cssi/SciSciGPT-SciSciNet huggingface dataset:
The Materiality of Virtual Learning Environments: Developing an Analytical Framework for the Study of Educational Platforms, Artifacts and Applications

The educational research community lacks a consistent methodology for the study of learning that does not begin with humans, their goals, and their concerns (Sorensen, 2009). While the modern practice of schooling is and always has been inextricably intertwined with its materials, the formative significance of materiality to the social project of education has received surprisingly little theoretical attention (Adams, 2010; Fenwick & Edwards, 2013; Edwards, 2010; Johri, 2011; Sorensen, 2009; Waltz, 2006). While educational artifacts are noticed, they are largely not considered integral to the educational program. “Artifacts remain interesting set pieces, but not participatory, interested actors” (Waltz, 2006, p.54). Waltz (2006) speculates that the reason educational theory disregards or underestimates the role of things, is because it treats nonhuman entities as categorically different from human ones. The natural and artifactual world are opposed to and separated from the social world. This clear-cut dichotomy between sociality and materiality, which traces back to Descartes’ notion of the internal and external (Barad, 2007) and which we find validated within the Positivistic tradition of scientific inquiry, have inscribed a division between the object and the subject that continues to define educational thought and research, which is itself deeply rooted in the sociological tradition (Waltz, 2006). According to this perspective, since human-to-human interaction is radically different from
Low-Temperature Synthesis of n-Type WS2 Thin Films via H2S Plasma Sulfurization of WO3

Thin tungsten disulfide (WS2) films were prepared on SnO2:F (FTO)-coated glass substrates by H2S plasma sulfurization of sputtered WO3. The reactive environment provided by the plasma enabled the complete transformation of a 75 nm oxide film to stoichiometric WS2 within 1 h at 500 °C. An apparent activation energy of 63.6 ± 1.9 kJ/mol was calculated for the plasma conversion process, which is less than half the barrier reported for the reaction of WO3 with H2S. The conversion followed Deal–Grove behavior, with the growing WS2 overlayer hindering diffusion to and from the reactive interface. The calibrated light absorption and relative intensity of the second-order Raman 2LA(M) peak were identified as two additional methods for progressively monitoring the thickness of the WS2 layer. The semiconducting WS2 layers exhibited n-type behavior with an indirect band gap at 1.4 eV and an absorption coefficient of ∼5 × 104 cm–1. Preliminary electrochemical measurements showed that the presence of WS2 reduced the o...
Modern Test on Humanist Consideration

In recent years,many western scholars cast their eyes to humanist tradition,trying to deconstruct consumerism,market economy,hedonism and material impact on society by restoring this tradition.Generally speaking,western humanism can be summarized into three stages:naturalism in pre-Socrates period,rationalism in Platonism and Christianity and the return to pre-Socrates age.Compared with the western counterpart,Chinese humanism always carries a naturalistic feature.However,no matter the western humanism or the Chinese one,the major issue is how it can help people cope with the rational crisis at present.
Does Loving-Kindness Meditation Reduce Anxiety? Results from a Randomized Controlled Trial

Although loving-kindness meditation (LKM) has shown some promise as a psychological intervention, little is known about the effectiveness of LKM for reducing one of the most prevalent mental health problems: anxiety. To build knowledge in this area, we conducted a randomized controlled trial, assigning non-clinical undergraduates to either a four-session, group-based LKM intervention (n = 38) or a waitlist control (n = 33). Self-reported anxiety, compassionate love, and self-compassion were assessed at pretreatment, posttreatment, and 8-week follow-up. Relative to control participants, participants in the LKM intervention reported higher compassionate love and self-compassion at posttreatment and higher self-kindness (a component of self-compassion) at follow-up. Anxiety ratings did not significantly differ between conditions at posttreatment or follow-up. Study limitations and directions for future research are discussed.
Xanthine Oxidase Mediates High Fat Diet-Induced Vascular Permeability via Junction Adhesion Molecule a Tyrosine Phosphorylation and Tight Junction Disruption

Abstract Previously we have shown that 15(S)-hydroxyeicosatetraenoic acid (15(S)-HETE), the 15-LO metabolite of arachidonic acid (AA), affects endothelial cell (EC) barrier function. In this study, we have examined the role of xanthine oxidase (XO) in 15(S)-HETE-induced EC barrier dysfunction. 15(S)-HETE induced JamA phosphorylation on tyrosine residues 164, 218 and 280 involving XO-mediated reactive oxygen species (ROS) production and Src and Pyk2 activation, resulting in its dissociation from Occludin and causing tight junction disruption with increased EC barrier permeability and enhanced leukocyte and monocyte transmigration in vitro using EC monolayer and ex vivo using arteries as models. The phosphorylation of JamA on tyrosine residues 164, 218, and 280 appear to be critical for its role in 15(S)-HETE-induced EC barrier dysfunction, as mutation of any one of these amino acid residues prevented its dissociation from Occludin and restored TJ integrity and barrier function. Feeding WT mice but not 12/15-LO-/- mice with HFD for 3 months resulted in enhanced XO expression and its activity in the artery, which was correlated with increased aortic EC TJ disruption and its barrier permeability with enhanced leukocyte adhesion. These observations provide additional support for the role of 12/15-LOX in the dysregulation of vascular permeability in response to HFD. Disclosures No relevant conflicts of interest to declare.
Structural Foundations of RNA Silencing by Argonaute

Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
Societal costs in displaced transverse olecranon fractures: using decision analysis tools to find the most cost-effective strategy between tension band wiring and locked plating.

Background Tension band wiring (TBW) and locked plating are common treatment options for Mayo IIA olecranon fractures. Clinical trials have shown excellent functional outcomes with both techniques. Although TBW implants are significantly less expensive than a locked olecranon plate, TBW often requires an additional operation for implant removal. To choose the most cost-effective treatment strategy, surgeons must understand how implant costs and return to the operating room influence the most cost-effective strategy. This cost-effective analysis study explored the optimal treatment strategies by using decision analysis tools. Methods An expected-value decision tree was constructed to estimate costs based on the 2 implant choices. Values for critical variables, such as implant removal rate, were obtained from the literature. A Monte Carlo simulation consisting of 100,000 trials was used to incorporate variability in medical costs and implant removal rates. Sensitivity analysis and strategy tables were used to show how different variables influence the most cost-effective strategy. Results TBW was the most cost-effective strategy, with a cost savings of approximately $1300. TBW was also the dominant strategy by being the most cost-effective solution in 63% of the Monte Carlo trials. Sensitivity analysis identified implant costs for plate fixation and surgical costs for implant removal as the most sensitive parameters influencing the cost-effective strategy. Strategy tables showed the most cost-effective solution as 2 parameters vary simultaneously. Conclusion TBW is the most cost-effective strategy in treating Mayo IIA olecranon fractures despite a higher rate of return to the operating room.
Manual Medicine Techniques Used in the Management of Musculoskeletal (Somatic) Dysfunction of the Lower Extremities

It is hoped that by reviewing this article the reader will understand the philosophy and methods of a comprehensive, hands-on evaluation of musculoskeletal injury and dysfunction of the lower extremities. An approach to management with effective application of manual medicine corrective techniques also should be learned. Risk factors are outlined that should be considered to prevent long-term chronic pain and dysfunction.
FAQs: Rapid Fire Answers to Pesky Clinical Questions – NGTs? Thiamine? PO Contrast? Nonsurgical Complications?

Bariatric patients encounter unique challenges. Blind placement of NG or OG tubes can be a risky procedure in those patients with altered anatomy. Clinicians should not place an NG tube blindly in those patients within 30 days of their surgery and consider fluoroscopic guidance when possible. Fluid intake, including oral contrast, should be limited to 6 oz (177 mL) for patients with stomach-altering bariatric surgeries, such as Roux-en-Y gastric bypass and sleeve gastrectomy, to accommodate the small gastric pouch. Nutritional deficiencies are common, and thiamine deficiency can lead to Wernicke’s encephalopathy in bariatric surgery patients. Venous thromboembolism and anastomotic leaks are both associated with significant morbidity and mortality in this population.
Science Diplomacy at ASM: The power of scientific societies in addressing global challenges

Despite incredible advancements in science and technology, the pace and intensity of global challenges have continued to escalate. Emerging diseases, increased drought, safety and availability of food, water quality, and environmental degradation respect no borders and create competition for natural resources that can only be addressed through collaboration and broad engagement of the international community. The expertise required to address these problems will increasingly draw on innovations across a variety of scientific, medical, and technological sources. Scientific societies, university networks, and nongovernmental organizations, with missions to educate, share knowledge, collaborate, and improve the human condition through science, have an increasingly important role to play in this arena. As the oldest and largest society of life scientists, ASM's member network is poised to make significant contributions through outreach and training of local and regional collaborators. Here we present an overview of the emerging topic of science diplomacy and offer a strategy for future Society engagement with international efforts to facilitate sustainable development.
The Notch pathway in CNS homeostasis and neurodegeneration

The role of the Notch signaling pathway in neural development has been well established over many years. More recent studies, however, have demonstrated that Notch continues to be expressed and active throughout adulthood in many areas of the central nervous system. Notch signals have been implicated in adult neurogenesis, memory formation, and synaptic plasticity in the adult organism, as well as linked to acute brain trauma and chronic neurodegenerative conditions. NOTCH3 mutations are responsible for the most common form of hereditary stroke, the progressive disorder cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. Notch has also been associated with several progressive neurodegenerative diseases, including Alzheimer's disease, multiple sclerosis, and amyotrophic lateral sclerosis. Although numerous studies link Notch activity with CNS homeostasis and neurodegenerative diseases, the data thus far are primarily correlative, rather than functional. Nevertheless, the evidence for Notch pathway activity in specific neural cellular contexts is strong, and certainly intriguing, and points to the possibility that the pathway carries therapeutic promise. This article is categorized under: Nervous System Development > Flies Signaling Pathways > Cell Fate Signaling Nervous System Development > Vertebrates: General Principles.
Completing the solution for the OSp(1|2) spin chain

Abstract The periodic O S p ( 1 | 2 ) quantum spin chain has both a graded and a non-graded version. Naively, the Bethe ansatz solution for the non-graded version does not account for the complete spectrum of the transfer matrix, and we propose a simple mechanism for achieving completeness. In contrast, for the graded version, this issue does not arise. We also clarify the symmetries of both versions of the model, and we show how these symmetries are manifested in the degeneracies and multiplicities of the transfer-matrix spectrum. While the graded version has O S p ( 1 | 2 ) symmetry, the non-graded version has only S U ( 2 ) symmetry. Moreover, we obtain conditions for selecting the physical singular solutions of the Bethe equations. This analysis solves a lasting controversy over signs in the Bethe equations.
Evaluation of Cord Blood Total Nucleated and CD34+ Cell Content, Cell Dose, and 8-Allele HLA Match by Patient Ancestry.

ABSTRACT How cord blood (CB) CD34+ cell content and dose and 8-allele HLA match vary by patient ancestry is unknown. We analyzed cell content, dose, and high-resolution HLA-match of units selected for CB transplantation (CBT) by recipient ancestry. Of 544 units (286 infused, 258 next-best backups) chosen for 144 racially diverse adult patients (median weight, 81 kg), the median total nucleated cell (TNC) and CD34+cell +contents were higher for Europeans than for non-Europeans: 216 × 107versus 197 × 107 (P = .002) and 160 × 105 versus 132 × 105 (P = .007), respectively. There were marked cell content disparities among ancestry groups, with units selected for Africans having the lowest TNC (189 × 107) and CD34+ cell (122 × 105) contents. Units for non-Europeans were also more HLA-mismatched (P = .017). When only the 286 transplanted units were analyzed, the adverse effect of reduced cell content was exacerbated by the higher weights in some groups. For example, northwestern Europeans (high patient weight, high unit cell content) had the best-dosed units, and Africans (high weight, low unit cell content) had the lowest. In Asians, low cell content was partially compensated for by lower weight. Marked differences in 8-allele HLA-match distribution were also observed by ancestry group; for example, 23% of units for northwestern Europeans were 3/8 to 4/8 HLA-matched, compared with 40% for southern Europeans, 46% for white Hispanics, and 51% for Africans. During the study period, 20 additional patients (17 non-Europeans; median weight, 98 kg) did not undergo CBT owing to the lack of a suitable graft. CB extends transplantation access to most patients, but racial disparities exist in cell content, dose, and HLA match.
Spatial and Temporal Dimensions of Weather Shocks and Migration in Nepal.

Research shows that environmental shocks can influence migration. However, studies vary widely in the shocks and type of migration measured, the context, and the strength and direction of environmental effects. In addition, existing theories provide opposing predictions for this relationship. There is a clear need for further theoretical development in the climate-migration literature. This study, in rural Nepal, examines four types of weather shocks, over various time frames, on four types of migration. Results suggest that the most substantial influence of weather shocks is not in a wholesale increase or decrease in migration. Instead, weather shocks are related to changes in the type of migration used, resulting in less long-term and more short-term migrations in the population. We use the ready-willing-and-able perspective to make sense of these patterns.
Complete Coding Sequence of Western Equine Encephalitis Virus Strain Fleming, Isolated from a Human Case.

ABSTRACT We sequenced the complete coding genome of the western equine encephalitis virus (WEEV) strain Fleming. This strain was originally isolated in 1938 from a human WEEV case.
Transactive Energy Framework for Critical Load Restoration Using Microgrids

As a new concept, the transactive energy framework manages both the supply and demand sides in a variant and generalized form of demand response. It targets future electric grids with an increase in distributed resources and intelligent devices. However, research works that consider the resiliency of electric power systems under the transactive energy framework are limited. In this paper, a new transactive energy framework is proposed for the service restoration of power distribution systems in extreme weather and/or abnormal conditions. A distributed heuristic algorithm is applied for the system restoration negotiation among microgrids and critical loads. The modified IEEE 37-node test feeder is used for validation. Contingency scenarios with both single and multiple critical loads outages in an emergency are performed. The transactive model and algorithms are implemented using Python and GridLAB-D.
NumbaSummarizer: A Python Library for Simplified Vectorization Reports

Python is a very popular programming language and has been adopted by many learning institutions as the first or only programming language taught to students. While its simple syntax and gentle learning curve makes it a very attractive option for new programmers, among its main drawbacks are that it obviates many key concepts of programming and computer architecture as well as rarely optimizing code to modern architectures.There are tools that provide optimizing capability for Python programmers. Numba is a JIT compiler for Python that among other things, optimizes Python and Numpy functions for better performance. Numba can exploit automatic parallelism and vectorization.In this paper we present NumbaSummarizer, a wrapper for Numba's vectorization module that works as a vectorization reporting tool. Students can use it to identify functions that are exploiting SIMD instructions. The main purpose of this tool is to teach students about Parallel Computing, Vectorization, Data Dependence, and Loop Transformations.We evaluated the use of NumbaSummarizer with 64 students during a course on intermediate programming. Most students had little to no background in Computer Architecture nor Parallel Computing. When asked to expose parallelism in a set of 8 loops, 95% percent of the students were able to transform and optimize at least 6 of these loops. When testing conceptual understanding, they scored an average of 95% for parallel computing concepts, and 62% for dependence analysis.
Next Generation Wi-Fi and 5G NR-U in the 6 GHz Bands: Opportunities and Challenges

The ever-increasing demand for unlicensed spectrum has prompted regulators in the US and Europe to consider opening up the 6 GHz bands for unlicensed access. These bands will open up 1.2 GHz of additional spectrum for unlicensed radio access technologies (RATs), such as Wi-Fi and 5G New Radio Unlicensed (NR-U), in the US and if permitted, 500 MHz of additional spectrum in Europe. The abundance of spectrum in these bands creates new opportunities for the design of mechanisms and features that can support the emerging bandwidth-intensive and latency-sensitive applications. However, coexistence of unlicensed devices both with the bands' incumbent users and across different unlicensed RATs present significant challenges. In this paper, we provide a comprehensive survey of the existing literature on various issues surrounding the operations of unlicensed RATs in the 6 GHz bands. In particular, we discuss how key features in next-generation Wi-Fi are being designed to leverage these additional unlicensed bands. We also shed light on the foreseeable challenges that designers of unlicensed RATs might face in the near future. Our survey encompasses key research papers, contributions submitted to standardization bodies and regulatory agencies, and documents presented at various other venues. Finally, we highlight a few key research problems that are likely to arise due to unlicensed operations in the 6 GHz bands. Tackling these research challenges effectively will be critical in ensuring that the new unlicensed bands are efficiently utilized while guaranteeing the interference-free operation of the bands' incumbent users.
Assessing debris strikes in spacecraft telemetry: Development and comparison of various techniques.

Abstract Debris strikes on operational spacecraft are becoming more common due to increasing numbers of space objects. Sample return missions indicate hundreds of minor strikes, but rigorous analysis is often only performed when a strike causes an anomaly in spacecraft performance. Developing techniques to identify and assess minor strikes that do not immediately cause anomalous behavior can help to validate models for debris populations, perform risk assessments, and aid in the attribution of future anomalies. This study introduces debris strikes to a spacecraft dynamics simulation and assesses the effect on spacecraft telemetry. Various signal processing and change detection techniques are used to identify strikes in noisy telemetry and estimate strike parameters. Matched filter wavelets are developed to identify the effects on state telemetry, where errors are autonomously corrected by the spacecraft attitude control system. A bank of matched filters is used to estimate the parameters of the strike based on a priori knowledge of the spacecraft's response characteristics. A sequential probability ratio test is used to highlight abrupt changes in the spacecraft's angular momentum. Monte-Carlo analyses are conducted to characterize the performance of these algorithms. The results of the various techniques are compared in terms of correctly identifying the debris strikes and accurately estimating the strike parameters. Developing the capability to catalog and characterize minor debris strikes allows any spacecraft to be used as an in situ debris sensor.
Influences of Environmental and Social Factors on Perceived Bio-Cultural Services and Disservices

Although the value of urban ecological infrastructure (UEI) is widely recognized, insufficient research has investigated how people perceive the wide variety of UEI. To address this gap, we investigated residents' perceptions of the coupled value of aesthetic and biological qualities as related to diverse UEI and other environmental and social factors (including personal beliefs and demographics), collectively referred to as bio-cultural services and disservices. We evaluated whether people positively view their neighborhood environments as natural-looking while providing diverse plants and wildlife habitat (services), in contrast to negatively perceived disservices that we evaluated as messy-looking with weeds and pests (disservices). We analyzed survey data from residents (n = 495) in metropolitan Phoenix, Arizona, United States, coupled with environmental variables (UEI and vegetative cover) compiled from diverse sources. We ran three regression models to compare the relative influence of social and environmental factors independently and combined on the perception of biocultural services and disservices. Our results demonstrate the influence of social factors, particularly place identity, neighborhood cohesion, and income, on both biocultural services and disservices. Additionally, environmental factors such as vegetation cover increased perceptions of bio-cultural services while decreasing perceived disservices. The effects of proximity to UEI were more varied. While proximity to cropland increased perceived bio-cultural disservices, proximity to desert parks reduced disservices. Although UEI can promote biodiversity and human well-being, all UEI are not perceived the same. Our results underscore the added value of considering both the form of UEI and perceptions among people who live nearby when designing and implementing infrastructure to promote bio-cultural services that are both ecologically and socially valued.
The Reach, Use, and Impact of a Free mHealth Mindfulness App in the General Population: Mobile Data Analysis.

Background: As smartphones are now used by most Americans, it is increasingly possible for mental health mobile apps to be disseminated to the general public. However, little is known about how mobile mental health apps are used by the general population outside of a controlled research design. Objective: Our objective is to describe how the general population engages with Mindfulness Coach, an iOS- and Android-based app designed to deliver a mindfulness training course. Methods: Using anonymous download and analytics data, we characterized the reach, usage, retention, and impact of Mindfulness Coach. We included mobile analytics data from all unique downloads of Mindfulness Coach between August 1, 2018, and April 8, 2019 (N=104,067) as well as starred reviews from all Mindfulness Coach users who provided reviews of the app as of March 1, 2020. Mindfulness characteristics were measured by an in-app assessment using the Five-Facet Mindfulness Questionnaire–Short Form (FFMQ-SF). Results: Users engaged, on average, in 4.3 visits to the app (SD 8.8; median 2; 90th percentile 8) and associated with an average total of 49.2 interactions with the app (ie, clicks within the app) (SD 113.8; median 19; 90th percentile 105). Users spent an average of 16.2 minutes (SD 63.1) engaged with the app over the full study time period. There were strong linear effects of app engagement on total FFMQ-SF scores. For example, FFMQ-SF scores were associated with more time spent engaged with the app (R2=.23; P<.001). Mindfulness Coach has been reviewed in the Google Play Store 3415 times, with an average rating of 4.7 out of 5 stars, and over 2000 times in the Apple App Store, with an average rating of 4.8 out of 5 stars. Conclusions: These findings suggest that Mindfulness Coach has achieved substantial and sustained reach in the general population; however, it was used less frequently by many downloaders than researchers and designers intended. There was a subpopulation of users who engaged in the app regularly over an extended period of time, and there was a clear relationship between app use and improvements in mindfulness. To strengthen Mindfulness Coach’s public health impact, more research is needed to understand who is using the app and how, and to design strategies to increase user engagement in order for users to receive a larger dose of mindfulness treatment.
The Systemic Immune-Inflammation Index Predicts Clinical Outcomes in Kidney Transplant Recipients

Background Outcomes after kidney transplantation (KTx) remain limited by delayed graft function (DGF) and acute rejection. Non-invasive biomarkers may help identify patients at increased risk for these events. We examined the association between the systemic immune-inflammation index (SII), a novel inflammatory biomarker, and outcomes after KTx and evaluated its ability to predict post-transplant prognosis. Patients and methods Adult patients who underwent primary KTx at our institution between 2016-2019 were included. SII was calculated from pre-transplant complete blood counts as the ratio of the neutrophil count to the lymphocyte count multiplied by the platelet count. The cutoff between high and low SII was determined by maximizing the area under the curve. Multivariable logistic and Cox regression were used to identify factors associated with DGF and patient, rejection-free, and graft survival respectively. Results Overall, 378 KTx recipients were included; 224 (59.3%) had high SII. On unadjusted analysis, high SII was associated with reduced odds of DGF, and improved patient and rejection-free survival. After adjustment, high SII was independently associated with improved patient survival alone. Multivariable models incorporating SII performed well for the prediction of DGF (c-statistic=0.755) and patient survival (c-statistic=0.786), though rejection-free survival was more difficult to predict (c-statistic=0.635). Conclusion SII demonstrated limited utility as an independent predictor of outcomes after KTx. However, in combination with other clinically relevant parameters, SII is a useful predictor of post-KTx prognosis. Validation of this novel inflammatory biomarker in a multi-institutional study is needed to further elucidate its practical applications in transplantation.
Entire functions with undecidable arithmetic properties

Abstract A basic problem in transcendental number theory is to determine the arithmetic properties of analytic functions of the form f ( z ) = ∑ k = 0 ∞ a k z k where the coefficients a k ∈ K belong to an algebraic number field. In particular, one of the most basic problems is to determine if f ( α ) is algebraic or transcendental for non-zero algebraic arguments α. For example, if f ( z ) is a transcendental Mahler function, then under generic conditions f ( α ) is transcendental for all non-zero algebraic numbers with | α | 1 . Also, if f ( z ) is an E-function, then there exist algorithms which completely determine the arithmetic properties of f ( n ) ( α ) for non-zero algebraic numbers α. In contrast to these and other algorithmic results, we construct three functions f ( z ) , g ( z ) , and h ( z ) with computable rational coefficients for which no algorithms exist that determine if f ( n ) ∈ Q , g ( n ) ( 1 ) ∈ Q , or ∫ 0 1 h ( z ) z n d z ∈ Q for integral n ≥ 0 . Our results are an application of an undecidable variant of the Collatz Problem due to Lehtonen [9] .
What the reproductive number R0 can and cannot tell us about COVID-19 dynamics.

The reproductive number R (or R0, the initial reproductive number in an immune-naive population) has long been successfully used to predict the likelihood of pathogen invasion, to gauge the potential severity of an epidemic, and to set policy around interventions. However, often ignored complexities have generated confusion around use of the metric. This is particularly apparent with the emergent pandemic virus SARS-CoV-2, the causative agent of COVID-19. We address some misconceptions about the predictive ability of the reproductive number, focusing on how it changes over time, varies over space, and relates to epidemic size by referencing the mathematical definition of R and examples from the current pandemic. We hope that a better appreciation of the uses, nuances, and limitations of R and R0 facilitates a better understanding of epidemic spread, epidemic severity, and the effects of interventions in the context of SARS-CoV-2.
Abstract PS17-29: Surgically induced weight loss corrects obesity associated tumor progression and improves responsiveness to immunotherapy

Background: Obesity leads to a higher risk of cancer invasion, metastases, recurrence, mortality, and impaired therapeutic response through various mechanisms. One of these mechanisms is microenvironment dysfunction, where changes in immune cells, microbes, metabolites, and growth factors contribute to tumor aggressiveness. We study obesity-induced changes to the tumor microenvironment in Triple Negative Breast Cancer (TNBC), an aggressive subtype associated with obesity. The goal to compare tumor progression in lean vs. obese vs. weight loss manipulations to identify causal and targetable pathways associated with reprogramming the tumor microenvironment. Clinically, bariatric surgery induced weight loss reduced the risk of BC, with the greatest benefit detected in pre-menopausal patients with ER- tumors, like TNBC. We hypothesize surgically-induced weight loss will diminish obesity-associated tumor progression. Methods: To study weight gain and loss that best mimics human adiposity, we utilized obesogenic C57BL/6 females with a syngeneic orthotopic transplant of TNBC cells. Female mice placed on a high fat diet (HFD) at weaning became obese compared to mice on a low fat diet (LFD). After 16 weeks on an HFD diet, mice underwent the bariatric surgery Vertical Sleeve Gastrectomy (VSG). The VSG resulted in reduced body weight, adiposity, and correction of metabolic profiles compared to obese mice. Two weeks post-surgery, TNBC cells were OT into the mammary fat. Results: As expected, tumor growth was increased in obese mice compared to lean. Importantly, surgical weight loss rescued obese tumor progression. We identified key changes in tumor infiltrating of immune cells that could be responsible for the beneficial effects of bariatric surgery on tumor progression. We then exploited these changes with immunotherapy, which was uniquely effective in mice that underwent bariatric surgery. Conclusions: In conclusion obesity promotes a pro-tumor microenvironment, that can be corrected through surgically induced weight loss. Citation Format: Laura Sipe, Mehdi Chaib, Emily B Korba, Mary C Lovely, Jared C Clements, Neena A John, Ajeeth K Pingili, Joseph F Pierre, Liza Makowski. Surgically induced weight loss corrects obesity associated tumor progression and improves responsiveness to immunotherapy [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS17-29.
Reporting of Infectious Diseases in the United States During the COVID-19 Pandemic.

Reporting of infectious diseases other than COVID-19 has been greatly decreased throughout the COVID-19 pandemic. We find this decrease varies by routes of transmission, reporting state, and COVID-19 incidence at the time of reporting. These results underscore the need for continual investment in routine surveillance efforts despite pandemic conditions.
Severe autoimmune hemolytic anemia following receipt of SARS-CoV-2 mRNA vaccine.

Large clinical trials have demonstrated the overall safety of vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, reports have emerged of autoimmune phenomena, including vaccine-associated myocarditis,1 immune thrombocytopenia,2 and immune thrombotic thrombocytopenia.3 4 Here we present a novel case of a young woman who developed life-threatening autoimmune hemolytic anemia (AIHA) after her first dose of a SARS-CoV-2 mRNA vaccine. Notably, initial direct antiglobulin testing was negative using standard anti-IgG reagents, which are "blind" to certain immunoglobulin (IgG) isotypes. Further testing using an antiglobulin reagent that detects all IgG isotypes was strongly positive and confirmed the diagnosis of AIHA. The patient required transfusion with 13 units of packed red blood cells, as well as treatment with corticosteroids, rituximab, mycophenolate mofetil, and immune globulin. As efforts to administer SARS-CoV-2 vaccines continue globally, clinicians must be aware of potential autoimmune sequelae of these therapies. This article is protected by copyright. All rights reserved.
Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize

Identification of the genetic mechanisms underlying phenotypic variation between and within populations is essential to understanding natural selection and evolution. Changes in gene expression are an important source of phenotypic variation and may arise as a result of a combination of cisregulatory and trans-regulatory variation within complex genetic networks (Wittkopp, 2005). This complexity has hindered identification of genomic targets of both natural and artificial selection. Long-term phenotypic selection experiments in plants and animals provide an invaluable resource for studying evolutionary change and regulatory variation, with implications for enhancing the efficiency of genetic gain in plant and animal breeding (Dudley and Lambert, 2004). Plants have the additional unique advantage of regeneration, where replicate selection experiments may be conducted in parallel. The Illinois Long-Term Selection Experiment for grain composition is a classic in plant genetics; 800 cycles of selection have been conducted from the same source population during the past century (Figure 12.1). Previous quantitative trait loci (QTL) mapping studies suggest that changes in both protein and oil concentration in the Illinois experiment are governed by many genes (Laurie et al., 2004; Dudley et al., 2007) with small phenotypic effect. However, there is also evidence that variation at relatively few loci can be associated with significant phenotypic differences. Advances in high-density genotyping coupled with functional genomics approaches enable a more thorough understanding of the genetic basis for the dramatic phenotypic responses observed. In this chapter, we provide an update on more recent phenotypic responses within the Illinois Long-Term Selection Experiment and related populations, a review of past efforts to characterize the genetic architecture of selection response, and a preliminary view of gene expression changes resulting from divergent selection for grain protein, and we introduce the use of promoter-reporter genes as tools to understand how selection has altered the regulation of seed storage protein genes. Collectively, these approaches illustrate that long-term selection for kernel composition has targeted variation in both trans-acting regulatory factors and specific genes known to influence oil or protein concentrations.
Reproducible Tall-Skinny QR

Reproducibility is the ability to obtain bitwise identical results from different runs of the same program on the same input data, regardless of the available computing resources, or how they are scheduled. Recently, techniques have been proposed to attain reproducibility for BLAS operations, all of which rely on reproducibly computing the floating-point sum and dot product. Nonetheless, a reproducible BLAS library does not automatically translate into a reproducible higher-level linear algebra library, especially when communication is optimized. For instance, for the QR factorization, conventional algorithms such as Householder transformation or Gram-Schmidt process can be used to reproducibly factorize a floating-point matrix by fixing the high-level order of computation, for example column-by-column from left to right, and by using reproducible versions of level-1 BLAS operations such as dot product and 2-norm. In a massively parallel environment, those algorithms have high communication cost due to the need for synchronization after each step. The Tall-Skinny QR algorithm obtains much better performance in massively parallel environments by reducing the number of messages by a factor of n to O(log(P)) where P is the processor count, by reducing the number of reduction operations to O(1). Those reduction operations however are highly dependent on the network topology, in particular the number of computing nodes, and therefore are difficult to implement reproducibly and with reasonable performance. In this paper we present a new technique to reproducibly compute a QR factorization for a tall skinny matrix, which is based on the Cholesky QR algorithm to attain reproducibility as well as to improve communication cost, and the iterative refinement technique to guarantee the accuracy of the computed results. Our technique exhibits strong scalability in massively parallel environments, and at the same time can provide results of almost the same accuracy as the conventional Householder QR algorithm unless the matrix is extremely badly conditioned, in which case a warning can be given. Initial experimental results in Matlab show that for not too ill-conditioned matrices whose condition number is smaller than sqrt(1/e) where e is the machine epsilon, our technique runs less than 4 times slower than the built-in Matlab qr() function, and always computes numerically stable results in terms of column-wise relative error.
Generating a Genome Assembly with PCAP

This unit describes how to use the Parallel Contig Assembly Program (PCAP) to assemble the data produced by a whole-genome shotgun sequencing project. We present a basic protocol for using PCAP on a multiprocessor computer in a 300-Mb genome assembly project. A support protocol to prepare input files for PCAP is also described. Another basic protocol for using PCAP on a distributed cluster of computers in a 3-Gb genome assembly project is presented, in addition to suggestions for understanding results from PCAP.
Secure data export and auditing using data diodes

Data diodes, that is, devices which permit only one-way communication, without even a reverse channel for acknowledgment, have many potential uses within voting systems. A practical design for a data diode is presented that is simpler and more nearly self-evident than previously published designs. Communication protocols appropriate for use in the voting context are described. Throughout, we emphasize designs that permit a relatively naive observer to determine that it meets key security constraints.
The positive deviance/hearth approach to reducing child malnutrition: systematic review.

Summary Objectives The Positive Deviance/Hearth approach aims to rehabilitate malnourished children using practices from mothers in the community who have well-nourished children despite living in poverty. This study assesses its effectiveness in a range of settings. Methods Systematic review of peer reviewed intervention trials and grey literature evaluation reports of child malnutrition programs using the Positive Deviance/Hearth approach. Results Ten peer reviewed studies and 14 grey literature reports met the inclusion criteria. These described results for 17 unique Positive Deviance/Hearth programs in 12 countries. Nine programs used a pre- and post-test design without a control, which limited the conclusions that could be drawn. Eight used more robust designs such as non-randomized trials, non-randomized cross-sectional sibling studies and randomized controlled trials (RCTs). Of the eight programs that reported nutritional outcomes, five reported some type of positive result in terms of nutritional status – although the improvement was not always as large as predicted, or across the entire target population. Both the two RCTs demonstrated improvements in carer feeding practices. Qualitative results unanimously reported high levels of satisfaction from participants and recipient communities. Conclusions Overall this study shows mixed results in terms of program effectiveness, although some Positive Deviance/Hearth programs have clearly been successful in particular settings. Sibling studies suggest that the Positive Deviance/Hearth approach may have a role in preventing malnutrition, not just rehabilitation. Further research is needed using more robust study designs and larger sample sizes. Issues related to community participation and consistency in reporting results need to be addressed.
Evaluation of Formagraph for Comparing Rennet Solutions

Abstract A new instrument for measuring milk clotting, the Formagraph, was evaluated. Measurement is movement of small pendulums immersed in linearly oscillating samples of coagulating milk. Pendulum movements are recorded on photographic paper, producing a diagram of firmness versus time. The instrument can be used for measuring milk-clotting enzyme activity in comparison to a standard, and in constrast to the rolling bottle method, it does not require continual observation. Coagulation times measured by the Formagraph are longer than those measured by the rolling bottle method, but both methods give linear standard curves between .2 and 1.0 rennet units/ml enzyme concentrations.
Student and Faculty Perceptions of the Quality of Online Learning Experiences

Some faculty members are reluctant to offer online courses because of significant concerns relative to the impact of such formats on the quality of instruction, learning, and participant interaction. Faculty members from The University of Southern Mississippi implemented synchronous interactive online instruction (SIOI) in the spring of 2007. This article explores the rationale for use of the particular technology, faculty conclusions regarding implementation of the technology, and the impact of the technology on instruction and learning. Comparisons by students of the quality of the learning experience in this environment with the quality of learning in face-to-face and asynchronous online learning environments were also analyzed. The study finds that instructors and students view SIOI favourably. The mean student ratings for the dimensions of instructional quality were the same for SIOI and face-to-face course formats in all but one dimension, but mean ratings for SIOI and face-to-face formats were consistently higher than those for asynchronous online instruction. The single exception was for the dimension, ease of access to the course; the SIOI and asynchronous online formats were rated higher than the face-to-face format in this quality dimension. These findings suggest that it is possible to achieve levels of effectiveness in an online instructional format similar to those that are realized in face-to-face delivery. However, there is slight, though not statistically significant, evidence of concern about the quality of student collaboration in SIOI-enabled courses. Thus, instructors will need to capitalize on available mechanisms for interaction and collaboration.
THEMATICS as a Tool for Functional Genomics

Structural genomics efforts are determining in high throughput the three-dimensional structures of thousands of gene products. Many of these protein structures are of unknown function. The next major step after genome sequencing and protein structure determination is the determination of the function of the thousands of newly-discovered gene products. This presentation focuses on THEMATICS [3, 4], a simple computational predictor of information about the function of a protein. In particular, THEMATICS predicts the location of, and some chemical characteristics of, the active site of an enzyme. Application of THEMATICS requires only the structure of the subject protein. Thus THEMATICS works for proteins that have no similarity in sequence or in structure to any protein of known function. The accuracy of THEMATICS predictions is verified using proteins whose functions and mechanisms have been well studied experimentally.
Cell cycle-dependent strand bias for UV-induced mutations in the transcribed strand of excision repair-proficient human fibroblasts but not in repair-deficient cells.

To study the effect of nucleotide excision repair on the spectrum of mutations induced in diploid human fibroblasts by UV light (wavelength, 254 nm), we synchronized repair-proficient cells and irradiated them when the HPRT gene was about to be replicated (early S phase) so that there would be no time for repair in that gene before replication, or in G1 phase 6 h prior to S, and determined the kinds and location of mutations in that gene. As a control, we also compared the spectra of mutations induced in synchronized populations of xeroderma pigmentosum cells (XP12BE cells, which are unable to excise UV-induced DNA damage). Among the 84 mutants sequenced, base substitutions predominated. Of the XP mutants from S or G1 and the repair-proficient mutants from S, approximately 62% were G.C----A.T. In the repair-proficient mutants from G1, 47% were. In mutants from the repair-proficient cells irradiated in S, 71% (10 of 14) of the premutagenic lesions were located in the transcribed strand; with mutants from such cells irradiated in G1, only 20% (3 of 15) were. In contrast, there was no statistically significant difference in the fraction of premutagenic lesions located in the transcribed strand of the XP12BE cells; approximately 75% (24 of 32) of the premutagenic lesions were located in that strand, i.e., 15 of 19 (79%) in the S-phase cells and 9 of 13 (69%) in the G1-phase cells. The switch in strand bias supports preferential nucleotide excision repair of UV-induced damage in the transcribed strand of the HPRT gene.