of interest, cohorts of co-regulated genes programs, and previously undetected patterns of expression.
Accelerating AES with Vector Permute Instructions

We demonstrate new techniques to speed up the Rijndael (AES) block cipher using vector permute instructions. Because these techniques avoid data- and key-dependent branches and memory references, they are immune to known timing attacks. This is the first constant-time software implementation of AES which is efficient for sequential modes of operation. This work can be adapted to several other primitives using the AES S-box such as the stream cipher LEX, the block cipher Camellia and the hash function Fugue. We focus on Intel's SSSE3 and Motorola's Altivec, but our techniques can be adapted to other systems with vector permute instructions, such as the IBM Xenon and Cell processors, the ARM Cortex series and the forthcoming AMD "Bulldozer" core.
Clay Strength Under Earthquake Loading Conditions

A procedure for determining the combinations of sustained stress and pulsating stress that will cause failure of a given soil is described and such data is presented for three soil types. The relationship depends on the nature of the loading conditions (one-directional or two-directional), the soil type, the principal stress ratio during consolidation, the frequency and duration of the pulsating stresses, the number of stress pulses, and the form of the stress pulse. Data is also presented on the strains resulting from different stress combinations. For typical field and earthquake conditions, it is shown that the relationship between total stress (sustained plus pulsating) and total strain for some soils will not differ greatly from the stress versus strain relationship for the soils determined by conventional undrained test procedures. Finally, it appears that in sensitive clay, a series of vibrations or stress pulses that will not in themselves cause failure, may induce an increase in pore water pressure and initiate creep movement that will lead to failure some time after the vibrations have ceased.
Power saving approaches in 2-hop relaying cellular networks

This paper discusses various approaches to save power in relay-based cellular networks. We introduce an optimization method based on the Hungarian assignment problem to globally minimize the power-based allocation of relays. We compare this approach with the greedy approach of choosing a relay. We introduce another approach based on the concept of intelligent relays. Here, based on the expected power values of mobiles at the relay's location, the relay chooses to carry call for a mobile. We show that this approach introduces less intra-cell interference
The role of deoxyribonucleic acid in ribonucleic acid synthesis. 13. Modified purification procedure and additional properties of ribonucleic acid polymerase from Escherichia coli W.

1. A modified procedure for the isolation and purification of RNA polymerase from Escherichia coli W is presented. The procedure described leads to the isolation of polymerase that is homogeneous by ultracentrifuge analysis and is free of detectable ribonuclease and deoxyribonuclease activities. Other enzyme activities that have been found to be absent from such preparations include inorganic pyrophosphatase, nucleoside diphosphokinase, DNA polymerase, nucleoside triphosphatase, polynucleotide phosphorylase, and polyriboadenylate polymerase. 2. Under the conditions used, the enzyme showed a single moving boundary of an s20,w of approximately 11 S in the analytical ultracentrifuge. Molecular weight determined by the sedimentation equilibrium method is approximately 370,000. The amino acid composition of the enzyme has been determined. 3. Once RNA synthesis has started from a template, subsequent addition of another variety of DNA hardly displaces the enzyme from the initial enzyme-DNA complex. 4. The enzyme does not catalyze pyrophosphorolysis of free RNA. In contrast, small but detectable pyrophosphorolysis of RNA from RNA-DNA hybrids has been demonstrated. 5. It has been calculated that there are approximately 1200 molecules of RNA polymerase per E. coli cell. This amount can account for the synthesis of only 10% of the total cellular RNA.
Self-renewal versus differentiation, a job for the mighty morphogens

The proliferation and differentiation of hematopoietic stem cells is regulated by BMP-4 and Shh. These factors collaborate with cytokines in the bone marrow to create an environment that maintains stem cell homeostasis
Two photon radiation in W and Z boson production at the Fermilab Tevatron collider

We present a calculation of two photon radiation in W and Z boson production in hadronic collisions, based on the complete matrix elements for the processes qq(bar sign){sup '}{yields}l{sup {+-}}{nu}{gamma}{gamma} and qq(bar sign){yields}l{sup +}l{sup -}{gamma}{gamma}, including finite charged lepton masses. In order to achieve stable numerical results over the full phase space, multiconfiguration Monte Carlo techniques are used to map the peaks in the differential cross section. Numerical results are presented for the Fermilab Tevatron. (c) 2000 The American Physical Society.
Gradient-free stochastic sensitivity analysis of the shipboard power system

United States. Office of Naval Research (N00014-02-1-0623); United States. Office of Naval Research (N00014-07-1-0846); Massachusetts Institute of Technology. Sea Grant College Program (NA060AR4170019 NOAA/DOC)
Probing RNA Structure and Metal-Binding Sites Using Terbium(III) Footprinting

The function of an RNA molecule is determined by its overall secondary and tertiary structure. The tertiary structure is facilitated and stabilized by the interaction with metal ions. The current chapter offers a detailed protocol on the use of the lanthanide metal ion terbium(III) as a powerful probe of RNA structure and metal-binding properties. When incubating RNA with low (micromolar) concentrations of terbium(III), specific backbone scission by partially deprotonated aqueous terbium(III) complexes can be used to detect high-affinity metal-binding sites, while incubation with high (millimolar) terbium(III) concentrations cleaves the RNA backbone preferentially at structurally accessible regions, providing a footprint of the RNA secondary and tertiary structure.
Safety and Efficacy of Chronic Extended Release Cornstarch Therapy for Glycogen Storage Disease Type I

Background: Glycogen storage disease type I (GSD I) causes severe hypoglycemia during periods of fasting since both glycogenolysis and gluconeogenesis are impaired. Primary treatment in North America consists of cornstarch therapy every 3–4 h. Waxy maize extended release cornstarch was introduced for maintaining overnight glucose concentrations, but no studies have assessed long-term safety and efficacy of the product.
Classification of hatchery and wild fish using natural geochemical signatures in otoliths, fin rays, and scales of an endangered catostomid

Endangered and endemic June sucker (JS, Chasmistes liorus) have been stocked for many years to prevent extinction in Utah Lake, Utah. When unmarked fish appeared in the lake at higher rates than expected from tag loss, we sought to determine if 87Sr/86Sr and Sr/Ca (signatures) in otoliths, fin rays, and scales could be used to identify whether stocking had created a naturally reproducing population. Signatures from otoliths and fin rays suggested that approximately 38% (12 of 31) of unmarked JS probably came from the Fisheries Experimental Station (FES) hatchery in Logan, Utah, and a minimum of 13% (four of 31) of unmarked JS had signatures that strongly indicated that they were of wild origin. The remaining JS (15 of 31) could not be assigned to any particular location because of signature overlap. While scales were not useful for determining fish provenance, we found a nearly 1:1 relationship between pelvic fin and otolith 87Sr/86Sr. Thus, fin sections appear to provide a nonlethal structure for laser a...
Map Hacking: On the use of inverse address- matching to discover individual identities from point-mapped information sources

The widespread availability of low-cost desktop GIS software now enables an unprecedented number of individuals to produce point-symbol maps from information considered confidential in its original, tabular, form. These maps, which are made by address-matching individual-level administrative records to street centerline files (e.g. TIGER) can be easily (and perhaps inadvertently) distributed in HTML format. These “raw” maps comprised of abstract map symbols do not directly disclose confidential information. However, a determined data spy can use GIS technology and other knowledge to “hack” the maps and make an estimate of the actual address (and hence, a good guess as the identity of an individual) associated with each point symbol. Though this process, called inverse address-matching, is supported by widely available GIS software, there has been almost no discussion in the GIS literature about factors that are important in successfully inverting the address-matching transformation. In this paper, we situate our work within current debates on privacy, and then conduct a set of controlled experiments that are designed to evaluate the performance of the address inversion process. We do this with the full understanding that such knowledge could be used for nefarious purposes. Such knowledge, however, can also be used to guard against individual-level identity disclosure by guiding the design and use of effective cartographic masking techniques. 1.0 Introduction and Background In the United States and most of the developed world, privacy is often thought to be a fundamental right. Though not explicitly protected under the U.S. Constitution and Bill of Rights, privacy issues have figured prominently in subsequent legislation and are recognized explicitly in many other national constitutions and in the UN Declaration of Human Rights. Moreover, many nations and organizations are developing standards that concern access to personal information, (e.g. EU Directive on the Protection of Individuals with Regard to the Processing of Personal Data and the Free Movement of Such Data 95/46/EC and URLs 2, 6, 8,
Plaque Reduction Technique for Demonstrating Neutralizing Antibodies for Chlamydia

Some members of the genus Chlamydia (Bedsonia or psittacosis-lymphogranuloma venereum-trachoma-inclusion conjunctivitis group of microorganisms) produce plaques in monolayers of mouse fibroblast (L-929) cells. Hyperimmune chicken antisera may be capable of specifically reducing plaque counts. When the test was applied to chlamydiae isolated from avian species, the results indicated that different isolates with a common source had similar antigenic reactivity. The plaque reduction test is a potentially useful method for serotyping chlamydiae. The difficult aspect of the method appears to be a readily reproducible means of producing neutralizing antiserum.