cssi/SciSciGPT-SciSciNet huggingface dataset:
Integrating information on genomics, transcriptomics, proteomics, and metabolomics into biosimulations for individualized personalized medicine

Current genomic tests reporting single nucleotide polymorphisms (SNPs) have limited predictability on individual patient responses to drugs. A novel method of using SNPs for homology proteomic modeling and drug docking of target proteins was tested in combination with transcriptomic determined kinetic biosimulations generating metabolomics and fluxomics of individual patients. Multiple informatics tools can generate individualized PK/PD predictions in silico before prescribing drugs to the same patients, for precise targeted therapy and pharmacogenomics.
Antioxidant Activity of Polyphenolic Extract from Shanxi Aged Vinegar

The in vitro antioxidant activity of polyphenolic extract from Shanxi aged vinegar was investigated using different antioxidant evaluation systems and compared with that of gallic acid and vitamin C.The results showed that the polyphenolic extract possessed antioxidant activity in a dosage-dependent manner which varied with the type of model systems.The reducing power and hydroxyl free radical scavenging activity of the samples under investigation were found to decrease in the following order: the polyphenolic extract gallic acid vitamin C.The decreasing order of superoxide anion radical scavenging activity among the samples was the polyphenolic extract vitamin C gallic acid.The DPPH radial scavenging activity was in the decreasing order of gallic acid the polyphenolic extract vitamin C.The nitrite scavenging activity of the extract was poorer than that of vitamin C.The samples decreased in total antioxidant capacity(at the same concentration) in the order of gallic acid vitamin C the polyphenolic extract.
Boundaries Not Drawn

The last five years have seen a global surge in political fact-checking, reporting that specializes in debunking political misinformation. A growing occupational movement, originating in the United States but increasingly international in scope, has sought to legitimize fact-checking as unbiased journalism, to establish common standards and practices, and to secure reliable funding for this emerging genre. As a genuinely transnational professional movement which includes practitioners from multiple journalistic cultures as well as other fields, fact-checking offers a new site to consider whether and how professional journalism is meaningfully becoming globalized. This paper models a novel approach to mapping a diverse organizational landscape in terms of institutional ties to the fields of journalism, academia, and politics. Drawing on fieldwork from two international gatherings of fact-checkers, I array fact-checking outlets on a ternary graph and review their competing understandings of the mission, the...
ELEMENTS OF PROBABILITY

This chapter introduces the idea of a probability experiment, explains the concept of the probability of an event, and presents the axioms of probability. The concept of the sample space and the events of an experiment are also studied. The chapter demonstrates how to apply probability theory to gain insight into real, everyday statistical problems, and situations. It provides an intuitive understanding of statistical procedures and strategies most often used by practicing engineers and scientists. The concept of the probability of a particular event of an experiment is subject to various interpretations. The two foregoing interpretations of the probability of an event are referred to as being the frequency interpretation and the subjective interpretation of probability. Probability is a subjective or personal concept and has no meaning outside of expressing a degree of belief. Conditional probability is the most important concepts in all of probability theory. The chapter also deals with the sample space, simple expression, use of Venn diagram, and Boole's inequality.
Chemical grouting and soil stabilization

Following shifting trends from remedial to preventive uses of grouting practices, this third edition covers all aspects of chemical grouting methods and applications. This reference highlights new ground improvement techniques as well as recent innovations in soil modification and stabilization procedures. It considers commercial alternatives to ground improvement, their relative advantages and disadvantages, and the engineering applications to which these methods are suited. Revised and expanded, this new edition assesses the role of new grouting techniques in the containment of hazardous waste and introduces numerous problems to illustrate concepts and facilitate instruction.
Hartree-Fock study of the ν = 0 quantum Hall state of monolayer graphene with short-range interactions

Recent experiments involving tilted graphene samples have shown evidence of a continuous phase transition in the $\ensuremath{\nu}=0$ quantum Hall bulk state. We present here a simple model that supports such a transition. In addition to a long-range SU(4) symmetric Coulomb interaction, we include Hubbard on-site and nearest neighbor interactions with tunable coupling strengths, and perform a self-consistent Hartree-Fock analysis. A large sea of negative energy Landau levels is retained, and is shown to have important qualitative and quantitative effects. Phase diagrams are constructed within the space of physically relevant parameters, yielding results consistent with experimental observation.
PLCG2 C2 domain mutations co-occur with BTK and PLCG2 resistance mutations in chronic lymphocytic leukemia undergoing ibrutinib treatment.

PLCG2 C2 domain mutations co-occur with BTK and PLCG2 resistance mutations in chronic lymphocytic leukemia undergoing ibrutinib treatment
Abstract 1157: Screening and identification of new generation glucose transporter inhibitors as anticancer therapeutics

Cancer is a top killer second only to cardiovascular diseases. Cellular metabolic reprogramming and altered energetics are key features of cancer. Opportunistic uptake of extracellular nutrients has recently been named as an emerging hallmark of cancer metabolism. Glucose is a key nutrient taken in by cancer cells for satisfying their high energy and biosynthesis needs. Drastic upregulation of glucose uptake and glycolytic activity, a phenomenon called the Warburg effect, is prevalent in cancers. Cancer cells overexpress specific glucose transporters (Gluts), particularly Glut1, on cell membranes for taking in glucose via facilitated diffusion. Considering the addiction of cancer cells for glucose and their sensitivity and vulnerability to changes in glucose supply, Gluts, especially Glut1, have been recognized as an attractive anticancer target. We previously reported the identification of first generation lead Glut1 inhibitor WZB117 (1). WZB117 treatment of human nonsmall cell lung cancer (NSCLC) A549 cells resulted in inhibition of glucose uptake, glycolysis and induction of apoptosis and necrosis. In addition, WZB-117 reduced tumor growth by ~70% in an A549 tumor mouse model. WZB117 inhibit cell growth of 7 cancer cell lines in 4 cancer types with IC50 values lower than 10 μM. Through a structure activity relationship (SAR) study of WZB117, a second generation lead, DRB18, has been identified. DRB-18 is much more stable and 5 to 10 times more potent than WZB117 in inhibiting growth and proliferation in about 90% of the 60 different cancer cell lines in 9 major cancer types as revealed in NCI-60 screenings. And its IC50s in many cancer cell lines are in the high nM range. In this study, we also report new compounds screening results for the objective of identifying novel compounds with higher glucose transport-inhibitory and cancer cell growth-inhibitory activities using nonsmall cell lung cancer cell lines as models. References: 1. Liu, Y., Cao, Y., Zhang, W., Bergmeier, S., Qian, Y., Akbar, H., Colvin, R., Ding, J., Tong, L., Wu, S. and Hines, J., 2012. A small-molecule inhibitor of glucose transporter 1 downregulates glycolysis, induces cell-cycle arrest, and inhibits cancer cell growth in vitro and in vivo. Molecular cancer therapeutics, 11(8):1672-1682. Citation Format: Yanrong Qian, Pratik Shriwas, Xuan Wang, Dennis Roberts, Emma Kessler, Stephen Bergmeier, Xiaozhuo Chen. Screening and identification of new generation glucose transporter inhibitors as anticancer therapeutics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1157. doi:10.1158/1538-7445.AM2017-1157
Robust Linear Regression Against Training Data Poisoning

The effectiveness of supervised learning techniques has made them ubiquitous in research and practice. In high-dimensional settings, supervised learning commonly relies on dimensionality reduction to improve performance and identify the most important factors in predicting outcomes. However, the economic importance of learning has made it a natural target for adversarial manipulation of training data, which we term poisoning attacks. Prior approaches to dealing with robust supervised learning rely on strong assumptions about the nature of the feature matrix, such as feature independence and sub-Gaussian noise with low variance. We propose an integrated method for robust regression that relaxes these assumptions, assuming only that the feature matrix can be well approximated by a low-rank matrix. Our techniques integrate improved robust low-rank matrix approximation and robust principle component regression, and yield strong performance guarantees. Moreover, we experimentally show that our methods significantly outperform state of the art both in running time and prediction error.
Reflected in a liquid crystal display: personalization and the use of avatars in serious games

Personalization, in the realm of Serious Games, is the extent to which users believe that the digital environment is tailored to their characteristics and preferences. This belief can have major repercussions for a user's experience with the game and can subsequently be used to maximize the return on investment for serious game designers. Other factors that influence users' personalization in games include how the game affects the users' perception of self, presence in the game, and social relationships developed in the game. Users' avatars influence all of these factors. This goal of this paper is to examine the research done into avatars and personalization and presents it in the context of serious games research.
Eleven quick tips for architecting biomedical informatics workflows with cloud computing

Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more. Despite these advantages that cloud-based workflows offer, the majority of scientific software developed in academia does not utilize cloud computing and must be migrated to the cloud by the user. In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing software and virtualized appliances on the world’s largest cloud. Researchers who follow these tips stand to benefit immediately by migrating their workflows to cloud computing and embracing the paradigm of abstraction.
Risk of infection from Legionella associated with spray irrigation of reclaimed water.

Abstract Legionella pneumophila has been detected in reclaimed water used for spray irrigation of turfgrass in public parks and golf courses. This study determined the risks of infection from exposure to various levels of Legionella in reclaimed waters considering: the method of spray application; and the duration and frequency of exposure. Evaluation of these factors resulted in a risk of infection greater than 1:10,000 for several scenarios when the number of Legionella in the reclaimed water exceeded 1000 colony-forming units (CFU) per ml. Most current guidelines for control of Legionella in distribution systems recommend that increased monitoring or remedial action be taken when Legionella levels exceed 1000 to 10,000 CFU/ml. Based upon our risk assessment, these guidelines seem appropriate for reclaimed water systems where spray irrigation is practiced.
Gene therapy strategies for the treatment of cancer. A review

This review summarizes current trends in cancer gene therapy. The diversity of approaches and rapid application of technical improvements reflects the interest in this emerging field. Major topics include the restoration of tumor suppressor genes and inhibition of oncogenes, stimulation of the immune response against tumors, and sensitization of cancer cells to systemically administered prodrugs. Special attention is focused on methodstumor targeting and the development of new vectors.
THE HISTORICAL LOGIC OF NON-VERBAL EXPRESSION IN EVERYDAY LIFE AND THE ARTS: THE PERCEPTUAL FOUNDATION OF THE PRECEPT

There is a figural basis of grammatical logic to be found in the norms of figural design within human expression. Husserl suggests this in his discussion of part and whole in the Logical Investigations. His notion of a “sprachlosen Denkungsform” “thought form without speech” emanates from this figural realm of knowing, a learning to express the visual field that begins from infancy. I explore “styles” of figuration which express the “part-whole” diaeresis of knowing natural to every human. These styles are pre-egoically formed, as a function of the “pure I” in its passive syntheses of judgment. The learning of verbal grammar accommodates one’s style of figural diaeresis.
Exosomal microRNA-21-5p Mediates Mesenchymal Stem Cell Paracrine Effects on Human Cardiac Tissue Contractility.

Rationale:The promising clinical benefits of delivering human mesenchymal stem cells (hMSCs) for treating heart disease warrant a better understanding of underlying mechanisms of action. hMSC exoso...
Leveraging Neighboring Cooperative Devices for Mobile Storage Offloading

With rising media technologies, increasing online presence, and newer high-quality file types, files on average have dramatically increased in size. However, to the consumer’s dissatisfaction, storage capacities on devices have not scaled well for acceptable prices. Moreover, privacy remains a concern in regards to personal data, where compromises in online storage services can be catastrophic. Manufacturers offer higher storage capacities on devices, in exchange for higher prices, and should the user opt to buy a low storage cheaper device, they become cornered into a limited number of options when their storage runs out. 1) utilizing cloud storage, which has raised a myriad of issues regarding privacy as of late. 2) manually moving their files from their device to storage disks.3) deleting some of their files, to free up space for new content. These options are non-autonomous and require a good deal of user intervention. The main contribution of this paper is proposing our Edge Storage Offloading Platform (ESOP), a mobile device middleware which capitalizes on the availability of unused devices within a user’s household. ESOP addresses the aforementioned privacy and cost concerns, through identifying unused files on a user’s device and offloading them to nearby user-owned, underutilized, and trusted devices.
DeepDx: A Deep Learning Approach for Predicting the Likelihood and Severity of Symptoms Post Concussion

In the United States alone, an estimated 1.7 million traumatic brain injuries (TBIs) occur each year, leading to more than 1.3 million TBI-related emergency room visits and hospitalizations, as well as thousands of deaths [9]. Following a mild TBI (mTBI) or concussion, patients may experience physical, psychological, and cognitive deficits lasting a period of hours, days, or for an extended period of time. Although most people recover within days to weeks of injury, some report persistent symptoms. Early detection, prognosis, and forecast of symptoms have the ability to improve the overall outcome of a patient, reduce the cost associated with treatment, and provide important insights into poorly understood brain injuries. This paper presents a deep learning approach for predicting the onset of a new diagnosis and its severity up to a year post concussion. Through the evaluation of our model we show that with thirty TBI-related symptoms, we are able to correctly predict the onset of a new symptom 93.49(±6.92)% of the time, and when predicting the entire 12-months trajectory of a patient’s symptoms we are able to exceed the expected 13.27% by more than doubling it to 33.53%. In addition, we introduce the concept of a deep recurrent neural network generating sample patients which can be used to derive the different types of patients that exist within the population.
Does ERAS impact outcomes of laparoscopic sleeve gastrectomy in adolescents

Abstract Background Enhanced recovery after surgery (ERAS) protocols have been successfully implemented in several surgical fields; however, the application of ERAS in the pediatric population is still limited. Objectives The aim is to determine if implementation of an ERAS protocol can improve outcomes of laparoscopic sleeve gastrectomy (LSG) in adolescents. Setting University Hospital, United States Methods A retrospective analysis of 112 adolescent patients who underwent LSG from February 2011 to July 2019 was conducted. An ERAS protocol was instituted in June 2016. Conventional care patients (n=51) were compared with ERAS patients (n=61). Comparisons were made using Chi-squared tests or Fisher’s exact for categorical data and Wilcoxon-rank sum tests for continuous data. Multiple linear regression was used to adjust length of stay (LOS) for patient characteristics. Results The two cohorts were similar in age, gender, race, number of comorbidities, and preoperative body mass index (BMI). The volume of intraoperative fluid, intraoperative and postoperative opioids were significantly reduced in the ERAS group (p Conclusions A LSG ERAS protocol is associated with significant reduction in perioperative opioid use and LOS with no increase in complications or readmission rates.
Pituitary Adenomas in Transgender Individuals

Transgender individuals may receive long-term hormonal treatment as part of their sexual transition; limited literature has suggested that they consequently may be predisposed to development of prolactinomas. We questioned whether we had encountered such cases. Pathology databases were searched for the years 2000-2019 for tissue specimens from transgender individuals; Sixty surgical specimens from 58 individuals and 8 cytology specimens were identified. Two of these 60 were pituitary adenomas, neither of which were lactotroph adenomas (prolactinomas).The first occurred in a 71-year-old transgender male-to-female who had undergone high-dose hormone therapy, followed by orchiectomy 30 years prior. Chronic hypertension, dizziness, and vertigo prompted an endocrine workup which revealed elevated IGF-1 and prolactin; The pituitary mass proved to be a mixed somatotroph/lactotroph adenoma. The second occurred in a 53-year-old transgender male-to-female who was being evaluated by an endocrinologist prior to initiating hormone therapy for transition when a slightly elevated prolactin level was discovered. This pituitary macroadenoma proved to be a gonadotroph adenoma. The most common surgical specimens were 33 bilateral mastectomies, 13 hysterectomies, and 4 orchiectomies, almost all for gender transition purposes rather than medical conditions. Pathologists may wish to be aware of the occurrence of pituitary adenomas in transgender individuals, although the incidence is quite low.
Transcriptional responses of soybean aphids to sublethal insecticide exposure

Insecticides are a key tool in the management of many insect pests of agriculture, including soybean aphids. The selection imposed by insecticide use has often lead to the evolution of resistance by the target pest through enhanced detoxification mechanisms. We hypothesised that exposure of insecticide-susceptible aphids to sublethal doses of insecticides would result in the up-regulation of genes involved in detoxification of insecticides, revealing the genes upon which selection might act in the field. We used the soybean aphid biotype 1 reference genome, version 6.0 as a reference to analyze RNA-Seq data. We identified multiple genes with potential detoxification roles that were up-regulated 12 h after sublethal exposure to esfenvalerate or thiamethoxam. However, these genes were part of a dramatic burst of differential gene expression in which thousands of genes were up- or down-regulated, rather than a defined response to insecticides. Interestingly, the transcriptional burst observed at 12 h s declined dramatically by 24-hrs post-exposure, suggesting a general stress response that may become fine-tuned over time.
Optimal Subarchitecture Extraction For BERT.

We extract an optimal subset of architectural parameters for the BERT architecture from Devlin et al. (2018) by applying recent breakthroughs in algorithms for neural architecture search. This optimal subset, which we refer to as "Bort", is demonstrably smaller, having an effective (that is, not counting the embedding layer) size of $5.5\%$ the original BERT-large architecture, and $16\%$ of the net size. Bort is also able to be pretrained in $288$ GPU hours, which is $1.2\%$ of the time required to pretrain the highest-performing BERT parametric architectural variant, RoBERTa-large (Liu et al., 2019), and about $33\%$ of that of the world-record, in GPU hours, required to train BERT-large on the same hardware. It is also $7.9$x faster on a CPU, as well as being better performing than other compressed variants of the architecture, and some of the non-compressed variants: it obtains performance improvements of between $0.3\%$ and $31\%$, absolute, with respect to BERT-large, on multiple public natural language understanding (NLU) benchmarks.
Retrospective observational study of temporal trends and outcomes of hepatitis B screening in patients receiving rituximab.

Objective Hepatitis B reactivation (HBr) is strongly associated with rituximab therapy. Guidelines advise hepatitis B screening and use of preventive nucleoside analogue (NA) in patients at risk. In this study, we examined screening trends, post-screening interventions and outcomes in patients receiving rituximab in light of recommendations. Design Retrospective, observational study. Setting Single, tertiary care centre in the USA. Participants Patients receiving rituximab from January 2005 to December 2017. Primary outcome Trends of hepatitis B screening prior to initiation of rituximab. Secondary outcome Results of hepatitis B screening, use of preventive NA therapy and HBr incidence. Results Over 13 years, 2219 patients received rituximab. Screening, with at least hepatitis B core antibody (anti-HBc) prior to the first dose of rituximab, improved from 20% to 97%. Because only 4.5% of patients had a positive anti-HBc, the overall HBr incidence was very low (0.42%). In susceptible patients, the incidence of HBr was 8%. In at-risk patients given preventive NA, 96% remained free of HBr. However, only 23% received a preventive NA and no temporal improvement in compliance was seen. Of those with HBr, 87.5% were hepatitis B surface antigen (HbsAg−)/anti-HBc+. Conclusions In those treated with rituximab, we demonstrated near-universal anti-HBc screening. Screening unlinked to preventive NA use, in those who are anti-HBc+, is ineffective in reducing HBr. HBr has a high fatality rate. The majority of cases occurred in those who were HBsAg negative. Efforts are needed to educate providers who use rituximab not only to screen for anti-HBc, but to provide preventive NA to those who test positive.
Plumage patterns: Ecological functions, evolutionary origins, and advances in quantification

Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed datasets of pattern phenotypes that were heretofore inaccessible. In this review, we synthesize recent and classic studies of plumage patterns at different evolutionary and organismal scales and discuss the various roles that plumage patterns play in avian biology. We dissect the role of plumage patches as signals within and among species. We also consider the evolutionary history of plumage patterns, including phylogenetic comparative studies and evolutionary developmental research of the genetic architecture underlying plumage patterns. We also survey an expanding toolbox of new methods that characterize and quantify the size, shape, and distribution of plumage patches. Finally, we provide a worked example to illustrate a potential workflow with dorsal plumage patterns among subspecies of the Horned Lark (Eremophila alpestris) in western North America. Studies of plumage patterning and coloration have played a prominent role in ornithology thus far, and recent methodological and conceptual advances have opened new avenues of research on the ecological functions and evolutionary origins of plumage patterns in birds.LAY SUMMARYBirds have many different plumage patterns that arise from coloration motifs within feathers as well as differences in color among body regions.Plumage patterns play various roles in bird biology. They are involved in mate choice and territoriality, social interactions, camouflage from predators, and many other functions.There is a rich history of detailed study on plumage patterns, which we review and synthesize in this manuscript.Recent advances in photography and image processing algorithms have opened new avenues of research on plumage patterns. These open-source methods enable efficient, repeatable, and scalable analytical pipelines.We illustrate one possible pipeline with a worked example of geographic variation in dorsal plumage patterns among populations of Horned Lark (Eremophila alpestris) in the western United States.Looking ahead, enhanced capacity and scalability for digital photography analyses will reveal new discoveries regarding the ecology and evolution of avian plumage patterns.
Comparative studies on speciation: 30 years since Coyne and Orr.

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr (1989) provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr (1989)'s influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today (Turelli and Begun 1997; Fitzpatrick 2002; Funk et al. 2006; Yukilevich 2012; Turelli et al. 2014). Now 30 years later, we revisit the five questions addressed by Coyne and Orr (1989), identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field. This article is protected by copyright. All rights reserved.
Baylor University Campus-Wide Deep Dive

Author(s): Zurawski, Jason; Schopf, Jennifer | Abstract: In January 2020, staff members from the Engagement and Performance Operations Center (EPOC) and the Lonestar Education And Research Network (LEARN) met with researchers and staff at Baylor University for the purpose of a Campus-Wide Deep Dive into research drivers. The goal of this meeting was to help characterize the requirements for five campus research use cases and to enable cyberinfrastructure support staff to better understand the needs of the researchers they support. Profiled scientific use cases included: - Experimental High Energy Physics (HEP) - Proton Computed Tomography (pCT) - Nutrition and Relation to Digestive Microbiome - Baylor University Core Research Facilities - Molecular Quantum-dot Cellular Automata (QCA), and Material Science of Quantum Computing - Modeling and Simulation of Low-Dimensional and Nano-Structured Materials - Computational Fluid Dynamics Material for this event included the written documentation from each of the research areas at Baylor University, documentation about the current state of technology support, and a write-up of the discussion that took place in person. The Case Studies highlighted the ongoing challenges that Baylor University has in supporting a cross-section of established and emerging research use cases. Each Case Study mentioned unique challenges which were summarized into common needs. These included: - Tradeoffs for network/software security, and usability of the resulting infrastructure. Better communication to set expectations and understand realities is required. - Computation use on campus is widespread and healthy. While no major problems were uncovered, upgrades to maintain current usage patterns and encourage growth will be required. - Storage is a critical need for enterprise use cases and research. In particular, a campus wide ‘storage architecture’ to support research use cases (e.g. instruments, data sharing) is required in the 2-5 year time window. - Instrumentation on campus is healthy and expanding. Technology must scale with this in the form of computation and storage. - Working with LEARN to upgrade network capacity (in multiples of 10G, or upgrades to 100G) will be required in the 1-3 year time frame. - Network monitoring and visibility will help to establish external science use cases. - Data sharing via portal systems is not currently a critical need, but growing in scope. EPOC can assist Baylor with options.
Techno-economic process modelling and Monte Carlo simulation data of uncertainty quantification in field-grown plant-based manufacturing

This data article is related to the research article, "M.J. McNulty, K. Kelada, D. Paul, S. Nandi, and K.A. McDonald, Introducing uncertainty quantification to techno-economic models of manufacturing field-grown plant-made products, Food Bioprod. Process. 128 (2021) 153-165." The raw and analyzed data presented are related to generation, analysis, and optimization of ultra-large-scale field-grown plant-based manufacturing of high-value recombinant protein under uncertainty. The data have been acquired using deterministic techno-economic process model simulation in SuperPro Designer integrated with stochastic Monte Carlo-based simulation in Microsoft Excel using the Crystal Ball plug-in. The purpose of the article is to make techno-economic and associated uncertainty data available to be leveraged and adapted for other research purposes.
Electoral Institutions and Substantive Representation in Local Politics: The Effects of Ranked Choice Voting

While significant progress has been made in studies of substantive representation in local politics in the past decade, we know less about the effects of institutions on local representation. In this paper, I explore the effect of an increasingly popular electoral institution---ranked choice voting (RCV)---on substantive representation. I examine a host of fiscal variables and the ideology of city councils using generalized synthetic controls, and I find that the municipalities adopting RCV saw no changes in policy outcomes or representation. Finally, I use roll call data to show that the behavior of legislators who served both before and after the use of RCV was unchanged and that intra-city responsiveness remained constant after RCV was implemented as well. My findings suggest that ranked choice voting may not produce the significant effects on representation for which its proponents hope.
Underrepresented Populations in Pediatric Epilepsy Surgery

As awareness of pediatric epilepsy increases, accompanied by advancements in technology and research, it is important to identify certain types of patients that are overlooked for surgical management of epilepsy. Identifying these populations will allow us to study and elucidate the factors contributing to the underutilization and/or delayed application of surgical interventions. Demographically, African-American and Hispanic patients, as well as patients of certain Asian ethnicities, have relatively lower rates of undergoing epilepsy surgery than non-Hispanic and white patients. Among patients with epilepsy, those with higher odds of seizure-freedom following surgery are more likely to be referred for surgical evaluation by their neurologists, with the most common diagnosis being lesional focal epilepsy. However, patients with multifocal or generalized epilepsy, genetic etiologies, or normal (non-lesional) brain magnetic resonance imaging (MRI) are less likely be to referred for evaluation for resective surgery. With an increasing number of high-quality imaging modalities to help localize the epileptogenic zone as well as new techniques for both curative and palliative epilepsy surgery, there are very few populations of patients and/or types of epilepsy that should be precluded from evaluation to determine the suitability of epilepsy surgery. Ultimately, a clearer understanding of the populations who are underrepresented among those considered for epilepsy surgery, coupled with further study of the underlying reasons for this trend, will lead to less disparity in access to this critical treatment among patients with epilepsy.
Minimizing development costs for efficient many-core visualization using MCD3

Abstract Scientific visualization software increasingly needs to support many-core architectures. However, development time is a significant challenge due to the breadth and diversity of both visualization algorithms and architectures. With this work, we introduce a development environment for visualization algorithms on many-core devices that extends the traditional data-parallel primitive (DPP) approach with several existing constructs and an important new construct: meta-DPPs. We refer to our approach as MCD3 — Meta-DPPs, Convenience routines, Data management, DPPs, and Devices. The twin goals of MCD3 are to reduce developer time and to deliver efficient performance on many-core architectures, and our evaluation considers both of these goals. For development time, we study 57 algorithms implemented in the VTK-m software library and determine that MCD3 leads to significant savings. For efficient performance, we survey ten studies looking at individual algorithms and determine that the MCD3 hardware-agnostic approach leads to performance comparable to hardware-specific approaches: sometimes better, sometimes worse, and better in the aggregate. In total, we find that MCD3 is an effective approach for scientific visualization libraries to support many-core architectures.
Mathematics for Business and Economics

A major challenge in writing a book on mathematics is to select appropriate topics and then present them with the necessary clarity. Another challenge is to motivate students in business and economics to study topics by convincingly demonstrating their power to deal with problems in areas of business and economics. These must be done without sacrificing anything in terms of the rigor and correctness of the mathematics itself. Keeping this in mind, the goal of this book is to help preparing students for academic courses: Mathematics for Business & Economics and Fundamental of Mathematics and then for the mathematical rigor of graduate economics by putting emphasis on its application. Specifically, mathematics is the backbone of economics and business in the sense that it forces learners to be very explicit about his or her assumptions and how s/he proves results by writing mathematical models. Furthermore, it helps establishing quantitatively causal links and to forecast the effects of policies and other economic phenomenon under conditions we might observe x causing y but also to what degree x can affect y. Particularly, calculus and dynamic programming for example enable economists to show how agents optimize their decisions over a time horizon and with uncertainty. Applications of mathematics in business and economics require the individuals to be creative and proficient in application of math techniques. It would not be overstated saying that without mathematics, all we could do is claim x causes y and not be able to show how it occurs except through vague wording and will still be unable to provide precise predictions as to how it works. Definitely, Mathematics is a problem solving subject and the key to succeeding in Mathematics is not to study Mathematics but working on mathematical problem solving. That raises question: what would be my advice on success? Answering question posed, I would suggest, in class, you simply need to pay attention to all work examples as it is expected to be shown by your class-teacher or from this textbook. And then you put your acquired knowledge into your solution working, covering a myriad variety of problems expected to be taken out from this course-book, all on your own. This textbook contains over 300 math-problems derived from subject areas of business & economics. Thus utilization of this book can serve you in multi-faucets: train you on the application of math-techniques, enhance your proficiency in the subject areas, which can be instrumental in your endeavors for better outcome. Finally, it is expected that students find this book useful as a guide to what they should expect to achieve; and professionals find this book as a resource in their professional endeavors.
Are Variable Environments Stochastic? A Review of Methods to Quantify Environmental Predictability

We review some methods for quantifying environmental predictability and discuss their advantages and disadvantages. Colwell’s (1974) index can be used to give an absolute measure of predictability, which can be partitioned into constancy and contingency (seasonality), and is applied to time series of categorical data. Spectral analysis is useful for measuring periodicity or seasonality of environments, and requires time series of continuous data. We compare the behavior of these measures for 15 wetland sites in tropical and subtropical portions of North and South America. Estimates of seasonality and predictability based on spectral densities were related positively to estimates of predictability and contingency, and to some extent negatively with constancy, derived from Colwell’s index. These methods performed better than simple statistical measures of variation such as the standard deviation or coefficient of variation. Studies seeking to characterize environmental variation and explore its implications for life-history evolution should employ these time series approaches.
What Parents Need to Know About Vitamin K Administration at Birth

Prophylactic treatment of newborns with intramuscular vitamin K has been the standard of care for many years in the United States. However, instances of parental refusal of routine prophylaxis are currently on the rise. Refusal of routine prophylaxis can have serious long-term neurodevelopmental consequences for some newborns, who may subsequently develop vitamin K deficiency-associated hemorrhagic disease of the newborn (HDN).
Identifying least affected parameters in analyzing Electrical Impedance Myography with alteration in subcutaneous fat thickness via finite element model

Electrical Impedance Myography (EIM) is a neurophysiologic technique in which high- frequency, low-intensity electrical current is applied via surface electrodes over a muscle or muscle group of interest and the resulting electrical parameters (resistance, reactance and phase) are analyzed to isolate diseased muscles from healthy one. Beside muscle properties, some other factors like subcutaneous fat (SF) thickness, inter-electrode distance, muscle thickness etc. also impact the major EIM parameters. The purpose of this study is to explore the effect of SF thickness variation on different EIM parameters and propose a parameter which is least affected and also can detect muscle conditions. We analyzed four different parameters in this study for various SF thicknesses and none of them possesses constant profile with alteration in SF thickness. For example, resistance in normal condition varies 24.48% with per millimeter SF thickness variation while phase varies 4.01%. Further investigation shows that among the observed parameters percentage changes in reactance is minimum with fat thickness variation while effectively identifying different muscle conditions.
User Defined Types

The aim of this chapter is to introduce the concepts and ideas involved in using the facilities offered in Fortran 90 for the construction and use of user defined types: the way in which we define our own types; the way in which we declare variables to be of a user defined type; the way in which we manipulate variables of our own types; the way in which we can nest types within types. The examples are simple and are designed to highlight the syntax. More complex and realistic examples of the use of user defined data types are to be found in later chapters.
Energy-bandwidth allocation in multiple orthogonal broadcast channels with energy harvesting

In this paper, we consider the energy-bandwidth allocation for a network with multiple orthogonal broadcast channels, where each transmitter communicates with multiple receivers orthogonally. We assume that the harvested energy and channel gain of each transmitter can be predicted for K slots a priori. To maximize the weighted throughput of the network, we formulate an optimization problem with O(MK) constraints, where M is the number of the receivers, making it hard to solve using a generic convex solver since the computational complexity of the solver becomes impractically high when the number of constraints is large. In order to use the iterative algorithm proposed in [1] to solve the problem efficiently, we decompose the problem into the energy and bandwidth allocation subproblems and propose algorithms to solve the two corresponding subproblems, so that the optimal energy-bandwidth allocation can be obtained with an overall complexity of O(MK2).
A review of the nutritional value of legumes and their effects on obesity and its related co-morbidities

Since the 1970s, the proportion of overweight and obese people in the United States has grown at an alarming rate. An awareness of the consequences of obesity on the health and well-being of individuals is evident in the plethora of strategic plans at the local and national levels, most of which have largely fallen short of their goals. If interventions continue to be unsuccessful, it is estimated that approximately three of four Americans will be overweight or obese by 2020. Prevention of excess weight gain can be accomplished with relatively small changes in lifestyle behaviours to control body weight. Small sustainable changes are perhaps better than efforts to achieve larger changes that cannot be sustained. Legumes can be a valuable food by which the needs of the undernourished or under-served populations could be met. They can be incorporated into meat products, such as sausages and burgers, to lower the energy density of these foods while providing important nutrients. Replacing energy-dense foods with legumes has been shown to have beneficial effects on the prevention and management of obesity and related disorders, such as cardiovascular disease, diabetes and the metabolic syndrome. This review explores the nutritional value and obesity-related health benefits of legume consumption while focusing on pulses.
Ameliorating Spinal Cord Injury in an Animal Model With Mechanical Tissue Resuscitation.

Background Traumatic spinal cord injury (SCI) is a major worldwide cause of mortality and disability with limited treatment options. Previous research applying controlled negative pressure to traumatic brain injury in rat and swine models resulted in smaller injuries and more rapid recovery. Objective To examine the effects of the application of a controlled vacuum (mechanical tissue resuscitation [MTR]) to SCI in a rat model under several magnitudes of vacuum. Methods Controlled contusion SCIs were created in rats. Vacuums of -50 and -75 mm Hg were compared. Analysis included open-field locomotor performance, magnetic resonance imaging (in vivo T2, ex vivo diffusion tensor imaging and fiber tractography), and histological assessments. Results MTR treatment significantly improved the locomotor recovery from a Basso, Beattie, and Bresnahan score of 7.8 ± 1.9 to 11.4 ± 1.2 and 10.7 ± 1.9 at -50- and -75-mm Hg pressures, respectively, 4 weeks after injury. Both pressures also reduced fluid accumulations > 10% by T2-imaging in SCI sites. The mean fiber number and mean fiber length were greater across injured sites after MTR treatment, especially with treatment with -50 mm Hg. Myelin volume was increased significantly by 60% in the group treated with -50 mm Hg. Conclusion MTR of SCI in a rat model is effective in reducing edema in the injured cord, preserving myelin survival, and improving the rate and quantity of functional recovery. Abbreviations BBB, Basso, Beattie, and BresnahanDTI, diffusion tensor imagingFA, fractional anisotropyMTR, mechanical tissue resuscitationMTR50, mechanical tissue resuscitation with 50-mm Hg subatmospheric pressureMTR75, mechanical tissue resuscitation with 75-mm Hg subatmospheric pressureROI, region of interestSCI, spinal cord injury.
Absorption of Ca45 and Sr85 from solid and liquid food at various levels of the alimentary tract of the rat.

The total absorption of Ca/sup 45/ and Sr/sup 85/ by the rat small intestine from a liquid dose of food averaged 45 and 28%, respectively; from solid dose it averaged 19 and 13%. The dtfferences were highly significant. Solid food left the stomach more slowly than liquid, but the time necessary for food to start entering the cecum was the same for both. Absorption of Ca/sup 45/ and Sr/sup 85/ occurred rapidly at first, but then tapered off and essentially ceased after about 2 hr for the liquid dose and 6 hr for the solid dose. The ratio of absorbed Sr/sup 85//Ca/sup 45/ per rat, averaged over time intervals of 15 min to 12 hr, was 0.67 plus or minus 0.020 for rats given labeled solid food. The ratio was independent of time or food consistency. The total relative per cent of Sr/sup 85/ and Ca/sup 45/ absorbed in each of the gut components was estimated after absorption had ceased. For liquid dose the values were: stomach 0, duodenum 15, jejunum 23, and ileum 62%. For the solid dose the corresponding values were 0, 8, 4, and 88%, respectively. The relative per cent absorption of Ca/sup 45/ and Sr/sup 85/more » was the same throughout the alimentary tract. It was postulated that an absorption mechanism exists throughout the entire small intestine, which is more efficient for Ca than for Sr but which handles both. (P.C.H.)« less