Miracle-dz/UniFAR-FTUs huggingface dataset:
A framework for scalable parameter estimation of gene circuit models using structural information

Motivation: Systematic and scalable parameter estimation is a key to construct complex gene regulatory models and to ultimately facilitate an integrative systems biology approach to quantitatively understand the molecular mechanisms underpinning gene regulation. Results: Here, we report a novel framework for efficient and scalable parameter estimation that focuses specifically on modeling of gene circuits. Exploiting the structure commonly found in gene circuit models, this framework decomposes a system of coupled rate equations into individual ones and efficiently integrates them separately to reconstruct the mean time evolution of the gene products. The accuracy of the parameter estimates is refined by iteratively increasing the accuracy of numerical integration using the model structure. As a case study, we applied our framework to four gene circuit models with complex dynamics based on three synthetic datasets and one time series microarray data set. We compared our framework to three state-of-the-art parameter estimation methods and found that our approach consistently generated higher quality parameter solutions efficiently. Although many general-purpose parameter estimation methods have been applied for modeling of gene circuits, our results suggest that the use of more tailored approaches to use domain-specific information may be a key to reverse engineering of complex biological systems. Availability: http://sfb.kaust.edu.sa/Pages/Software.aspx Contact: xin.gao@kaust.edu.sa Supplementary information: Supplementary data are available at Bioinformatics online.
Investigating Decision Support System ( DSS ) Success : A Partial Least Squares Structural Equation Modeling Approach

The central contribution of the study is the development of a DSS success model explores the effects of the quality features of DSS systems, including system quality, information quality, accompanied with perceived ease of use and perceived usefulness on decision support satisfaction and DSS net benefits. A detailed questionnaire was developed to measure the relationship between the aforementioned variables and data was collected from employees in Royal Jordanian Airlines in Jordan who had experience using DSS at their workplace. Partial least squares-structural equation modelling (PLS-SEM) methods were employed to test the research model. The results revealed that system quality had positive effects on both perceived usefulness and decision support satisfaction. Information quality had positive effects on decision support satisfaction; ease of use had positive effects on perceived usefulness, and decision support satisfaction positive effects on net benefits. However, information quality effects on the perceived usefulness, ease of use effects on decision support satisfaction, perceived usefulness effects on decision support satisfaction and benefits were not significant. The findings provide several important implications for DSS research and practice. This paper concludes by discussing the limitations of the study, which should be addressed in future research.
Participation as a tool for interactional work on Twitter: A sociolinguistic approach to social media 'engagement'

This work approaches the concept of social media engagement through a lens of participation theory. Following the work of Goffman (1981) and others, this dissertation uses the concepts of the participation framework and the participant role to explore engagement as a function of participation in interaction. The purposes of this dissertation are three-fold: to model participant roles as they are built in interaction on Twitter, to discover the ways in which participation is established through the linguistic choices enacted by participants, and to demonstrate the role of the medium as an important factor influencing possibilities for participation. Using discourse analysis as a methodology, tweets from accounts associated with National Hockey League (NHL) organizations are analyzed for the linguistic resources that are used to reference interactional roles traditionally understood as “speaker” and “hearer”. In turn, the linguistic and discursive resources deployed in team tweets are used to reveal these speaker and hearer roles as more detailed and complex production and reception frameworks. The modal affordances of Twitter are also investigated as to their role in influencing the building of participation frameworks through talk, including unique linguistic forms that are available to Twitter users and possibilities for hiding or revealing participants through the Twitter screen. The findings of this investigation reveal three primary models for production frameworks for NHL accounts: an Impersonal Model that eschews identification of the parties in production roles, an Interpersonal Model that highlights the individuals involved in the interaction, and a Team Model that obscures the individual to focus on the team or organization as a primary participant. Additionally, a framework for understanding recipient audiences on Twitter is proposed, incorporating both actual and intended audiences. Consistent patterns in the language choices used to construct participatory identities for production and reception roles are demonstrated, highlighting the value of using linguistic data as a resource for investigations of participation. Finally, Twitter’s modal affordances are shown to be an integral part of the ways that users enact participatory concepts, such as co-presence and address, revealing the importance of considering the role of the medium in participation studies.
Electroweak and Flavour Structure of a Warped Extra Dimension with Custodial Protection

We present the electroweak and flavour structure of a model with a warped extra dimension and the bulk gauge group SU(3)c × SU(2)L × SU(2)R × PLR × U(1)X. The presence of SU(2)R implies an unbroken custodial symmetry in the Higgs system allowing to eliminate large contributions to the T parameter, whereas the PLR symmetry and the enlarged fermion representations provide a custodial symmetry for flavour diagonal and flavour changing couplings of the SM Z boson to left-handed down-type quarks. We diagonalise analytically the mass matrices of charged and neutral gauge bosons including the first KK modes. We present the mass matrices for quarks including heavy KK modes and discuss the neutral and charged currents involving light and heavy fields. We give the corresponding complete set of Feynman rules in the unitary gauge.
The Stretch Factor of the Delaunay Triangulation Is Less than 1.998

Let $S$ be a finite set of points in the Euclidean plane. Let $D$ be a Delaunay triangulation of $S$. The stretch factor (also known as dilation or spanning ratio) of $D$ is the maximum ratio, among all points $p$ and $q$ in $S$, of the shortest path distance from $p$ to $q$ in $D$ over the Euclidean distance $||pq||$. Proving a tight bound on the stretch factor of the Delaunay triangulation has been a long-standing open problem in computational geometry. In this paper we prove that the stretch factor of the Delaunay triangulation is less than $\rho = 1.998$, significantly improving the current best upper bound of 2.42 by Keil and Gutwin [``The Delaunay triangulation closely approximates the complete Euclidean graph,” in Proceedings of the 1st Workshop on Algorithms and Data Structures (WADS), 1989, pp. 47--56]. Our bound of 1.998 also improves the upper bound of the best stretch factor that can be achieved by a plane spanner of a Euclidean graph (the current best upper bound is 2). Our result has a direc.
Association between cholesterol level and mortality in dialysis patients: role of inflammation and malnutrition.

CONTEXT Total cholesterol level is inversely associated with mortality in dialysis patients, a group at high risk of cardiovascular disease (CVD). This paradox may be explained by systemic inflammation and/or malnutrition, which are associated with lower cholesterol levels and higher mortality. OBJECTIVE To determine the relationship between cholesterol level and outcome in patients undergoing dialysis, accounting for inflammation and malnutrition. DESIGN, SETTING, AND PARTICIPANTS Prospective study of 823 patients enrolled from October 1995 to June 1998 who recently initiated dialysis, from 79 clinics, classified by absence or presence of inflammation and/or malnutrition (defined as serum albumin levels <3.6 mg/dL, C-reactive protein > or =10 mg/L, or interleukin 6 > or =3.09 pg/mL). MAIN OUTCOME MEASURES All-cause and cardiovascular disease mortality. RESULTS During a median follow-up of 2.4 years, 324 deaths (159 CVD deaths), 153 renal transplantations, and 10 losses to follow-up occurred. Average serum cholesterol level was lower in the presence of inflammation/malnutrition than in its absence. In a Cox model adjusted for age, race, and sex, a 40-mg/dL (1.0-mmol/L) increment in baseline total serum cholesterol level was associated with a decreased risk of all-cause mortality overall (relative hazard [RH], 0.92; 95% confidence interval [CI], 0.87-0.98) and in the presence of inflammation/malnutrition (RH, 0.89; CI, 0.84-0.95). In contrast, serum cholesterol level was associated with an increased risk in the absence of inflammation/malnutrition (RH, 1.32; 95% CI, 1.07-1.63). For CVD mortality, an inverse trend was not statistically significant in the presence of inflammation/malnutrition, and a positive association was evident in the absence of inflammation/malnutrition (RH, 1.41; 95% CI, 1.04-1.89). Further adjustment for traditional CVD risk factors, dialysis modality, comorbidity, and inflammatory markers attenuated the inverse association but strengthened the positive association. CONCLUSIONS The inverse association of total cholesterol level with mortality in dialysis patients is likely due to the cholesterol-lowering effect of systemic inflammation and malnutrition, not to a protective effect of high cholesterol concentrations. These findings support treatment of hypercholesterolemia in this population.
Complex event processing for RFID-enabled retail store

Out-of-stock is considered to be a major problem for retailers and suppliers. In this paper, we study the problem of complex event processing in a RFID enabled retail store operation, particularly aiming to provide automated shelf replenishment decisions. We define different event queries to simulate retailer store workflow in the area of backroom (warehouse) and the sales floor over the RFID data streams with item level and case-level tagging. With these queries to detect different levels of objects movement, the retail store can quickly replenish the shelves without long time delays. We utilize a simulated RFID enabled retail store to verify the effectiveness of our method.
Multi-Wiener SURE-LET Deconvolution

In this paper, we propose a novel deconvolution algorithm based on the minimization of a regularized Stein's unbiased risk estimate (SURE), which is a good estimate of the mean squared error. We linearly parametrize the deconvolution process by using multiple Wiener filters as elementary functions, followed by undecimated Haar-wavelet thresholding. Due to the quadratic nature of SURE and the linear parametrization, the deconvolution problem finally boils down to solving a linear system of equations, which is very fast and exact. The linear coefficients, i.e., the solution of the linear system of equations, constitute the best approximation of the optimal processing on the Wiener-Haar-threshold basis that we consider. In addition, the proposed multi-Wiener SURE-LET approach is applicable for both periodic and symmetric boundary conditions, and can thus be used in various practical scenarios. The very competitive (both in computation time and quality) results show that the proposed algorithm, which can be interpreted as a kind of nonlinear Wiener processing, can be used as a basic tool for building more sophisticated deconvolution algorithms.
3D and sequential representations of spatial relationships among photos

This paper proposes automatic representations of spatial relationships among photos for structure analysis and review of a photographic subject. Based on camera tracking, photos are shown in a 3D virtual reality space to represent global spatial relationships. At the same time, the spatial relationships between two of the photos are represented in slide show sequences. This proposal allows people to organize photos quickly in spatial representations with qualitative meaning.
An Efficient Double Auction Mechanism for On-Demand Transport Services in Cloud-Based Mobile Commerce

Current cloud-based solutions of mobile commerce (m-commerce) for on-demand transport services, such as Uber and Didi Dache, uses a take-it-or-leave-it market mechanism, in which passengers and drivers have no option but to accept or reject given market prices determined by transport companies. Such a market mechanism does not consider the actual needs of passengers and drivers, e.g., high-urgency situations of passengers and different operating cost of vehicles, which are valuable for determining a reasonable market value of a trip. In this paper, we introduce a double auction mechanism for on-demand transport services, which allows multiple passengers and drivers to submit their bids simultaneously. In a double auction, with bids from both passengers and drivers, the marketplace can fairly determine a reasonable price based on the current supply and demand of the market. The proposed approach, which extends the McAfee's mechanism, ensures that honesty is a dominant strategy for bidders with winning preferences. It is different from existing market mechanisms for transport services as it allows users to specify their own prices based on the actual cost of transport services as well as their urgency situations.
Sleep Neuroimaging and Models of Consciousness

Human deep sleep is characterized by reduced sensory activity, responsiveness to stimuli, and conscious awareness. Given its ubiquity and reversible nature, it represents an attractive paradigm to study the neural changes which accompany the loss of consciousness in humans. In particular, the deepest stages of sleep can serve as an empirical test for the predictions of theoretical models relating the phenomenology of consciousness with underlying neural activity. A relatively recent shift of attention from the analysis of evoked responses toward spontaneous (or “resting state”) activity has taken place in the neuroimaging community, together with the development of tools suitable to study distributed functional interactions. In this review we focus on recent functional Magnetic Resonance Imaging (fMRI) studies of spontaneous activity during sleep and their relationship with theoretical models for human consciousness generation, considering the global workspace theory, the information integration theory, and the dynamical core hypothesis. We discuss the venues of research opened by these results, emphasizing the need to extend the analytic methodology in order to obtain a dynamical picture of how functional interactions change over time and how their evolution is modulated during different conscious states. Finally, we discuss the need to experimentally establish absent or reduced conscious content, even when studying the deepest sleep stages.
Influenza detection and prediction algorithms: comparative accuracy trial in Östergötland county, Sweden, 2008–2012

SUMMARY Methods for the detection of influenza epidemics and prediction of their progress have seldom been comparatively evaluated using prospective designs. This study aimed to perform a prospective comparative trial of algorithms for the detection and prediction of increased local influenza activity. Data on clinical influenza diagnoses recorded by physicians and syndromic data from a telenursing service were used. Five detection and three prediction algorithms previously evaluated in public health settings were calibrated and then evaluated over 3 years. When applied on diagnostic data, only detection using the Serfling regression method and prediction using the non-adaptive log-linear regression method showed acceptable performances during winter influenza seasons. For the syndromic data, none of the detection algorithms displayed a satisfactory performance, while non-adaptive log-linear regression was the best performing prediction method. We conclude that evidence was found for that available algorithms for influenza detection and prediction display satisfactory performance when applied on local diagnostic data during winter influenza seasons. When applied on local syndromic data, the evaluated algorithms did not display consistent performance. Further evaluations and research on combination of methods of these types in public health information infrastructures for ‘nowcasting’ (integrated detection and prediction) of influenza activity are warranted.
Enhancing amplifiers/filters bandwidth by transfer function zeroes

The paper describes an extension, at the approximation level, of shunt-peaking technique to increase the filter/amplifier bandwidth. The frequency dependent delay function of a Bessel filter and the modifications of this function consisting in deleting one or more frequency terms in the delay function numerator are considered as “squared-moduli” for a group of filters with transmission zeroes. Using a standard procedure of restoration one finds the transfer functions of this group. The number of filters in each group is defined by the order of the denominator. The paper provides the transfer functions parameters, frequency properties and the parameters of step-transient responses for the filter orders from two to six.
Molt, Orientation, and Avian Speciation

The Auk, Vol. 128, Number 2, pages 419−425. ISSN 0004-8038, electronic ISSN 1938-4254.  2011 by The American Ornithologists’ Union. All rights reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Rights and Permissions website, http://www.ucpressjournals. com/reprintInfo.asp. DOI: 10.1525/auk.2011. 10176 Sievert rohwer1,3 and darren e. irwin2
Restoration of blurred images using Blind Deconvolution Algorithm

Image restoration is the process of recovering the original image from the degraded image. Aspire of the project is to restore the blurred/degraded images using Blind Deconvolution algorithm. The fundamental task of Image deblurring is to de-convolute the degraded image with the PSF that exactly describe the distortion. Firstly, the original image is degraded using the Degradation Model. It can be done by Gaussian filter which is a low-pass filter used to blur an image. In the edges of the blurred image, the ringing effect can be detected using Canny Edge Detection method and then it can be removed before restoration process. Blind Deconvolution algorithm is applied to the blurred image. It is possible to renovate the original image without having specific knowledge of degradation filter, additive noise and PSF. To get the effective results, the Penalized Maximum Likelihood (PML) Estimation Technique is used with our proposed Blind Deconvolution Algorithm.
An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation

Mechanosensitive channels act as molecular transducers of mechanical force exerted on the membrane of living cells by opening in response to membrane bilayer deformations occurring in physiological processes such as touch, hearing, blood pressure regulation, and osmoregulation. Here, we determine the likely structure of the open state of the mechanosensitive channel of large conductance using a combination of patch clamp, fluorescence resonance energy transfer (FRET) spectroscopy, data from previous electron paramagnetic resonance experiments, and molecular and Brownian dynamics simulations. We show that structural rearrangements of the protein can be measured in similar conditions as patch clamp recordings while controlling the state of the pore in its natural lipid environment by modifying the lateral pressure distribution via the lipid bilayer. Transition to the open state is less dramatic than previously proposed, while the N terminus remains anchored at the surface of the membrane where it can either guide the tilt of or directly translate membrane tension to the conformation of the pore-lining helix. Combining FRET data obtained in physiological conditions with simulations is likely to be of great value for studying conformational changes in a range of multimeric membrane proteins.
Metabolic Oxidation of Glucose During Early Myocardial Reperfusion

We have previously studied the relation between long-chain fatty acid and pyruvate metabolism in reperfused myocardium and noted a rapid return of fatty acid oxidation to at least preischemic values accompanied by a marked decrease in pyruvate oxidation. The purpose of the present report is to further characterize carbohydrate metabolism during reflow by describing rates of glucose oxidation using [6-14C]glucose. Chddative performance was determinedwith and without preserved fatty acid utilization; the latter condition was effected byoxfenicine, which inhibits palmitoylcarnitine transferase I. In the main protocol, two groups ofworking swine hearts (n =18) were perfused aeroblcaUy for 30 minutes, rendered regionallyischemic (−60 Δ% in anterior descending coronary flow) for 45 minutes, and reperfused atcontrol flows for a final 50 minutes of perfusion. An emulsion of Intralipid with heparin wasadministered systemically throughout the studies to augment serum fatty acids (average fattyacid values, 1.05 ± 0.05 μmol/ml for both groups). Serum glucose was monitored and maintainedat or about 100 rag/dl with additional infusions of glucose as needed. Oxfenicine (33mg/kg) was administered systemically by bolus injection at time 0 and 60 minutes of perfusionin nine animals. Decreased mechanical performance, that is, stunning, during reflow wasevident in both groups (−50 Δ% in regional systolic shortening, p < .0.05 compared with aerobicvalues in the control group, and -32 Δ%, p ≤ 0.05 compared with aerobic values in treatedhearts). This stunning was associated with concordant reductions in myocardial oxygenconsumption during recovery (−15 Δ%, p ≤ 0.02 for the control group, and -21 Δ%, p ≤ 0.01 for the treated group). 14CO2 production from labeled glucose was strongly suppressed duringpreischemic perfusion in both groups, rose slightly during ischemia, and continued to rise in theoxfenicine group during reperfusion to twice the values measured in control hearts (p ≤ 0.01). These responses were contrasted with data from five additional, similarly perfused hearts thatdid not receive Intralipid. Reducing fatty acids twofold In the perfusate caused no majorchanges in glucose oxidation as compared with control hearts. Tissue glycogen was detected inboth aerobic and reperfused myocardium and was unaffected by oxfenicine treatment. Thesedata confirm previous findings and do not support an argument for increased glucose oxidation. Rather, the results support the concept of competitive inhibition of glucose and/or itsintermediates by the preferred use of fatty acids.