Miracle-dz/UniFAR-FTUs huggingface dataset:
The VEGFC/VEGFR3 pathway in the malignancy of ovarian carcinoma

Vascular endothelial growth factor C (VEGFC) promotes tumor progression in several tumor types, mainly through the stimulation of lymphangiogenesis and lymphatic metastasis. The expression and biological significance of the VEGFCNEGFR3 pathway in ovarian cancer growth and dissemination has been investigated in this thesis using ovarian carcinoma cell lines and tumor animal models. In patient-derived ovarian carcinoma xenografts (HOC), high levels of soluble VEGFC in ascites and serum were detected, in association with disease progression and tumor burden. Peak VEGFC expression preceded para-aortic lymph node infiltration by HOCS neoplastic cells. Histological detection of tumor cells in blood and lymphatic vessels indicated both hematogenous and lymphatic dissemination. VEGFC was over-expressed in the VEGFR3-positive and luciferase-expressing 1A9 and IGROV1 ovarian cancer cells. In vitro, VEGFC released by the expressing turnor cells stimulated turnor cell migration in an autocrine manner. In vivo, over-expression of VEGFC promoted . IGROVl dissemination after orthotopic intraovarian transplantation in nude mice. VEGFC released in serum of mice correlated with tumor burden and metastasis. Cediranib, a small molecule receptor tyrosine kinase inhibitor of VEGFR1-3 and c-Kit, inhibited in vivo metastasis of VEGFC-overexpressing [GROVI and in vitro autocrine effects on turnor cell migration; cediranib improved the survival of mice bearing the four HOC xenografts analyzed. The therapeutic benefit was proportional to soluble VEGFC levels in serum and ascites and to VEGFR3 expression by tumor cells. Different schedules of cediranib were tested on HOC8 xenograft, The survival benefit of cediranib in maintenance regimen (14 weeks) was superior to 3-weeks treatment. A significant prolongation of mice survival was observed in mice treated with advanced tumor. Treatment benefits were improved combining cediranib with chemotherapy (paclitaxel plus cisplatin). These findings suggest that the VEGFC/VEGFR3 pathway acts as an enhancer of ovarian cancer progression through autocrine and paracrine mechanisms, hence offering a potential target for therapy.
Immunoglobulin heavy chains are sufficient to determine most B cell clonal relationships1

B cell clonal expansion is vital for adaptive immunity. High-throughput B cell receptor (BCR) sequencing enables investigating this process, but requires computational inference to identify clonal relationships. This inference usually relies on only the BCR heavy chain, as most current protocols do not preserve heavy:light chain pairing. The extent to which paired light chains aids inference is unknown. Using human single-cell paired BCR datasets, we assessed the ability of heavy chain-based clonal clustering to identify clones. Of the expanded clones identified, <20% grouped cells expressing inconsistent light chains. Heavy chains from these misclustered clones contained more distant junction sequences and shared fewer V segment mutations than the accurate clones. This suggests that additional heavy chain information could be leveraged to refine clonal relationships. Conversely, light chains were insufficient to refine heavy chain-based clonal clusters. Overall, the BCR heavy chain alone is sufficient to identify clonal relationships with confidence.
3D light sheet fluorescence microscopy of lungs to dissect local host immune - Aspergillus fumigatus interactions

Aspergillus fumigatus is an opportunistic fungal pathogen that can cause life-threatening invasive lung infections in immunodeficient patients. The cellular and molecular processes of infection during onset, establishment and progression are highly complex and depend on both fungal attributes and the immune status of the host. Therefore, preclinical animal models are paramount to investigate and gain better insight into the infection process. Yet, despite their extensive use, commonly employed murine models of invasive pulmonary aspergillosis are not well understood due to analytical limitations. Here we present quantitative light sheet fluorescence microscopy (LSFM) to describe fungal growth and the local immune response in whole lungs at cellular resolution within its anatomical context. We analyzed three very common murine models of pulmonary aspergillosis based on immunosuppression with corticosteroids, chemotherapy-induced leukopenia or myeloablative irradiation. LSFM uncovered distinct architectures of fungal growth and degrees of tissue invasion in each model. Furthermore, LSFM revealed the spatial distribution, interaction and activation of two key immune cell populations in antifungal defense: alveolar macrophages and polymorphonuclear neutrophils. Interestingly, the patterns of fungal growth correlated with the detected effects of the immunosuppressive regimens on the local immune cell populations. Moreover, LSFM demonstrates that the commonly used intranasal route of spore administration did not result in the desired intra-alveolar deposition, as more than 60% of fungal growth occurred outside of the alveolar space. Hence, LSFM allows for more rigorous characterization of murine models of invasive pulmonary aspergillosis and pinpointing their strengths and limitations. IMPORTANCE The use of animal models of infection is essential to advance our understanding of complex host-pathogen interactions that take place during Aspergillus fumigatus lung infections. As in the case of humans, mice need to be immunosuppressed to become susceptible to invasive pulmonary aspergillosis, the most serious infection caused by A. fumigatus. There are several immunosuppressive regimens that are routinely used to investigate fungal growth and/or immune responses in murine models of invasive pulmonary aspergillosis (IPA). However, the precise consequences that each immunosuppressive model has on the local immune populations and for fungal growth are not completely understood. Here we employed light sheet fluorescence microscopy (LSFM) to analyze whole lungs at cellular resolution, to pin down the scenario commonly used IPA models. Our results will be valuable to optimize and refine animal models to maximize their use in future research. VISUAL ABSTRACT Quantitative light sheet fluorescence microscopy to dissect local host-pathogen interactions in the lung after A. fumigatus airway infection.
A homeopathic drug proving of Anthropoides paradiseus 30CH with subsequent comparison to the ethology of the substance

Introduction The purpose of this study was to conduct a homoeopathic drug proving of Anthropoides paradiseus 30CH and to subsequently compare the symptoms derived during the proving to the ethology of the animal from which the proving substance was derived. Methodology The homoeopathic proving of Anthropoides paradiseus 30CH was conducted as a randomised double-blinded placebo-controlled trial at the Durban University of Technology on thirty participants. Twenty percent of the participants received a placebo while the remaining eighty percent received the active substance of Anthropoides paradiseus 30CH which was manufactured according to methods 6, 8a and 10 of the German Homoeopathic Pharmacopoeia. After recruitment, a two-phase consent and a comprehensive initial consultation, participants who met the inclusion criteria were accepted into this study. Powders were ingested over a two-day period and thereafter the provers were monitored for a further five weeks. During the proving period, participants subjectively recorded their experiences in a journal and were monitored by the researcher. Following the proving period, journals were collected, and the data analysis took place. The symptoms of the verum group were converted to standard repertory and materia medica formats. The symptoms were then compared to the ethology of the animal from which the substance was derived so that similarities between the behaviour of the animal and the expressed symptom picture of the provers could be assessed. Results The proving of Anthropoides paradiseus 30CH produced symptoms in keeping with five hundred and seventy-four existing rubrics, and fifty-five new rubrics were created. The majority of rubrics were represented in the MIND, NOSE, STOMACH and DREAMS sections of the repertory. The general themes of dryness, thirst, increased or decreased energy, large appetite and laterality were seen. The common sensations were itching and heaviness. The mental themes which were clearly evident were: focus, lack of concentration, isolation, sociability, music, dance, exercise, anxiety, calmness and spirituality. Correlations between the behavioural, anatomical and physiological features of Anthropoides paradisus and the symptom picture produced by provers during the proving period was clearly evident. Conclusion Clearly observable symptoms were produced in healthy individuals following the administration of Anthropoides paradiseus 30CH. A clear correlation existed between the symptomatology produced during this proving and the ethology of Anthropoides paradiseus.
Design Pattern Detection and Visualization using Reverse Engineering

—Design Patterns are the most valuable and approachable solution for any software design issues. Pattern identification delivers important information to the designers. The proposed work here gives a detailed analysis of this solution and also helps in fulfilling the detection of design patterns in java. Since design is not tangible, it is hard to detect. The proposed application is functioned for all kinds of java based software where any person interested in understanding the code can use. The focus here is to detect the java design patterns and display them with the help of a proper GUI for easier understanding. Functionally, this tool gives an overall idea of the design pattern and its detection.
The influence of experienced effort on learning and choice of solution paths in a simple navigation task

In my dissertation, I am going to study the influence of experienced effort on learning and problem-solving behavior. In a simple navigation task on a computersimulated map, subjects have to acquire information on various levels of effort in different solution paths through experience. The experienced effort information allows subjects to improve their performance by finding faster solution paths on the map. I am planning to build ACT-R model to understand the underlying mechanisms. Specifically, I am interested in modeling the learning of the "current" effort and the "downstream" effort in ACTR theory, and how each of them can influence problemsolving behavior in the task.
Linear-time algorithms for dominators and related problems

This dissertation deals with several topics related to the problem of finding dominators in flowgraphs. The concept of dominators has applications in various fields, including program optimization, circuit testing and theoretical biology. We are interested both in asymptotically fast algorithms and in algorithms that are practical. We begin with an experimental study of various algorithms that compute dominators efficiently in practice. We describe two practical algorithms that have been proposed in the related literature: an iterative algorithm initially presented by Allen and Cocke and later refined by Cooper, Harvey and Kennedy, and the well-known algorithm of Lengauer and Tarjan. We discuss how to achieve efficient implementations, and furthermore, introduce a new practical algorithm. We present a thorough empirical analysis using real as well as artificial data. Then we present a linear-time algorithm for dominators implementable on the pointer machine model of computation. Previously, Alstrup, Harel, Lauridsen and Thorup gave a complicated linear-time algorithm for the random-access model. Buchsbaum, Kaplan, Rogers and Westbrook presented a simpler dominators algorithm, implementable on a pointer machine and claimed linear running time. However, as we show, one of their techniques cannot be applied to the dominators problem and, consequently, their algorithm does not run in linear time. Nonetheless, based on this algorithm, we show how to achieve linear running time on a pointer machine. Next we address the question of how to verify dominators. We derive a linear-time verification algorithm, which is much simpler than the known algorithms that compute dominators in linear time. Still, this algorithm is non-trivial and we believe it provides some new intuition and ideas towards a simpler dominators algorithm. Finally we study the relation of dominators to spanning trees. Our central result is a linear-time algorithm that constructs two spanning trees of any input flowgraph G, such that corresponding paths in the two trees satisfy a vertex-disjointness property we call ancestor-dominance . This result is related to the concepts of independent spanning trees and directed st-numberings, previously studied by various authors, and implies linear-time algorithms for these constructions.
FJM: fast join mechanism for end host multicast

We propose fast join mechanism to search potential parents for new members in end host multicast. An existing method searches EM-tree one step at a time to find a potential parent. The existing search method causes long join latency. To search quickly, we search EM-tree two steps at a time. In other words, we search children and grandchildren at the same time. We look at the performance of fast join mechanism using the following metrics: cost and search time by the number of group members and degree limit. Simulation results show that our mechanism searches potential faster than the existing method.
The coupling mechanism of reassembly quality with uncertainty of remanufactured parts

Purpose The uncertainty of remanufacturing parts is a key factor affecting the quality of remanufactured products. Therefore, the purpose of this paper is to measure the uncertainty of remanufactured parts and study the coupling mechanism of reassembly quality. Design/methodology/approach First, uncertainty of remanufactured parts is analyzed, and the uncertainty measure model for remanufacturing parts based on entropy is constructed. Second, the nonlinear mapping model between the uncertainty and reassembly quality were studied using Gauss-Newton iterative method to reveal the coupling mechanism between uncertainty of remanufacturing parts and reassembly quality. Finally, the model is verified in the reassembly process of remanufacturing cylinder head. Findings The method can guide reassembly operations to improve the reassembly quality with uncertainty of remanufactured parts. Originality/value This study provides practical implications by developing a multivariate nonlinear mapping model for reassembly quality based on entropy to determine the uncertainty factors that affect the reassembly quality significantly and then correct the reassembly operation to better optimize the allocation of remanufacturing production resources. The study also theoretically contributes to reveal the coupling mechanism of reassembly quality with the uncertainty of remanufactured parts.
CellMix: a comprehensive toolbox for gene expression

Summary: Gene expression data are typically generated from heterogeneous biological samples that are composed of multiple cell or tissue types, in varying proportions, each contributing to global gene expression. This heterogeneity is a major confounder in standard analysis such as differential expression analysis, where differences in the relative proportions of the constituent cells may prevent or bias the detection of cell-specific differences. Computational deconvolution of global gene expression is an appealing alternative to costly physical sample separation techniques and enables a more detailed analysis of the underlying biological processes at the cell-type level. To facilitate and popularize the application of such methods, we developed CellMix ,a nR package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples. Availability and Implementation: The CellMix package builds on R/BioConductor and is available from http://web.cbio.uct.ac.za/ � renaud/CRAN/web/CellMix. It is currently being submitted to BioConductor. The package’s vignettes notably contain additional information, examples and references. Contact: renaud@cbio.uct.ac.za
The small noncoding RNA sr8384 determines solvent synthesis and cell growth in industrial solventogenic clostridia

Small noncoding RNAs (sncRNAs) are crucial regulatory molecules in organisms and are well known not only for their roles in the control of diverse essential biological processes but also for their value in genetic modification. However, to date, in gram-positive anaerobic solventogenic clostridia (which are a group of important industrial bacteria with exceptional substrate and product diversity), sncRNAs remain minimally explored, leading to a lack of detailed understanding regarding these important molecules and their use as targets for genetic improvement. Here, we performed large-scale phenotypic screens of a transposon-mediated mutant library of Clostridium acetobutylicum, a typical solventogenic clostridial species, and discovered a novel sncRNA (sr8384) that functions as a determinant positive regulator of growth and solvent synthesis. Comparative transcriptomic data combined with genetic and biochemical analyses revealed that sr8384 acts as a pleiotropic regulator and controls multiple targets that are associated with crucial biological processes, through direct or indirect interactions. Notably, modulation of the expression level of either sr8384 or its core target genes significantly increased the growth rate, solvent titer and productivity of the cells, indicating the importance of sr8384-mediated regulatory network in C. acetobutylicum. Furthermore, a homolog of sr8384 was discovered and proven to be functional in another important Clostridium species, C. beijerinckii, suggesting the potential broad role of this sncRNA in clostridia. Our work showcases a previously unknown potent and complex role of sncRNAs in clostridia, providing new opportunities for understanding and engineering these anaerobes, including pathogenic Clostridium species. IMPORTANCE The discovery of sncRNAs as new resources for functional studies and strain modifications are promising strategies in microorganisms. However, these crucial regulatory molecules have hardly been explored in industrially important solventogenic clostridia. Here, we identified sr8384 as a novel determinant sncRNA controlling cellular performance of solventogenic Clostridium acetobutylicum and performed detailed functional analysis, which is the most in-depth study of sncRNAs in clostridia to date. We reveal the pleiotropic function of sr8384 and its multiple direct and indirect crucial targets, which represents a valuable source for understanding and optimizing this anaerobe. Of note, manipulation of these targets leads to improved cell growth and solvent synthesis. Our findings provide a new perspective for future studies on regulatory sncRNAs in clostridia.
Evaluating Reference Services: A Practical Guide

The author's proven techniques will explain how to: create a planning strategy to avoid future pitfalls; select the best evaluation tools for specific needs; understand the strengths and weaknesses of various collection tools; collect and analyze data more effectively; communicate results to improve reference services and maintain funding; and satisfy the needs of library users.
Trust-Based Service Selection

Service Oriented Architecture (SOA) is an architectural style that builds enterprise solutions based on services. In SOA, the lack of trust between different parties affects the adoption of such architecture. Trust is as significant a factor for successful online interactions as it is in real life communities, and consequently, it is an important factor that is used as a criterion for service selection. In the context of online services and SOA, the literature review shows that trust is not mature and does not reflect trust as it is in the online world in terms of trust definition and the consideration of the essentials trust aspects that reflects the nature of trust. This thesis proposes a trust-based service selection solution, which requires establishing trust for services and supporting service selection based on trust. This work considers building trust for service providers besides rating services, an area that is neglected in the services trust literature. This work follows progressive steps to arrive at a solution. First, this work develops a trust definition and identifies trust principles, which cover different aspects of trust. Next, SOA is extended to build a trust-based SOA that supports trust-based service selection. In particular, a new component, the trust mediator, which is responsible for trust establishment is added to the architecture. Accordingly, a trust mediator framework is built according to the trust definition and principles to identify its main components. Subsequently, this work identifies the trust information, or metrics, for services and service providers. Accordingly, trust models are built to evaluate trust rates for the applicable metrics, services, and service providers. Moreover, this work addresses the trust bootstrapping challenge in the literature. The proposed trust bootstrapping approach addresses different challenges in the literature such as whitewashing and cold start challenges. This approach is implemented through experiments, evaluations, and scenarios.
A combined CELP/Reed-Solomon codec for mobile radio applications

The performance of an error-protected speech codec for mobile radio applications is investigated. The speech codec is a 4 kb/s variation of the proposed Federal Standard 1016 CELP. The major difference is the use of a trained codebook (as opposed to a stochastic codebook in the proposed standard). The channel codec on the other hand, consists of a bank of rate-compatible punctured Reed-Solomon (RS) codes. The two subsystems are combined in an optimal fashion, according to the sensitivity of the speech elements. This implies that the most sensitive bits are protected by the most powerful RS codes, while the least sensitive bits are (either uncoded or) protected by the least powerful code. The performance of such a combined codec under different sets of system parameters and channel conditions is studied. In all cases, though, the aggregate rate is fixed at about 6.4 kb/s. The simulation results show that under the condition that there is no interleaving delay, the resulting codec can provide good quality speech at a channel bit error rate as high as 10/sup -2/. <<ETX>>
Multiple models and parallel solving with Mosel

This paper describes several examples of sequential and parallel solving of multiple models with Mosel. Without being able to give an exhaustive list of possible configurations, the examples showcase different uses of the Mosel module mmjobs, such as concurrent execution of several instances of a model, the (sequential) embedding of a submodel into a master, and the implementation of decomposition algorithms (Dantzig-Wolfe and Benders decomposition). From a more technical point of view, topics discussed in this paper include model management, synchronization of concurrent models, and the use of the shared memory IO driver.