Miracle-dz/UniFAR-FTUs huggingface dataset:
Waiting Time Models of Cancer Progression

Cancer progression is an evolutionary process driven by mutation and selection in a population of tumor cells. In multistage models of cancer progression, each stage is associated with the occurrence of genetic alterations and their fixation in the population. The accumulation of mutations is described using conjunctive Bayesian networks, an exponential family of waiting time models in which the occurrence of mutations is constrained by a partial temporal order. Two opposing limit cases arise if mutations either follow a linear order or occur independently. Exact analytical expressions for the waiting time until a specific number of mutations have accumulated are derived in these limit cases as well as for the general conjunctive Bayesian network. In a stochastic population genetics model that accounts for mutation and selection, waves of clonal expansions sweep through the population at equidistant intervals. An approximate analytical expression for the waiting time is compared to the results obtained with conjunctive Bayesian networks.
Current Status of Biomarkers for Prostate Cancer

Prostate cancer (PCa) is a leading cause of cancer-related death of men globally. Since its introduction, there has been intense debate as to the effectiveness of the prostate specific antigen (PSA) test as a screening tool for PCa. It is now evident that the PSA test produces unacceptably high rates of false positive results and is not prognostic. Here we review the current status of molecular biomarkers that promise to be prognostic and that might inform individual patient management. It highlights current efforts to identify biomarkers obtained by minimally invasive methods and discusses current knowledge with regard to gene fusions, mRNA and microRNAs, immunology, and cancer-associated microparticles.
Process Safety Behavioral Systems: Behaviors Interlock in Complex Metacontingencies

ABSTRACT This paper seeks to identify behavioral components active in process safety. Three types of behavior classes are identified as contributors to process safety: task-specific behaviors, safety-directed behaviors, and behaviors associated with situational awareness. Behavioral systems analysis is used to provide a framework for identifying the cross-functional interlocking behavioral contingencies that can, even over a period of years, contribute to process safety incidents. Leadership behaviors are also identified that can create the context in the form of metacontingencies that maintain these interlocking contingencies.
Do Dogs Know Calculus?

Tim Pennings (pennings@hope.edu) is an Associate 4-i> "4 RProfessor of Mathematics at Hope College in Holland, Michigan. His research, done collaboratively with undergraduate students, is in dynamical systems and modeling. He also directs the Hope College NSF-REU Mathematics Summer Research Program. Other reasons for living include ultimate frisbee, racquetball, nature photography, choral music, folk song guitar gigs, and playing with Elvis at the beach.
Disorder-induced phases in the S=1 antiferromagnetic Heisenberg chain

We use extensive density matrix renormalization group (DMRG) calculations to explore the phase diagram of the random S=1 antiferromagnetic Heisenberg chain with a power-law distribution of the exchange couplings. We use open chains and monitor the lowest gaps, the end-to-end correlation function, and the string order parameter. For this distribution at weak disorder, the systems is in the gapless Haldane phase with a disorder dependent dynamical exponent, z, and z=1 signals, the border between the nonsingular and singular regions of the local susceptibility. For strong enough disorder, which approximately corresponds to a uniform distribution, a transition into the random singlet phase is detected, at which the string order parameter as well as the average end-to-end correlation function are vanishing and at the same time the dynamical exponent is divergent. Singularities of physical quantities are found to be somewhat different in the random singlet phase and in the critical point.
Evaluations of tropospheric aerosol properties simulated by the community earth system model with a sectional aerosol microphysics scheme

A sectional aerosol model (CARMA) has been developed and coupled with the Community Earth System Model (CESM1). Aerosol microphysics, radiative properties, and interactions with clouds are simulated in the size‐resolving model. The model described here uses 20 particle size bins for each aerosol component including freshly nucleated sulfate particles, as well as mixed particles containing sulfate, primary organics, black carbon, dust, and sea salt. The model also includes five types of bulk secondary organic aerosols with four volatility bins. The overall cost of CESM1‐CARMA is approximately ∼2.6 times as much computer time as the standard three‐mode aerosol model in CESM1 (CESM1‐MAM3) and twice as much computer time as the seven‐mode aerosol model in CESM1 (CESM1‐MAM7) using similar gas phase chemistry codes. Aerosol spatial‐temporal distributions are simulated and compared with a large set of observations from satellites, ground‐based measurements, and airborne field campaigns. Simulated annual average aerosol optical depths are lower than MODIS/MISR satellite observations and AERONET observations by ∼32%. This difference is within the uncertainty of the satellite observations. CESM1/CARMA reproduces sulfate aerosol mass within 8%, organic aerosol mass within 20%, and black carbon aerosol mass within 50% compared with a multiyear average of the IMPROVE/EPA data over United States, but differences vary considerably at individual locations. Other data sets show similar levels of comparison with model simulations. The model suggests that in addition to sulfate, organic aerosols also significantly contribute to aerosol mass in the tropical UTLS, which is consistent with limited data.
Robust guaranteed cost control for discrete-time uncertain systems with delay

The uncertain systems under considered depend on norm-bounded time-varying matrices of uncertain parameters. The authors develop a quadratic guaranteed cost control method for robust stabilisation via linear memoryless state feedback and static output feedback. Also presented is a robust state feedback controller and static output feedback controller. It is shown that the state feedback controller and output feedback controller can be constructed by solving a linear matrix inequality.
A study of athlete engagement, athlete identity and individualism: Collectivism cultural behaviours among Filipino Athletes compared with US American Athletes

The focus of this study is the Filipino athlete, how they engage with their sport and the influence in this process of their cultural background and the way in which they construct their personal identity as athletes. These aspects are further studied in comparison with a sample of their US American counterparts. Athlete Engagement (AE) is a fairly new concept in sport psychology. It has been developed from the concept of employee engagement in industrial/organizational psychology where it was operationalised with the dimensions of vigour, dedication and absorption (Hakanen, Schaufeli & Aloha, 2008). Similar dimensions were explored in the first two research studies on AE by Lonsdale, Hodge and Raedeke (2007) and Lonsdale, Hodge and Jackson (2007). AE has been found to be “a persistent, positive, cognitive-affective experience in sport characterized by confidence, dedication and vigour” (2007, p.451). The first study in the present enquiry surveyed 70 Filipino and 62 US American athletes. AE was explored in relation to the athletic identity and the individualismcollectivism cultural behaviours of these athletes. AE was measured through the use of the Athlete Engagement Questionnaire (AEQ); athletic identity was measured through the Athletic Identity Measurement Scale-Plus (AIMS-Plus); and individualismcollectivism cultural behaviours were measured through the Auckland Individualism Collectivism Scale (AICS). No differences were found between the levels of global AE reported for the two national groups (p=.489). However at the level of the subscales the US sample engaged with greater confidence (p=.014) and dedication (p=.001) whereas the Filipino group engaged with more vigor (p=.023) and enthusiasm (p=.044). There was no difference found between the two groups for their individualist behaviours (p=.236) or the strength of their athletic identities (p=.739). It was therefore concluded on the basis of these findings that, regardless of their national cultural background, athletes were primarily individualistic and had high levels of athletic identity. The second study sought to explore these differences further through the use of qualitative techniques. Following the model applied by Lonsdale, Hodge and Raedeke (2007) with a sample of New Zealand athletes, the Scanlan Collaborative Interview Method was used to gather information from 10 Filipino and 10 US American athletes. It was found that although both samples experienced the same engagement dimensions,
A novel design of a 6-GHz 8 /spl times/ 8-b pipelined multiplier

This paper presents a design of 8-bit /spl times/ 8-bit unsigned multiplier for high-speed digital signal processing (DSP) applications. High-speed is achieved by a new architecture implementing our earlier multiplication technique based in A. Khatibzadeh et a. (2005) in conventional register pipelining at the bit level. The multiplier is designed employing 0.18-/spl mu/m CMOS process. HSPICE simulation results indicate that the proposed design performs multiplication rates up to 6 GHz under the supply voltage of 1.8V or 3.3 GHz under 1.4 V with about 25% times less power consumption. The comparison with Baugh-Wooley multiplier with same topology of the common elements shows that our multiplier consumes only 63% of the power of Baugh-Wooley multiplier with 40% reduction in latency.
Dimensional Affect Recognition from HRV: An Approach Based on Supervised SOM and ELM

Dimensional affect recognition is a challenging topic and current techniques do not yet provide the accuracy necessary for HCI applications. In this work we propose two new methods. The first is a novel self-organizing model that learns from similarity between features and affects. This method produces a graphical representation of the multidimensional data which may assist the expert analysis. The second method uses extreme learning machines, an emerging artificial neural network model. Aiming for minimum intrusiveness, we use only the heart rate variability, which can be recorded using a small set of sensors. The methods were validated with two datasets. The first is composed of 16 sessions with different participants and was used to evaluate the models in a classification task. The second one was the publicly available Remote Collaborative and Affective Interaction (RECOLA) dataset, which was used for dimensional affect estimation. The performance evaluation used the kappa score, unweighted average recall and the concordance correlation coefficient. The concordance coefficient on the RECOLA test partition was 0.421 in arousal and 0.321 in valence. Results show that our models outperform state-of-the-art models on the same data and provides new ways to analyze affective states.
A Lantern-Tree-Based QoS On-Demand Multicast Protocol for a Wireless Mobile Ad Hoc Network

SUMMARY The multimedia applications have recently generated much interest in wireless network infrastructure with supporting the quality-of-service (QoS) communications. In this paper, we propose a lantern-tree-based QoS on-demand multicast protocol for wireless ad hoc networks. Our proposed scheme offers a bandwidth routing protocol for QoS support in a multihop mobile network, where the MAC sub-layer adopts the CDMA-over-TDMA channel model. The QoS on-demand multicast protocol determines the end-to-end bandwidth calculation and bandwidth allocation from a source to a group of destinations. In this paper, we identify a lantern-tree for developing the QoS multicast protocol to satisfy certain bandwidth requirement, while the lantern-tree is served as the multicast-tree. Our lantern-tree-based scheme offers a higher success rate to construct the QoS multicast tree due to using the lantern-tree. The lantern-tree is a tree whose sub-path is constituted by the lantern-path, where the lantern-path is a kind of multi-path structure. This obviously improves the success rate by means of multi-path routing. In particular, our proposed scheme can be easily applied to most existing on-demand multicast protocols. Performance analysis results demonstrate the achievements
A unified view of linear AR(1) models

We review and synthesize the wide range of non-Gaussian first order linear autoregressive models that have appeared in the literature. Models are organized into broad classes to clarify similarities and differences and facilitate application in particular situations. General properties for process mean, variance and correlation are derived, unifying many separate results appearing in the literature. Examples illustrate the wide range of properties that can appear even under the autoregressive assumption. These results are used in analysing a variety of real data sets, illustrating general methods of estimation, model diagnostics and model selection.
Augmentation of Radiation Response by Motesanib, a Multikinase Inhibitor that Targets Vascular Endothelial Growth Factor Receptors

Background: Motesanib is a potent inhibitor of vascular endothelial growth factor receptors (VEGFR) 1, 2, and 3, platelet-derived growth factor receptor, and Kit receptors. In this report we examine the interaction between motesanib and radiation in vitro and in head and neck squamous cell carcinoma (HNSCC) xenograft models. Experimental Design: In vitro assays were done to assess the impact of motesanib on VEGFR2 signaling pathways in human umbilical vein endothelial cells (HUVEC). HNSCC lines grown as tumor xenografts in athymic nude mice were utilized to assess the in vivo activity of motesanib alone and in combination with radiation. Results: Motesanib inhibited VEGF-stimulated HUVEC proliferation in vitro, as well as VEGFR2 kinase activity. Additionally, motesanib and fractionated radiation showed additive inhibitory effects on HUVEC proliferation. In vivo combination therapy with motesanib and radiation showed increased response compared with drug or radiation alone in UM-SCC1 (P < 0.002) and SCC-1483 xenografts (P = 0.001); however, the combination was not significantly more efficacious than radiation alone in UM-SCC6 xenografts. Xenografts treated with motesanib showed a reduction of vessel penetration into tumor parenchyma, compared with control tumors. Furthermore, triple immunohistochemical staining for vasculature, proliferation, and hypoxia showed well-defined spatial relationships among these parameters in HNSCC xenografts. Motesanib significantly enhanced intratumoral hypoxia in the presence and absence of fractionated radiation. Conclusions: These studies identify a favorable interaction when combining radiation and motesanib in HNSCC models. The data presented suggest that motesanib reduces blood vessel penetration into tumors and thereby increases intratumoral hypoxia. These findings suggest that clinical investigations examining combinations of radiation and motesanib are warranted in HNSCC. Clin Cancer Res; 16(14); 3639–47. ©2010 AACR.
The interaction of a giant planet with a disc with MHD turbulence — II. The interaction of the planet with the disc

We present a global magnetohydrodynamics (MHD) simulation of a turbulent accretion disc interacting with a giant protoplanet of 5 Jupiter masses in a fixed circular orbit. The disc model had an aspect ratio H/r= 0.1, and in the absence of the protoplanet a typical value of the Shakura–Sunyaev stress parameter α= 5 × 10−3. As expected from previous work, the protoplanet was found to open and maintain a significant gap in the disc, with the interaction leading to inward migration of the protoplanet orbit on the expected time-scale. No evidence for a persistent net mass flow through the gap was found. However, this may be because an extensive inner cavity could not be formed for the model adopted. Spiral waves were launched by the protoplanet and, although these appeared to be diffused and dissipated through interaction with the turbulence, they produced an outward angular momentum flow which compensated for a reduced flux associated with the MHD turbulence near the planet, so maintaining the gap. When compared with laminar disc models, with the same estimated α in the absence of the planet, the gap was found to be deeper and wider, indicating that the turbulent disc behaved as if it in fact possessed a smaller α, even though analysis of the turbulent stress indicated that it was not significantly affected by the planet in the region away from the gap. This may arise for two reasons. First, unlike a Navier–Stokes viscosity with anomalous viscosity coefficient, the turbulence does not provide a source of constantly acting friction in the near vicinity of the planet that leads to steady mass flow into the gap region. Instead, the turbulence is characterized by large fluctuations in the radial velocity, and time averaging of these fluctuations over significant time-scales is required to recover the underlying mass flow through the disc. In the vicinity of the planet, the disc material experiences high amplitude periodic perturbations on time-scales that are short relative to the time-scale required for averaging. Consequently the disc response is likely to be significantly altered relative to that expected from a Navier–Stokes model. Secondly, the simulation indicates that an ordered magnetic connection between the inner and outer disc can occur enabling angular momentum to flow out across the gap, helping to maintain it independently of the protoplanet's tide. This type of effect may assist gap formation for smaller mass protoplanets which otherwise would not be able to maintain them. There is also some evidence that magnetic connection between the circumstellar disc and material that flows into the protoplanet's Hill sphere may lead to significant magnetic braking of the resulting circumplanetary disc, thereby modifying the expected gas accretion rate on to forming gas giant planets.
Agrobacterium-mediated transformation of indica rice under Acetosyringone - free conditions.

The possibility of developing transgenic indica rices through Agrobacterium -mediated transformation in the absence of Acetosyringone at bacterial preinduction or cocultivation or both stages was assessed. Six weeks old, scutellum derived calluses of indica rice viz., ASD 16, White Ponni, Pusa Basmati, Pusa Sugandh 4, Pusa Sugandh 5 were cocultivated with A. tumifaciens strain EHA 105, harbouring the binary vector pCAMBIA 1305.1 with the P-glucouronidase (GUS) and hygromycin phospho transferase genes in the T-DNA region. Addition of Acetosyringone (AS) to the pre induction medium and cocultivation medium induced higher levels of transient GUS expression than that obtained with the addition of AS to either of the stages. Adddition of sucrose to both the media revealed that the transient expression levels were similar to those obtained by the addition of AS. The resultant fertile plants were stable ttransformants as revealed by GUS histochemical assay and PCR analysis for the GUS and HPT genes. The results indicated that the addition of phenolics like AS may not be essential for the induction of vir genes and development of transgenic indica rices are also possible under AS free conditions.
Returning to that which was never lost: Indigenous Australian saltwater identities, a history of land claims and the paradox of return

ABSTRACT In this paper I explore the kincentric ecologies that define sea country for Indigenous Australians, in particular the Yanyuwa of Northern Australia. Despite colonial alienation from their coastal territories, Yanyuwa have sustained a four-decade long legal fight for restitution. Using the framework of ‘urgent patience’ as resistance against ‘social death’, this paper tracks the historical legacy of legislative land rights for saltwater peoples.
Eigenvector 1: An Optimal Correlation Space for Active Galactic Nuclei

We identify a correlation space involving optical and UV emission-line parameters as well as the soft X-ray spectral index that provides optimal discrimination between all principal classes of active galactic nuclei (AGNs). Most of the sources in our three high-quality data samples show a strong intercorrelation with narrow-line Seyfert 1 (NLSy1) galaxies and steep-spectrum radio galaxies occupying opposite extrema in the space. NLSy1 sources show a clear continuity with broader line sources, indicating that they are not a disjoint class of AGN as is sometimes suggested. We interpret the principal intercorrelation in the parameter space as being driven by the AGN luminosity-to-black hole mass ratio (L/M is proportional to the Eddington ratio). Source orientation no doubt also plays an important role, but it is not yet clear whether FWHM Hβ or C IV λ1549 line shift is the better indicator. We tentatively identify two radio-quiet populations: an almost pure radio-quiet population A, with FWHM ≤ 4000, and population B, which occupies the same parameter domain as the flat-spectrum radio-loud sources. A possible interpretation sees population A/NLSy1 as lower mass/high accretion rate sources and population B/radio-loud sources as the opposite.
Derivative processes for modelling metabolic fluxes

Motivation: One of the challenging questions in modelling biological systems is to characterize the functional forms of the processes that control and orchestrate molecular and cellular phenotypes. Recently proposed methods for the analysis of metabolic pathways, for example, dynamic flux estimation, can only provide estimates of the underlying fluxes at discrete time points but fail to capture the complete temporal behaviour. To describe the dynamic variation of the fluxes, we additionally require the assumption of specific functional forms that can capture the temporal behaviour. However, it also remains unclear how to address the noise which might be present in experimentally measured metabolite concentrations. Results: Here we propose a novel approach to modelling metabolic fluxes: derivative processes that are based on multiple-output Gaussian processes (MGPs), which are a flexible non-parametric Bayesian modelling technique. The main advantages that follow from MGPs approach include the natural non-parametric representation of the fluxes and ability to impute the missing data in between the measurements. Our derivative process approach allows us to model changes in metabolite derivative concentrations and to characterize the temporal behaviour of metabolic fluxes from time course data. Because the derivative of a Gaussian process is itself a Gaussian process, we can readily link metabolite concentrations to metabolic fluxes and vice versa. Here we discuss how this can be implemented in an MGP framework and illustrate its application to simple models, including nitrogen metabolism in Escherichia coli. Availability and implementation: R code is available from the authors upon request. Contact: j.norkunaite@imperial.ac. uk; m.stumpf@imperial.ac. uk Supplementary information: Supplementary data are available at Bioinformatics online.
The Geometry of Tamagawa Numbers of Algebraic Groups

Let X be a smooth projective geometrically connected curve over a finite field with function field K. Let G be a connected semisimple group scheme over X . Under certain hypothesis we prove the equality of two numbers associated with G. The first is an arithmetic invariant, its Tamagawa number. The second, is a geometric invariant, the number of connected components of the moduli stack of G-torsors on X .