Miracle-dz/UniFAR-FTUs huggingface dataset:
The Deoxyribonucleases of Pathogenic Lancefield Streptococci

Deoxyribonucleases (DNases) are abundant among the pathogenic streptococci, with most species 19 harbouring genes for at least one. Despite their prevalence, however, the role for these extracellular 20 enzymes is still relatively unclear. The DNases of the Lancefield group A Streptococcus , S. pyogenes 21 are the best characterised, with a total of eight DNase genes identified so far. Six are known to be 22 associated with integrated prophages. Two are chromosomally encoded, and one of these is cell-wall 23 anchored. Homologues of both prophage-associated and chromosomally encoded S. pyogenes 24 DNases have been identified in other streptococcal species, as well as other unique DNases. A major 25 role identified for streptococcal DNases appears to be in the destruction of extracellular traps 26 produced by immune cells, such as neutrophils, to ensnare bacteria and kill them. These traps are 27 composed primarily of DNA which can be degraded by the secreted and cell wall anchored 28 streptococcal DNases. DNases can also reduce TLR-9 signalling to dampen the immune response and 29 produce cytotoxic deoxyadenosine to limit phagocytosis. Upper respiratory tract infection models of 30 S. pyogenes have identified a role for DNases in potentiating infection and transmission, possibly by 31 limiting the immune response or through some other unknown mechanism. Streptococcal DNases 32 may also be involved in interacting with other microbial communities through communication, 33 bacterial killing and disruption of competitive biofilms, or control of their own biofilm production. The 34 contribution of DNases to pathogenesis may therefore be wide ranging and extend beyond direct 35 interference with the host immune response. The DNases of group A Streptococcus are by far the best characterised and currently eight have been 90 identified; spnA , spdB , sda1 , sda2 , spd1 , spd3 , spd4 and sdn . Both spn A and spdB are encoded on the 91 chromosome and have been shown to be common to all S. pyogenes isolates tested, existing as different alleles related to the emm genotype of the isolate [18, 19]. We confirmed the presence of both spnA and spdB in all available completed S. pyogenes genomes (NCBI, n=54) representing 25 different emm genotypes. SpnA is the only S. pyogenes DNase to be identified that is cell wall anchored via an LPXTG motif [19].
TransplantationMicroglia in Relation to Neuronal Retina T Cell Immunity Induced by Allogeneic

Microglia share a lineage relationship with bone marrow-derived monocytes/macrophages and dendritic cells, and their inclusion in retinal and brain transplants may function as “passenger leukocytes. ” In other solid allografts, passenger leukocytes are the primary sources of immunogenicity, triggering alloimmune rejection. We have conducted a series of in vitro and in vivo studies examining the capacity of microglia cultured from forebrain to activate alloreactive T cells and to induce and elicit alloimmunity. Cultured microglia expressed class II MHC molecules and costimulatory molecules (B7-1, B7-2, and CD40), and they secreted IL-12. Cultured microglia injected s.c. into naive recipients induced allospeciﬁc delayed hypersensitivity and elicited delayed hypersensitivity directed at alloantigens. Cultured microglia differed from conventional APCs by secreting signiﬁcant amounts of mature TGF- b 2, but smaller amounts of IL-12. Moreover, while both cultured microglia and conventional APC stimulated T cell proliferation in vitro, microglia directed the responding T cells toward the Th2 pathway in which IL-4, but not IL-2 and IFN- g , was secreted. The abilities of microglia to secrete TGF- b 2, to stimulate alloreactive Th2 cells, and to induce anterior chamber associated immune deviation when injected into the eye of naive allogeneic mice suggest that they are not typical passenger leukocytes. The unique functional properties of cultured microglia may account for the capacity of neonatal retinal tissue transplanted into the eye to alter the systemic alloimmune response in a manner that delays, but does not prevent, graft rejection. The Journal of Immunology, 1999, 162: 4482–4489. alloreactive T
The DynB Sparse Matrix Format Using Variable Sized 2D Blocks for Efﬁcient Sparse Matrix Vector Multiplications with General Matrix Structures

—The Sparse Matrix Vector Multiplication is an important operation on sparse matrices. This operation is the most time consuming operation in iterative solvers and therefore an efﬁcient execution of that operation is of great importance for many applications. Numerous different storage formats that store sparse matrices efﬁciently have already been established. Often, these storage formats utilize the sparsity pattern of a matrix in an appropiate manner. For one class of sparse matrices the nonzero values occur in small dense blocks and appropriate block storage formats are well suited for such patterns. But on the other side, these formats perform often poor on general matrices without an explicit / regular block structure. In this paper, the newly developed sparse matrix format DynB is introduced. The aim is to efﬁciently use several optimization approaches and vectorization with current processors, even for matrices without an explicit block structure of nonzero elements. The DynB matrix format uses 2D rectangular blocks of variable size, allowing ﬁll-ins per block of explicit zero values up to a user controllable threshold. We give a simple and fast heuristic to detect such 2D blocks in a sparse matrix. The performance of the Sparse Matrix Vector Multiplication for a selection of different block formats and matrices with different sparsity structures is compared. Results show that the beneﬁt of blocking formats depend – as to be expected – on the structure of the matrix and that variable sized block formats like DynB can have advantages over ﬁxed size formats and deliver good performance results even for general sparse matrices.
University of Birmingham Time correlation functions of equilibrium and nonequilibrium Langevin dynamics

We study the time correlation functions of coupled linear Langevin dynamics with and without inertial eﬀects, both analytically and numerically. The model equation represents the physical behavior of a harmonic oscillator in two or three dimensions in the presence of friction, additive noise, and an external ﬁeld with both rotational and deformational components. This simple model plays pivotal roles in understanding more complicated processes. The analytical solution presented serves as a test of numerical integration schemes, and its derivation is presented in a fashion that allows it to be repeated directly in a classroom. While the results in the absence of ﬁelds (equilibrium) or conﬁnement (free particle) are omnipresent in the literature, we write down, apparently for the ﬁrst time, the full nonequilibrium results that may correspond, e.g., to a Hookean dumbbell embedded in a macroscopically homogeneous shear or mixed ﬂow ﬁeld. We demonstrate how the inertial results reduce to their noninertial counterparts in the nontrivial limit of vanishing mass. While the results are derived using basic integrations over Dirac delta dis- tributions, we also provide alternative approaches involving (i) Fourier transforms, which seem advantageous only if the measured quantities also reside in Fourier space, and (ii) a Fokker–Planck equation and the moments of the probability distribution. The results, veriﬁed by numerical experiments, provide additional means of measuring the performance of numerical methods for such systems. It should be emphasized that this article provides speciﬁc details regarding the derivations of the time correlation functions as well as the implementations of various numerical methods, so that it can serve as a standalone piece for lessons in the framework of Itˆo stochastic diﬀerential equations and calculus.
Measuring Self-Efﬁcacy in Engineering Courses – Impact of Learning Style Preferences

Self-efficacy is an important outcome of engineering education as it relates to students' feelings, thoughts, motivations and behaviors. The key element of self-efficacy construct is a self-belief in one's abilities and has been described in detail in terms of Bandura's Social Cognitive Theory. Measuring self-efficacy of students in engineering courses is an important element of evaluating the overall effectiveness of engineering education. Traditional methods of judging student learning outcomes include quizzes, homework, exams, and course projects, with a primary focus on measuring student skills. It is important that, along with mastering the skills, students should also possess self-belief that they will be able to perform required tasks with those skills. An important research question is: How should self-efficacy be measured in engineering courses? This paper addresses this question by highlighting the results of a longitudinal study conducted on students in engineering modeling and design (junior-level) courses at Arkansas Tech University. This course is selected because the teaching method is based on project-based learning activities. Using the collected data, we have analyzed the effect of learning style preference on the perception of self-efficacy. Previous research has demonstrated that students have different preferred learning styles, and they approach learning new information in different ways. Our collected data includes student responses on their learning styles, including lectures/discussions, books/related written material, video/movies/media, hands-on activities, and a hybrid method. Paired sample t-tests and one-way analysis of variance (ANOVA) are used to analyze the collected data. These methods allow us to determine any statistically significant differences between the self-efficacy scores at the start and end of the course. We also determine the impact of learning style preference on students’ perception of self-efficacy. Based on the collected data, results indicated that the self-efficacy of students improved equally using project-based learning techniques, regardless of their learning style preferences.
Association between male circumcision and human papillomavirus infection in males and females: a systematic review, meta-analysis, and meta-regression

Background: Human papillomavirus (HPV) infection is a necessary cause of cervical cancer and is associated with anal, penile, vaginal, and vulvar cancers. Previous studies have suggested a protective effect of male circumcision (MC) on HPV infections in males, and that this protection may be conferred to their female sexual partners. We synthesized the available evidence on the association between MC and HPV infections in males and females. Methods: We performed a systematic review and meta-analysis of the effect of MC on the prevalence, incidence, and clearance of genital HPV infections in heterosexual males and their female sexual partners. We searched multiple databases for studies that assessed MC status and tested for the presence of genital HPV DNA. We used random-effects meta-analysis models to estimate summary measures of effect and 95% confidence intervals (CI) for the prevalence, incidence, and clearance of HPV infections in males and females. We assessed effect modification for prevalence in males using random-effects meta-regression. Findings: We included 32 publications encompassing 25 unique study populations. MC was associated with decreased odds of prevalent HPV infections (odds ratio 0.45, CI 0.34-0.61), a reduced rate of incident HPV infections (incidence rate ratio 0.69, CI 0.57-0.83), and an increased risk of clearing HPV infections (risk ratio 1.44, CI 1.28-1.61) at the glans penis. Effect modification by sampling site was observed for HPV prevalence in males, with greater protection conferred by MC at the glans than the shaft (OR 0.68, 95% CI 0.48-0.98). Females with circumcised sexual partners were at reduced risk for all outcomes. Interpretation: MC protects against various HPV infection outcomes, especially at the glans, and may be a viable prophylactic strategy in regions with a high burden of HPV-associated disease where the HPV vaccine is not commercially available. That the protective effect of MC on HPV infection prevalence varies by penile site has important implications for epidemiologic studies of HPV transmission.
On properties of local additive estimation based on the smooth backfitting estimator.

We study properties of local additive estimation based on the smooth backfitting estimator by Mammen, Linton and Nielsen (1999). The local additive estimator defined as a restricted additive estimator and thus inherits locally properties of additive estimator. Our asymptotic analysis shows that this provides a new class of nonparametric regression estimators for high dimensional problem. Simulation studies are used to assess finite sample performance.
Comparison of Estimators of the Weibull Distribution

We compare the small sample performance (in terms of bias and root mean squared error) of the L-moment estimator of a three-parameter Weibull distribution with maximum likelihood estimation (MLE), moment estimation (MoE), least-square estimation (LSE), the modified MLE (MMLE), the modified MoE (MMoE), and the maximum product of spacing (MPS). Overall, the LM method has a tendency to perform well as it is almost always close to the best method of estimation. The ML performance is remarkable even at a small sample size of n = 10 when the shape parameter β lies in the [1.5, 4] range. The MPS estimator dominates others when 0.5 ≤ β < 1.5. For large β ≥ 6, MMLE outweighs others in samples of size n ≥ 50, whereas LM is preferred in samples of size n ≤ 20.
Data Center Workload Analysis in Multi-Source RSMAD’s Test Environment

—The paper presents the system model of Radio System for Monitoring and Acquisition of Data from Traffic Enforcement Cameras, noting the used network connections and their effective throughput. The article presents the results of test verifying the performance of selected elements of designed system, in terms of image data transmission from multiple sources. Threats that could be caused by large amounts of data transmitted from multiple sources to the database server have been identified.
Retinoic Acid Bone Marrow Reveals a Critical Role of Generation of Mucosal Dendritic Cells from

It is unknown how dendritic cells (DCs) become specialized as mucosal DCs and maintain intestinal homeostasis. We report that a subset of bone marrow cells freshly isolated from C57BL/6 mice express the retinoic acid (RA)-synthesizing enzyme aldehyde dehydrogenase family 1, subfamily A2 (ALDH1a2) and are capable of providing RA to DC precursors in the bone marrow microenvironment. RA induced bone marrow-derived DCs to express CCR9 and ALDH1a2 and conferred upon them mucosal DC functions, including induction of Foxp3 + regulatory T cells, IgA-secreting B cells, and gut-homing molecules. This response of DCs to RA was dependent on a narrow time window and stringent dose effect. RA promoted bone marrow-derived DC production of bioactive TGF- b by inhibiting suppressor of cytokine signaling 3 expression and thereby enhancing STAT3 activation. These RA effects were evident in vivo, in that mucosal DCs from vitamin A-deﬁcient mice had reduced mucosal DC function, namely failure to induce Foxp3 + regulatory T cells. Furthermore, MyD88 signaling enhanced RA-educated DC ALDH1a2 expression and was required for optimal TGF- b production. These data indicate that RA plays a critical role in the generation of mucosal DCs from bone marrow and in their functional activity. The Journal of Immunology , 2010, 185: 000–000. time and stringent for
Strategic Schemas and Corporate Environmental Performance: Theorizing, Testing, and Enriching an Interpretive Framework

Environmental science draws public and scholarly attention to the disquieting deterioration of the global ecosystem and its impacts on human activities. Environment and management researchers have been looking at the role of business organizations in this phenomenon, both as contributors to degradation and as leaders in restoration, thus bringing forth the issue of corporate environmental performance (CEP). Research on the antecedents of CEP has examined a variety of internal and external predictors, but has surprisingly overlooked strategic schemas, which are often implied in this research and recognized as prompters for social and environmental actions. Management research needs further exploration of strategic schemas and lacks a framework that relates schemas to corporate environmental performance. The three papers in this doctoral thesis attempt to fill these gaps. The first paper proposes an interpretive framework on CEP that integrates literatures on schemas and sustainability. This framework offers an original view of schema interaction and evolution, where schema interaction models traditionally understood as discrete are shown to be interrelated. The framework also provides an explanation for business organizations’ limited success in addressing global environmental issues. The second paper validates part of the framework by testing a set of relationships between schemas, organizational actions, and CEP. Combining content analysis with quantification techniques, this paper finds that although firms gather information and learn about natural environmental issues, they fail to translate their knowledge into appropriate actions. Perhaps as a result, corporate environmental initiatives correlate with a deterioration of CEP. The third paper employs cognitive mapping to examine the discourse on sustainability produced by an international trade association and four member companies over a period of eleven years. This study reveals that disclosed schemas change through two fundamental mechanisms of growth and reduction which can be used to explain all schema evolution. It also unveils the existence of two distinct types of schema content: core and peripheral content. Although schemas tend to grow incrementally, peripheral content undergoes frequent growth and reduction, while core content grows and shapes the meaning attributed to newer content. Larger companies use the trade association as a vector to disseminate their schemas on sustainability and influence the schemas of smaller firms and possibly of the industry as whole by adopting and promoting new sustainability practices early. Together, these three papers provide an original and testable framework to understand CEP from a cognitive perspective, qualify the relationship between strategic schemas and CEP, and reveal underlying mechanisms of schema evolution.
A Survey of Internet Protocol and Architectures in the Context of Emerging Technologies

—The Internet technologies need an overhaul to support next-generation of applications requiring communications between machines and humans. This paper is a survey of the state of current internetworking architecture and its engineering properties. The purpose of this paper is to highlight the aging of original design goals and motivations. We aim to formulate a new set of guidelines that maybe used to postulate design principles of the new network architectures.
Cutoff-cladding waveguides: Subdiffraction guided modes near cutoff

We propose a class of waveguides operating near cutoff such that electromagnetic energy is mainly bound to the cladding rather than the dielectric core to achieve subdiffraction confinement of light. The cladding incorporates an alternating stack of thin films that exhibit uniaxial form birefringence with a high contrast between the effective principal dielectric constants. In contrast to conventional dielectric waveguides, the effective modal length for the fundamental mode of the proposed waveguide diverges at a much slower rate for core thicknesses less than a twentieth of the illumination wavelength, and is comparable to that attainable for plasmonic waveguides. The proposed waveguide can be exploited for important applications such as optoelectronic integration, and the fundamental mode exhibits a near-uniform spatial field distribution potentially allowing for position-independent spontaneous emission enhancement effects.
Comparison on Channel Characteristics at 3.5 GHz and 28 GHz

In this paper, the channel measurements at 28 GHz and 3.5 GHz were conducted in the same indoor shopping mall scenario for the purpose of comparing the channel propagation characteristics between millimeter wave and centimeter wave. In the measurement of 28 GHz, a high gain steerable horn antenna is rotated with the step of 5 degrees in azimuth to synthesize the omnidirectional signal array for collecting the angular information at receiver (Rx) while a sector antenna at transmitter (Tx). And the raw data at 3.5 GHz is collected by a MIMO measurement equipment of an omnidirectional array (ODA) at Rx with an uniform array (UPA) at Tx. Based on the raw data and channel estimation algorithm space-alternating generalized expectation-maximization (SAGE), Power Angular Spectrum (PAS) and Root Mean Square (RMS) Angular Spread of Azimuth of arrive (ASA) are calculated. After that, the PAS at each measured spot are compared and analyzed. Meanwhile, the relationship between RMS ASA and distance in the Line of sight (LoS) are observed at 3.5 GHz and 28 GHz. Finally, the fitted distributions and parameters of the RMS ASA at 3.5 GHz and 28 GHz are compared with the Model-A proposed in IMT-2020 channel model.
Pseudorandom-Frequency Sinusoidal Injection for Position Sensorless IPMSM Drives Considering Sample and Hold Effect

The acoustic noises caused by the fixed-frequency signal injection scheme limit the applications of saliency tracking based sensorless control methods for interior permanent magnet synchronous machine (IPMSM) drives at low-speed operation. In this paper, a pseudorandom-frequency sinusoidal injection (PRFSI) considering the sample and hold effect in practical applications is proposed to reduce the undesired acoustic noises. Since the power spectral density (PSD) of the excited high-frequency (HF) current could be dispersed and continuously distributed with PRFSI, the additional HF acoustic noises can be reduced. Through the comparative analysis of HF response currents PSD results for PRFSI and fixed-frequency sinusoidal injection (FFSI), the principle of acoustic noises reduction with PRFSI is analyzed theoretically. Furthermore, the optimal selection of the injection signals is derived considering the sample and hold effect. Whereby, a comparative evaluation of the proposed PRFSI versus FFSI is carried out on a 2.2-kW position sensorless IPMSM drive, in terms of position estimation and PSD results, which verifies the effectiveness of the proposed scheme.
Homogenisation model for calculating multi‐point grounding current of transformer core

Multi-point grounding of the core is one of the common transformer faults. In this study, a homogenisation model based on the finite element method is developed for calculating multi-point grounding current of the transformer core. The equivalent conductivity in the direction normal to the laminations is determined by the analysis of fault current distribution and calculation of anisotropic resistances of the iron core, especially, considering the influence of insulation coating on the silicon steel sheet. The validity of the proposed model is verified by comparing the three-dimensional finite element simulation results with the experimental results. Finally, two typical faults are simulated to further study the characteristics of multi-point grounding current based on a distribution transformer, which may be useful for the optimisation of transformer core design.