Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced shedding of extracellular vesicles from amoeboid prostate cancer cells

The gene encoding the cytoskeletal regulator DIAPH3 is lost at high frequency in metastatic prostate cancer, and DIAPH3 silencing evokes a transition to an amoeboid tumor phenotype in multiple cell backgrounds. This amoeboid transformation is accompanied by increased tumor cell migration, invasion, and metastasis. DIAPH3 silencing also promotes the formation of atypically large (>1 μm) membrane blebs that can be shed as extracellular vesicles (EV) containing bioactive cargo. Whether loss of DIAPH3 also stimulates the release of nano-sized EV (e.g., exosomes) is not established. Here we examined the mechanism of release and potential biological functions of EV shed from DIAPH3-silenced and other prostate cancer cells. We observed that stimulation of LNCaP cells with the prostate stroma-derived growth factor heparin-binding EGF-like growth factor (HB-EGF), combined with p38MAPK inhibition caused EV shedding, a process mediated by ERK1/2 hyperactivation. DIAPH3 silencing in DU145 cells also increased rates of EV production. EV isolated from DIAPH3-silenced cells activated AKT1 and androgen signaling, increased proliferation of recipient tumor cells, and suppressed proliferation of human macrophages and peripheral blood mononuclear cells. DU145 EV contained miR-125a, which suppressed AKT1 expression and proliferation in recipient human peripheral blood mononuclear cells and macrophages. Our findings suggest that EV produced as a result of DIAPH3 loss or growth factor stimulation may condition the tumor microenvironment through multiple mechanisms, including the proliferation of cancer cells and suppression of tumor-infiltrating immune cells.
Large scale MANET emulations using U.S. Army waveforms with application: VoIP

Large scale experimentation and analysis of mobile ad-hoc networks (MANETs) is an expensive and time consuming task. Even with the best planning, the environment at the time of the experiment is unpredictable, making large scale controlled experiments difficult to impossible to perform. At the U.S. Army Research Laboratory (ARL) we are using the EMANE (Extensible Mobile Ad-hoc Network Emulation) environment to supplement and extend live experiments in a controlled environment. Our emulation environment includes locally developed tools for real-time path loss calculations using the Longley-Rice irregular terrain model implemented on GPGPUs (General Purpose Graphics Processing Units). This real-time path loss calculation capability allows for the integration of virtual devices with live experiments and forces modeling and simulations. Live experiment integration is identified as one method to increase the perceived scale of the MANET to live participants and increase the repeatability of the experiment. This emulation system is currently being scaled to 1000s of CPU cores and emulated radios through the use of high performance computing assets and approaches. We will present this emulation platform in the context of the performance analysis of a MANET application, namely VoIP (Voice over IP).
Quantum-holographic and classical Hopfield-like associative nnets: implications for modeling two cognitive modes of consciousness

Quantum bases of consciousness are considered with psychosomatic implications of three front lines of psychosomatic medicine (hesychastic spirituality, holistic Eastern medicine, and symptomatic Western medicine), as well as cognitive implications of two modes of individual consciousness (quantum-coherent transitional and altered states, and classically reduced normal states) alongside with conditions of transformations of one mode into another (considering consciousness quantum-coherence/classical-decoherence acupuncture system/nervous system interaction, direct and reverse, with and without threshold limits, respectively) - by using theoretical methods of associative neural networks and quantum neural holography combined with quantum decoherence theory. © 2005 Optical Society of America
Rapid Identification of Staphylococcus aureus and Methicillin Resistance by Flow Cytometry Using a Peptide Nucleic Acid Probe

ABSTRACT A total of 56 Staphylococcus aureus isolates incubated for 2 h in the presence or absence of oxacillin were analyzed by flow cytometry after labeling with an S. aureus-specific peptide nucleic acid (PNA) probe. Two defined ratios, the paired signal count ratio (PSCR) and the gate signal count ratio (GSCR), differentiated methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) with sensitivities of 100% each and specificities of 96% and 100%, respectively.
SOPHOROSE AS AN INDUCER OF CELLULASE IN TRICHODERMA VIRIDE

Mandels, Mary (Quartermaster Research and Engineering Center, Natick, Mass.), Fredrick W. Parrish, and Elwyn T. Reese. Sophorose as an inducer of cellulase in Trichoderma viride. J. Bacteriol. 83:400–408. 1962. —The impurity in glucose responsible for cellulase induction in Trichoderma viride QM 6a has been isolated and characterized as sophorose (2-O-β-d-glucopyranosyl-d-glucose). It is present at 0.0058% in reagent grade glucose. Sophorose is a very powerful inducer of cellulase for Trichoderma viride, being 2500 times as active as cellobiose. Modifications of sophorose, such as reduction or glycoside formation, destroy its inducing ability. The high activity of sophorose as an inducer is specific for T. viride.
Soluble syndecan‐1 level at diagnosis is an independent prognostic factor in multiple myeloma and the extent of fall from diagnosis to plateau predicts for overall survival

Syndecan‐1 (CD138) is a heparin sulphate proteoglycan that is over expressed on the surface of both normal and malignant plasma cells and actively shed from the cell surface (soluble syndecan‐1). Soluble syndecan‐1 has been shown to be an independent prognostic factor in myeloma but its role in prognostic classification requires further investigation. We have retrospectively measured soluble syndecan‐1 in 324 presentation samples and 154 plateau phase samples from the UK Medical Research Council Myeloma VIth trial. Log‐rank analysis showed that the presentation value of soluble syndecan‐1 is a highly significant prognostic factor when assessing survival from entry (χ2 = 14·92, P < 0·0001) and remains an important independent prognostic factor when considered in Cox regression models (P ≤ 0·02) with known independent factors. The magnitude of fall in soluble syndecan‐1 from presentation to plateau also had prognostic value when assessing overall survival from plateau (χ2 = 3·79, P = 0·05). In conclusion, this large study confirms that soluble syndecan‐1 level is a powerful independent prognostic factor both at diagnosis and at plateau phase.
BF-PSO-TS: Hybrid Heuristic Algorithms for Optimizing Task Schedulingon Cloud Computing Environment

Task Scheduling is a major problem in Cloud computing because the cloud provider has to serve many users. Also, a good scheduling algorithm helps in the proper and efficient utilization of the resources. So, task scheduling is considered as one of the major issues on the Cloud computing systems. The objective of this paper is to assign the tasks to multiple computing resources. Consequently, the total cost of execution is to be minimum and load to be shared between these computing resources. Therefore, two hybrid algorithms based on Particle Swarm Optimization (PSO) have been introduced to schedule the tasks; Best-Fit-PSO (BFPSO) and PSO-Tabu Search (PSOTS). According to BFPSO algorithm, Best-Fit (BF) algorithm has been merged into the PSO algorithm to improve the performance. The main principle of the modified BFSOP algorithm is that BF algorithm is used to generate the initial population of the standard PSO algorithm instead of being initiated randomly. According to the proposed PSOTS algorithm, the Tabu-Search (TS) has been used to improve the local research by avoiding the trap of the local optimality which could be occurred using the standard PSO algorithm. The two proposed algorithms (i.e., BFPSO and PSOTS) have been implemented using Cloudsim and evaluated comparing to the standard PSO algorithm using five problems with different number of independent tasks and resources. The performance parameters have been considered are the execution time (Makspan), cost, and resources utilization. The implementation results prove that the proposed hybrid algorithms (i.e., BFPSO, PSOTS) outperform the standard PSO algorithm
Knowledge‐based proteome profiling: Considering identified proteins to evaluate separation efficiency by 2‐D PAGE

Proteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biologically not significant. It was the aim of this study to use the knowledge of the biological context of proteins in order to establish optimised proteome profiling protocols. While 2‐D spot patterns of total cell protein fractions were found to poorly represent the true protein composition, purified subcellular protein fractions were found to better represent the protein composition of the analysed sample. The application of a standardised protocol to different kinds of cells revealed several striking observations. Firstly, the protein composition of cultured cells of various origins is very similar. Secondly, proteome alterations observed with the described protocols do make sense from a biologic point of view and may thus be considered as truly representative for the analysed samples. Thirdly, primary white blood cells isolated from different donors were found to show minor, but reproducible and significant individual differences. We designate the consideration of known properties of identified proteins in proteome profiles as a knowledge‐based approach. The present data suggest that this approach may tremendously help to improve the applied techniques and assess the results. We demonstrate that the fulfilment of well‐defined criteria of proteome profiles eventually results in reliable and biologically relevant data.
Robotically assisted treadmill exercise training for improving peak fitness in chronic motor incomplete spinal cord injury: A randomized controlled trial

Objective: To assess the effectiveness of robotically assisted body weight supported treadmill training (RABWSTT) for improving cardiovascular fitness in chronic motor incomplete spinal cord injury (CMISCI). Design: Pilot prospective randomized, controlled clinical trial. Setting: Outpatient rehabilitation specialty hospital. Participants: Eighteen individuals with CMISCI with American Spinal Injury Association (ASIA) level between C4 and L2 and at least one-year post injury. Interventions: CMISCI participants were randomized to RABWSTT or a home stretching program (HSP) three times per week for three months. Those in the home stretching group were crossed over to three months of RABWSTT following completion of the initial three month phase. Outcome measures: Peak oxygen consumption (peak VO2) was measured during both robotic treadmill walking and arm cycle ergometry: twice at baseline, once at six weeks (mid-training) and twice at three months (post-training). Peak VO2 values were normalized for body mass. Results: The RABWSTT group improved peak VO2 by 12.3% during robotic treadmill walking (20.2 ± 7.4 to 22.7 ± 7.5 ml/kg/min, P = 0.018), compared to a non-significant 3.9% within group change observed in HSP controls (P = 0.37). Neither group displayed a significant change in peak VO2 during arm cycle ergometry (RABWSTT, 8.5% (P = 0.25); HSP, 1.76% (P = 0.72)). A repeated measures analysis showed statistically significant differences between treatments for peak VO2 during both robotic treadmill walking (P = 0.002) and arm cycle ergometry (P = 0.001). Conclusion: RABWSTT is an effective intervention model for improving peak fitness levels assessed during robotic treadmill walking in persons with CMISCI.
The use of gene-expression profiling to identify candidate genes in human sepsis.

RATIONALE Our understanding of the pathophysiology of sepsis remains incomplete. Genomewide study offers an unbiased, system biology approach to examine the expression patterns of circulating leukocytes and may reveal novel insights into the host response to sepsis. OBJECTIVES We examined whether gene-expression profiling of neutrophils could identify signature genes and important pathways in the clinical syndrome of sepsis. METHODS Gene-expression profiling was performed using oligonucleotide microarrays on peripheral blood samples of 94 critically ill patients (71 septic and 23 nonseptic). Using a supervised learning algorithm based on support vector machine, a molecular signature of sepsis was generated from a training set of 44 samples and validated in an independent set of 50 samples. The diagnostic performance of the signature genes was assessed against a reference standard based on the International Sepsis Forum Consensus Conference definition of infection. MEASUREMENTS AND MAIN RESULTS A set of 50 signature genes correctly identified sepsis with a prediction accuracy of 91 and 88% in the training and validation sets, respectively. The diagnostic performance remained high regardless of patient's age, comorbidities, or prior antibiotic treatment. Compared with controls, genes involved in immune modulation and inflammatory response had reduced expression in patients with sepsis. In particular, the activation of nuclear factor-kappaB pathway was reduced, whereas its inhibitor gene, NFKBIA, was significantly up-regulated. CONCLUSIONS The signature genes reflect suppression of neutrophils' immune and inflammatory function by sepsis. Gene-expression profiling therefore provides a novel approach to advance our understanding of the host response in sepsis.
Incorporating Geometric Registration With Pc-Cluster Rendering For Flexible Tiled Displays

We describe a display system that automatically registers an array of casually positioned projectors and drives the display with a PC cluster. The display system uses a camera to compute the necessary transformations to geometrically align multiple overlapping projectors. Geometric alignment is realized through real-time corrective warping applied in the rendering pipeline. This combination of camera-aided display alignment with the PC-cluster rendering engine provides a display system that is easy to configure and reconfigure, accommodates casually tiled projectors and arbitrary display surfaces, and can be operational in a very short period of time.
Anger Among Prospective Adoptive Parents: Structural Determinants and Management Strategies

This paper focuses on anger experienced by prospective adoptive parents as they go through infertility and the formal adoption process. Qualitative interviews were done with seventy-four infertile couples who were at various stages in their consideration of adoption. Using a sociology of emotions perspective, I examine the source of their anger by focusing on the structural power imbalance between infertile couples and the physicians and adoption agency personnel to whom they turn for help in becoming parents. I analyze the way that this power unbalance constrains their anger and examine the way it is managed according to the "feeling rules" that then come into play. The implications of this anger for practice are discussed. The anger experienced by prospective adoptive parents as they go through infertility and the formal adoption process will be examined along two axes. First, the structural power imbalance between infertile couples and those who they turn to for help in becoming parents will be considered. Typically, couples turn to, and become dependent on, physicians for help in becoming biological parents; when that doesn't work they turn to, and become dependent on, adoption agency personnel in an effort to become adoptive parents. In both instances, their dependence on others results in a sense of powerlessness and feelings of anger. Second, the way that this power imbalance constrains the expression of this anger will be analyzed, specifically, the way anger is managed in interactive situations by prospective adoptive couples according to the "feeling rules" that come into play (Kemper, 1981:346). The powerlessness that couples experience is compounded by the structural restrictions that inhibit the expression of anger
Generating an Algebraic Specification from an ER-Model

Entity-Relationship modelling is a visual, hence a rather intuitive technique for specifying the structure of complex data. The technique is popular in part because the structure of an ER-model is easily grasped, and it is usually supported by diagrams or other visualizing tools. This paper deals with a detailed analysis of ER-modelling with the goal of deriving an algebraic specification for a given ER-model. This is motivated by considerations regarding program specification for data intensive applications. We indicate how the technique demonstrated here may be combined with formal techniques for specifying the functional behavior of a system.
Vers l'exogiciel - Une approche de la construction d'infrastructures logicielles radicalement configurables

La problematique de cette these est celle de la construction de systemes auto-administrables, c'est-a-dire de systemes prenant eux-memes en charge les fonctions d'administration classiquement devolues a des humains. La construction de tels systemes requiert a la fois l'utilisation d'une technologie logicielle adaptee et la mise en place d'une algorithmique dediee. Concernant la technologie logicielle, nous proposons une demarche de construction d'infrastructures logicielles radicalement configurables, appelee « exogiciel ». Cette demarche, inspiree de la philosophie exo-noyaux, vise a minimiser le nombre d'abstractions - fonctionnelles, non fonctionnelles et architecturales - imposees au developpeur d'applications. Nous illustrons ce concept d'exogiciel a travers la presentation de DREAM, un canevas logiciel a composants pour la construction d'intergiciels de communication. Concernant les aspects algorithmiques de la construction de systemes autonomes, une approche classique, adoptee par la theorie de la commande, est de mettre en place des boucles de commande. Dans cette these, nous presentons deux elements de base des boucles de commande : LeWYS, un canevas logiciel a composants permettant de construire des systemes d'observation de systemes distribues, et FREECAST, un protocole de diffusion de groupe avec ordre total uniforme. Par ailleurs, nous montrons comment les differents logiciels presentes dans cette these peuvent s'integrer dans JADE, un intergiciel developpe au sein du projet SARDES pour construire des boucles de commande pour l'administration autonome de systemes.
New methods for Quantum Compiling

The efficiency of compiling high-level quantum algorithms into instruction sets native to quantum computers defines the moment in the future when we will be able to solve interesting and important problems on quantum computers. In my work I focus on the new methods for compiling single qubit operations that appear in many quantum algorithms into single qubit operations natively supported by several popular architectures. In addition, I study several questions related to synthesis and optimization of multiqubit operations. When studying the single qubit case, I consider two native instruction sets. The first one is Clifford+T; it is supported by conventional quantum computers implementing fault tolerance protocols based on concatenated and surface codes, and by topological quantum computers based on Ising anyons. The second instruction set is the one supported by topological quantum computers based on Fibonacci anyons. I show that in both cases one can use the number theoretic structure of the problem and methods of computational algebraic number theory to achieve improvements over the previous state of the art by factors ranging from 10 to 1000 for instances of the problem interesting in practice. This order of improvement might make certain interesting quantum computations possible several years earlier. The work related to multiqubit operations is on exact synthesis and optimization of Clifford+T and Clifford circuits. I show an exact synthesis algorithm for unitaries generated by Clifford+T circuits requiring exponentially less number of gates than previous state of the art. For Clifford circuits two directions are studied: the algorithm for finding optimal circuits acting on a small number of qubits and heuristics for larger circuits optimization. The techniques developed allows one to reduce the size of encoding and decoding circuits for quantum error correcting codes by 40-50% and also finds their applications in randomized benchmarking protocols.
Thymolipoma in child: a case diagnosed by correlation of ultrasound‐guided fine needle aspiration (EUS‐FNA) cytology and computed tomography with histological confirmation

Dear Editor, Thymolipomas are infrequently occurring benign neoplasms of the anterior mediastinum, typically seen in children and young adults. A search of the available indexed English literature yielded fewer than 50 cases of paediatric thymolipoma. We describe the clinical, radiological, cytological and histopathological features of a case of mediastinal thymolipoma in a young child diagnosed by correlation of ultrasound-guided fine needle aspiration (EUS-FNA) cytology and computed tomography (CT). An 11-year-old boy presented to the hospital with a history of recurrent chest pain for the past month. There were no associated respiratory symptoms, and there was no fever or surgical history. Physical examination, including that of cardiovascular and respiratory systems, was unremarkable. Plain radiographs showed a lobulated soft tissue density mass in the right parahilar region with a broad base towards the mediastinum silhouetting the right upper mediastinal border. Contrast-enhanced computed tomography showed a lobulated mixed soft tissue and fat density mass lesion measuring 45 9 35 9 33 mm located in the antero-superior mediastinum closely abutting the thymus. The mass lesion showed homogenous enhancement (Figure 1). A radiological impression of mediastinal teratoma or thymolipoma was rendered. The child underwent EUS-FNA. Cytological smears were cellular and showed predominantly lymphocytes in various stages of maturation (Figure 2a). Scattered epithelial cells with squamoid features were also seen (Figure 2b). There was no evidence of a teratomatous component. The cytological features were suggestive of thymic tissue. Considering the radiological and FNA smear features, a cytological possibility of thymolipoma was rendered and excision biopsy was advised. A right thoracotomy with excision of the mass was performed. Intraoperatively, a 5 9 4-cm firm mass was seen near the right atrium and thymus. The mass was dissected free from the thymus and submitted for histopathology. On gross examination, the mass was encapsulated and lobulated, and measured 5.2 9 4.1 9 2.0 cm (Figure 2c). Cut section showed a grey–brown to yellowish lobulated lesion lacking haemorrhage or necrosis. The mass was extensively sampled for histopathological examination. Microscopically, a lobulated lesion was seen composed of thymic tissue in the form of lymphoid component and Hassall’s corpuscles, together with varying amounts of mature adipose tissue (Figure 2d). No teratomatous component was seen in the numerous sections examined. No evidence of malignancy was noted. A final histopathological diagnosis of mediastinal thymolipoma