Miracle-dz/UniFAR-FTUs huggingface dataset:
Applications of non-linear algebra to biology

Author(s): Cartwright, Dustin Alexander | Advisor(s): Sturmfels, Bernd | Abstract: We present two applications of non-linear algebra to biology. Our first application is to the analysis of gene expression data from Arabidoposis roots. In Chapter 2, we present a method forcomputing non-negative roots to certain systems of polynomials. This algorithm is based on a generalization of the Expectation-Maximization and Iterative Proportional Fitting from statistics. In Chapter 3, this method is applied to a model for gene expression coming from roots of the Arabidopsis plant. Variation in gene expression is one method in which different tissue types develop different functional characteristics. Our model for gene expression in these roots is non-linear and so we apply the method from Chapter 2.Our second application is the use of secant varieties to study mixture models for the distribution of single-nucleotide polymorphisms in genes. In Chapter 4, we give generators for the defining ideal of the first 5 secant varieties of P^2 x P^{n-1} embedded by O(1,2). Our equations come from a generalization of the flattening of a tensor, which we call an exterior flattening. The study of secant varieties is a classical subject in algebraic geometry, which has recently been connected to applications in algebraic statistics. In Chapter 5, this connection is used in order to understand how single-nucleotide polymorphisms occur within human genes. Because genes perform important functions, there is selective pressure against mutations which affect the gene's behavior. As we show, these selective pressures are closely tied to the nature by which genetic sequence codes for the constituent amino acids of a protein.
AI agency vs. human agency: understanding human-AI interactions on TikTok and their implications for user engagement

Artificial intelligence (AI) technology has vastly reshaped user experiences on social media. AI-powered social media use and its outcomes largely depend on how users collaborate with AI that exercises agency. Through in-depth interviews with TikTok users, this study investigates how users collaborate with AI when using AI-powered social media and how such dynamics shape user engagement. We found that TikTok users are receptive to personalized experiences enabled by machine agency. However, by influencing each other, user agency and machine agency also led to user–AI synergy. Users deliberately influence content curation algorithms to make them cater more precisely to their needs; AI also facilitates users’ content creation and networking. Such AI–user collaboration on TikTok significantly influences medium engagement and social-interactive engagement. These findings advance our understanding of the dynamics between human agency and machine agency and, thus, how AI transforms user experiences on social media.
Eigenvalues in Filled Julia Sets

Summary We show how Julia sets can be introduced very naturally in a junior-level linear algebra course, as a way of exposing students to the contemporary area of complex dynamics. The standard definition of the filled Julia set of a polynomial is generalized to the setting of polynomial iteration of matrices. We prove that the eigenvalues of any matrix bounded under iteration by a polynomial must lie in the corresponding filled Julia set. A partial converse is obtained if the matrix is assumed to be diagonalizable. Still another partial converse is proven by assuming the spectrum of the matrix is contained in the interior of corresponding filled Julia set.
WORKING PAPER SERIES ASSET SPECIFICITY OF NON-FINANCIAL FIRMS

The specificity of firms' assets affects a wide range of economic issues. We study asset specificity of U.S. non-financial firms using a new dataset on the liquidation recovery rates of all major asset categories across industries. First, we find that non-financial firms' assets are generally highly specific. The average recovery rate (liquidation value over cost net of depreciation) is 35% for plant, property, and equipment (PPE). Second, across industries, physical attributes such as mobility, durability, and standardization account for around 40% of variations in PPE recovery rates. Over time, macroeconomic and industry conditions have the most impact on recovery rates when PPE is not firm-specific. Third, higher asset specificity is associated with less asset sales, greater investment response to uncertainty, and more Q dispersion, consistent with theories of investment irreversibility. Finally, the data suggests that rising intangibles have had a limited impact on firms' liquidation values. Amir Kermani Haas School of Business University of California, Berkeley 545 Student Services Building #1900 Berkeley, CA 94720 and NBER kermani@berkeley.edu Yueran Ma The University of Chicago Booth School of Business 5807 S. Woodlawn Ave. Chicago, IL 60637 United States Yueran.Ma@chicagobooth.edu
BUTLER: Increasing the Availability of Low-Power Wireless Communication Protocols

Over the past years, various low-power wireless protocols based on synchronous transmissions (ST) have been developed to meet the high dependability requirements of emerging cyber-physical applications. For example, Wireless Paxos provides consensus, a key mechanism for building fault-tolerant systems through replication. However, Wireless Paxos and other ST-based protocols are themselves not fault-tolerant: They suffer from a single point of failure that fundamentally impairs the availability of the communication service in the presence of node crashes and network partitions. We present B UTLER , a mechanism that allows removing the single point of failure in many ST-based protocols. B UTLER synchronizes all nodes in the network so that the communication process can be jointly started by multiple randomly chosen nodes rather than a single dedicated node. We analyze and formally prove the correctness of B UTLER and implement it on the state-of-the-art nRF52840 platform. Experiments on the FlockLab testbed demonstrate that B UTLER reliably synchronizes the network to within ± 3 µs despite large initial offsets, unpredictable node failures, and network partitions. B UTLER ’s temporal overhead ranges well below 1 %. Because of this efficiency and effectiveness, our results further indicate that B UTLER can dramatically improve the availability of an existing ST-based protocol without any noticeable impact on the overall communication reliability and efficiency.
Exploring split ticket voting motives

Split ticket voting is becoming increasingly common in most political systems. Tendencies to split votes has grown steadily during the last decades (Dalton, 2014: 197). Split ticket voting refers to the act of splitting one’s vote on several candidates or parties in elections and can occur in two different ways: by the division of votes to several, equivalent offices (horizontal voting) or to multiple levels of government (vertical voting) (Burden & Helmke, 2009:2). But why does it occur, who is the split ticket voter and how can we understand its steady increase among the electorate? This report investigates split ticket voting motives in Sweden using data from the 2018 Swedish National Election Study. The special circumstances offered by Sweden’s concurrent elections enable comparisons of voting motives on the national and local levels. The results show that sincere voting motives are most salient among split ticket voters in Sweden, and that strategic motives are relevant as a measure of threshold-insurance. Furthermore, the results show high salience of issue politics, and local level politics prominently referenced among split voters. Additionally, the analyses reveal differences between groups based on social and political cleavages, suggesting that motives for split-ticket voting vary across different groups.
Cardiovascular and Renal Outcomes among Patients with Type 2 Diabetes using SGLT2 Inhibitors added to Metformin: A Population-Based Cohort Study from the United Kingdom

Introduction : As large numbers of patients with type 2 diabetes receive treatment with a sodium-glucose co-transporter-2 inhibitor (SGLT2i), we investigated whether the cardio-renal preventative effects found in clinical trials are also seen in clinical practice where patient characteristics and adherence to treatment differs. Research design and methods : Using UK primary care electronic health records, we followed two cohorts of patients with type 2 diabetes prescribed metformin: SGLT2is (N=12,978) and a matched comparator of patients not using a SGLT2i at the start of follow-up (N=44,286). Independent follow-ups were performed to identify the study outcomes – Cox regression to estimate adjusted hazard ratios (HRs) for the study outcomes: cardiovascular (CV) composite outcome (comprising non-fatal myocardial infarction [MI]/ischaemic stroke [IS] requiring hospitalisation and CV death), severe renal disease, and all-cause mortality. Results: Mean follow-up was 2.3 years (SGLTi cohort) and 2.1 years (comparison cohort). Mean age was 60.4 years (SD ±10.2, SGLTi cohort) and 60.4 years (SD ± 10.0, comparison cohort). SGLT2i new users were associated with a reduced risk of the CV composite (HR 0.75, 95% CI: 0.61–0.93), severe renal disease (HR 0.55, 95% CI: 0.46– 0.67), and all-cause mortality (HR 0.56, 95% CI: 0.49–0.63), with risk reductions similar irrespective of baseline CKD. Reduced risks were seen for IS (HR 0.51, 95% CI: 0.36–0.74) but not MI (HR 0.98, 95% CI: 0.74–1.28). Results were consistent in sensitivity analyses. Conclusions: In population-based study, SGLT2is were associated significant CV, the stroke.
Business model innovation in small- and medium-sized enterprises

Purpose Industry 4.0 is expected to significantly transform industrial value creation. However, research on business models affected through Industry 4.0, and on small- and medium-sized enterprises (SMEs), remains scarce. In response, the purpose of this paper is to address both aspects, further elaborating on the role that SMEs can take toward Industry 4.0 as provider or user. Design/methodology/approach The paper used an exploratory research design based on 43 in-depth expert interviews within the three most important German industry sectors, mechanical and plant engineering, electrical engineering and automotive suppliers. Interviews were conducted with leading personnel of the respective enterprises, including 22 CEOs. They assign business model implications through Industry 4.0, referring to the Business Model Canvas, while the paper delineates between Industry 4.0 providers and users. Findings The paper finds that key resources and value proposition are among the most affected elements of the business model, whereas channels are the least affected. Furthermore, distinct characteristics between Industry 4.0 providers and users can be delineated. In general, Industry 4.0 providers’ business models are significantly more affected than users, except for key partners and customer relationships. Research limitations/implications Industry 4.0 remains at its early stages of implementation. As a result, many interviewees’ answers remain at a rather general level. Practical implications Strategies for the further alignment of the business models are provided for Industry 4.0 providers and users. Originality/value The paper is among the few that investigate Industry 4.0 in the context of SMEs and business models.
A comparison of lung cancer in HIV-positive and HIV-negative populations

Background Lung cancer is the most common cancer worldwide and is the greatest contributor to malignancy-associated deaths. Human immunodeficiency virus (HIV) is an epidemic in many developing countries and South Africa carries the largest burden of this disease in the world. With the introduction of antiretroviral therapy (ART), acquired immune deficiency syndrome (AIDS)-defining malignancies (ADMs) are on the decline and non-AIDS-defining malignancies (NADMs) are becoming more common, with lung cancer being the most common among these. Objectives To describe and compare a cohort of HIV-positive lung cancer patients and a cohort of HIV-negative lung cancer patients. Methods A retrospective study of 188 patients with histologically confirmed bronchogenic carcinoma was conducted. Smoking history, cancer sub-type, cancer stage, HIV parameters and demographic data were collected. Results There were 31 (16.94%) HIV-positive patients. They presented at a younger age (53.94 years) than the HIV-negative group (61.64 years) (p=0.0001). Adenocarcinoma was the most common sub-type in the HIV-negative cohort while squamous cell carcinoma was slightly more common in the HIV-positive cohort. Both groups predominantly presented with locally advanced or metastatic disease. Conclusion HIV-positive patients present at a younger age than HIV-negative patients and both groups show a male-predominant pattern.
Mixture of multiple copies of maximally entangled states is quasipure

Employing the general bilateral controlled-NOT operation and local state discrimination, the mixed state of the form {rho}{sub d}{sup (k)}=(1/d{sup 2}){sigma}{sub m,n=0}{sup d-1}(vertical bar {phi}{sub mn}> {r_brace} is the canonical set of mutually orthogonal maximally entangled states in dxd. Therefore irreversibility does not occur in the process of distillation for this family of states. Also, the distillable entanglement is calculated explicitly.
Metabolic and morphological profile in skeletal muscle of healthy boys and girls

It was hypothesized that the typical adult pattern of higher glycolytic capacity in skeletal muscle of males compared to females is not observed in children and that fiber cross‐sectional area (CSA) is a determinant of glycolytic capacity in children. Biopsies were performed in vastus lateralis in 9–12 years‐old healthy boys and girls (N = 27). Fiber types were classified by myofibrillar ATPase staining and CSA was measured using planimetry. Citrate synthase (CS) and lactate dehydrogenase (LD) were analyzed using fluorometric and spectrophotometric methods. There was no significant difference between boys and girls in CS activity (0.45 ± 0.1 μkat g−1 dry muscle in boys and 0.42 ± 0.1 in girls) or LD activity (24 ± 6 μkat g−1 dry muscle in boys and 25 ± 7 in girls). CSA did not differ between boys and girls. CS was inversely related to type I CSA (r = −0.62, p < 0.001) and LD was directly related to type IIA (r = 0.63, p < 0.001) and type IIB CSA (r = 0.72, p < 0.001). CSA was a significant determinant of CS and LD, even after adjusting for sex and relative fiber type area in multiple regression analysis. This suggests that the typical adult pattern of higher muscle glycolytic capacity in males than in females, as estimated by LD activity, was not observed in children. Sex‐specific patterns in glycolytic capacity thus appear to develop during the transition from childhood to adulthood. In addition, fiber CSA was a strong determinant of both muscle glycolytic and oxidative capacity in children, regardless of sex.
Scoping review of models and frameworks of patient engagement in health services research

Objective To count and describe the elements that overlap (ie, present in two or more) and diverge between models and frameworks of patient engagement in health services research. Our specific research question was ‘what are the elements that underlie models and frameworks of patient engagement in health services research? ’ Design Scoping review. Data sources On 6–7 July 2021, we searched six electronic databases (ie, CINAHL, Cochrane Database of Systematic Reviews, Joanna Briggs Institute Evidence Based Practice Database, MEDLINE, PsycINFO and Scopus) and Google Scholar for published literature, and ProQuest Dissertations & Theses, Conference Proceedings Citation Index, Google, and key agencies’ websites for unpublished (ie, grey) literature, with no date restrictions. These searches were supplemented by snowball sampling. Eligibility criteria We included published and unpublished literature that presented (a) models or frameworks (b) of patient engagement (c) in health services research. We excluded articles unavailable as full text or not written in English. Data extraction and synthesis Two independent reviewers extracted data from included articles using an a priori developed standardised form. Data were synthesised using both quantitative (ie, counts) and qualitative (ie, mapping) analyses. Results We identified a total of 8069 articles and ultimately included 14 models and frameworks in the review. These models and frameworks were comprised of 18 overlapping and 57 diverging elements, that were organised into six conceptual categories (ie, principles, foundational components, contexts, actions, levels and outcomes) and spanned intrapersonal, interpersonal, process, environmental, and health systems and outcomes domains. Conclusions There is little overlap between the elements that comprise existing models and frameworks of patient engagement in health services research. Those seeking to apply these models and frameworks should consider the ‘fit’ of each element, by conceptual category and domain, within the context of their study.
Objective evaluation of facial features in Congolese newborns by facial measurements. The need for population‐specific measurements

The evaluation of dysmorphism is often subjective because many continuous traits are not easily measured or lack normal values. Because many common morphologic profiles vary between populations, population‐specific reference ranges of relevant traits are needed. We aim to evaluate the objective assessment of facial dysmorphism in 553 Congolese newborns based on facial measurements. Measurements taken with a ruler were on average larger compared to those with a caliper, but the bias did not depend on the size of the measurement. We therefore introduced a correction factor that allows to use both techniques for facial measurements interchangeably in future studies. The outer canthal distance, palpebral fissure length, and mouth width were significantly larger in Congolese newborns (respectively mean 6.59 [SD 0.48]; mean 2.20 [SD 0.24]; mean 2.78 [SD 0.26]) when compared to references based on European newborns (respectively mean 3.59 [SD 1.76]; mean 4.20 [SD 2.26]; mean 0.47 [SD 1.21]), while the rest of measurements were significantly smaller. The interpupillary distance (IPD) calculated from inner canthal distance and outer canthal distance was not significantly different. We observed a poor agreement between clinical evaluation and measured features (kappa of 0.432). Clinicians were more likely to recognize a face as having wide‐spaced eyes when it had been recognized as such during the clinical examination, more than if the child had a high interpupillary distance. This suggests that the measured IPD is not precisely reflecting what is clinically evaluated as wide‐spaced eyes.
Investigation of the effect of hesperidin on some reproductive parameters in testicular toxicity induced by Bisphenol A

Bisphenol A (BPA) is one of the chemicals that cause dysfunction and infertility in testicles. Therefore, it is crucial to develop effective treatments against this damage. In this study, the effects of Hesperidin (HESP), a flavonoid in testicular toxicity induced by BPA in rats, on oxidative stress, inflammation, apoptosis, histological damage, spermatogenesis, steroidogenic enzymes and reproductive hormones were investigated. Our study used 52 Sprague Dawley male rats weighing 250–300 g, and four experimental groups were formed. From the experimental groups, 1 ml of olive oil was administered to the control group, HESP at a dose of 50 mg/kg to the HESP group, BPA at a dose of 100 mg/kg to the BPA group, HESP at a dose of 50 mg/kg to the BPA + HESP group and 100 mg/kg BPA was administered intragastrically (ig) for 14 days. We determined that BPA administration causes apoptosis, histological damage, inflammation, oxidative stress and toxic effects on spermatogenesis and steroidogenic enzymes in testicles. We observed that the administration of HESP with BPA attenuated oxidative stress, inflammation and apoptosis resulting in therapeutic effects on both steroidogenic enzymes and spermatogenesis and reproductive hormones (FSH, LH and testosterone). Our findings from this study clearly showed that while HESP treatment alleviates oxidative damage, inflammation and apoptosis in testicles of rats treated with BPA, it has regulatory effects on steroidogenic enzymes, spermatogenesis and serum reproductive hormones.
High-performance controllable ambipolar infrared phototransistors based on graphene-quantum dot hybrid

The field effect transistors (FETs) exhibited ultrahigh responsivity (107 A/W) to infrared light with great improvement of mobility in graphene / PbS quantum dot (QD) hybrid. These reported transistors are either unipolar or depletion mode devices. In this paper, we presented and fabricated conveniently-controlled grapheme / PbS QD hybrid FETs. Through the investigation on electric and optoelectronic properties, the ambipolar FETs (normally OFF) can be switched ON by raising gate voltage (VG) up to 3.7 V and -0.8 V in the first and third quadrants. Near these thresholds (VT) each carrier species shows comparable mobility (~ 300 cm2V-1s-1). Photo-responsivity reach ~ 107 A/W near each threshold and it will linearly increases with (VG-VT). These hybrid FETs become strongly competitive candidates for devices in flexible integrated circuits with low cost, large area, low-energy consumption and high performances.
Apolygus lucorum effector Al6 promotes insect feeding performance on soybean plants: RNAi analysis and feeding behaviour study with electrical penetration graph

The mirid bug Apolygus lucorum, a dominant mirid species in northern China, is a notorious polyphagous pest with more than 200 hosts, including several major crops such as cotton and soybean, resulting in massive economic loss. Studies of insect salivary effectors may provide a novel control strategy for A. lucorum. An A. lucorum effector, that is, Al6, that inhibits plant immunity by using glutathione peroxidase to repress reactive oxidase accumulation was previously identified. In this study, we further explored the molecular functions of Al6 associated with feeding behaviour and insect survival on soybean, a major host of A. lucorum, using RNA interference and electrical penetration graph (EPG) techniques. We initially observed the injury symptom of this mirid bug and characterized feeding behaviour on soybean leaves using EPG. Our results revealed that A. lucorum preferred to feed on young plant organs such as tender leaves, shoots and buds. This mirid bug used cell rupture as a feeding strategy to ingest cell contents from plant tissues. Subsequently, we silenced the Al6 gene using RNAi and investigated the feeding behaviour, honeydew excretion, body weight, and survival rates of A. lucorum on soybean after Al6 knockdown. Our results demonstrated that silencing of Al6 significantly reduced feeding duration, amount of honeydew secretion, body weight, and survival rates of A. lucorum. Thus, our findings provide a novel molecular target of plant‐mediated RNAi for the control of A. lucorum.
Hopf bifurcation and symmetry: travelling and standing waves on the circle

Synopsis In this paper we consider Hopf bifurcation in the presence of O(2) symmetry. The system of reaction diffusion equations ut, = D(µ)uxx + f(µ, u) provided with periodic boundary conditions may serve as a model problem. We prove the bifurcation of a torus of standing waves and two circles of travelling waves and we compute the stability (with asymptotic phase) of these periodic solutions, giving explicit formulae. Finally we demonstrate how a small perturbation which breaks part of the symmetry leads to secondary bifurcation.