Miracle-dz/UniFAR-FTUs huggingface dataset:
Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations

ABSTRACT A fluorescence in situ hybridization-flow cytometry (FISH/FC)-based method was optimized using artificial mixtures of pure cultures of methanotrophic bacteria. Traditional oligonucleotide probes targeting 16S rRNAs of type I (MG84/705 probe) and type II (MA450 probe) methanotrophs were labeled with fluorescein or Alexa fluor and used for FISH, followed by fluorescence-activated FC analysis and cell sorting (FACS). The method resulted in efficient separation of target cells (type I or type II methanotrophs) from the artificial mixtures. The method was then applied for detection and enrichment of type I and type II methanotroph populations from a natural sample, Lake Washington sediment. Cells were extracted from the sediment, fixed, and subjected to FISH/FC/FACS. The resulting subpopulations were analyzed by reverse transcriptase PCR surveys of 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehyde-activating enzyme) genes. The functional gene analysis indicated specific separation of the type I and type II methanotroph populations. 16S rRNA gene analysis revealed that type I methanotrophs comprised 59% of the subpopulation separated using the type I-specific probe and that type II methanotrophs comprised 47.5% of the subpopulation separated using the type II-specific probe. Our data indicate that the FISH/FC/FACS protocol described can provide significant enrichment of microbial populations of interest from complex natural communities and that these can be used for genetic tests. We further tested the possibility of direct whole-genome amplification (WGA) from limited numbers of sorted cells, using artificial mixtures of microbes whose genome sequences are known. We demonstrated that efficient WGA can be achieved using 104 or more cells separated by 16S rRNA-specific FISH/FC/FACS, while fewer cells resulted in less specific WGA.
Predicting audience responses to movie content from electro-dermal activity signals

The ability to assess fine-scale user responses has applications in advertising, content creation, recommendation, and psychology research. Unfortunately, current approaches, such as focus groups and audience surveys, are limited in size and scope. In this paper, we propose a combined biometric sensing and analysis methodology to leverage audience-scale electro-dermal activity (EDA) data for the purpose of evaluating user responses to video. We provide detailed characterization of how temporal physiological responses to video stimulus can be modeled, along with first-of-its-kind audience-scale EDA group experiments in uncontrolled real-world environments. Our study provides insights into the techniques used to analyze EDA, the effectiveness of the different temporal features, and group dynamics of audiences. Our experiments demonstrate the ability to classify movie ratings with accuracy of over 70% on specific films. Results of this study suggest the ability to assess emotional reactions of groups using minimally invasive sensing modalities in uncontrolled environments.
Geometry of the Proximal Phalanx of Hallux and First Metatarsal Bone to Predict Hallux Abducto Valgus: A Radiological Study

Background Hallux abducto valgus (HAV) is one of the most common forefoot deformities in adulthood with a variable prevalence but has been reported as high as 48%. The study proposed that HAV development involves a skeletal parameter of the first metatarsal bone and proximal phalanx hallux (PPH) to determine if the length measurements of the metatarsal and PPH can be used to infer adult HAV. Methods All consecutive patients over 21 years of age with HAV by roentgenographic evaluation were included in a cross-sectional study. The control group included patients without HAV. The study included 160 individuals. We identified and assessed the following radiographic measurements to evaluate HAV: the distances from the medial (LDM), central (LDC), and lateral (LDL) aspects of the base to the corresponding regions of the head of the PPH. The difference between the medial and lateral aspect of PPH was also calculated. Results The reliability of the variables measured in 40 radiographic films show perfect reliability ranging from 0.941 to 1 with a small error ranging from 0.762 to 0. Also, there were no systematic errors between the two measurements for any variable (P > 0.05). The LDM PPH showed the highest reliability and lowest error. Conclusion It is more suitable to measure the LDM PPH instead of the LDC PPH when calculating the hallux valgus angle based on our reliability results. When the differences of the medial and lateral PPH are greater, the risk for developing HAV increases.
Condensation-sorting events in the rough endoplasmic reticulum of exocrine pancreatic cells

In guinea pig exocrine pancreatic cells intracisternal granules (ICGs) occur at a low frequency within the lumen of the RER. By starving and refeeding guinea pigs or injecting them in CoCl2 solution, the number of these granules is greatly increased. We show here that ICGs contain the complete set of secreted pancreatic digestive enzymes and proenzymes. Two other soluble proteins in the lumen of the RER, GRP 78/BiP and protein disulphide isomerase (PDI), are specifically excluded from ICGs. The formation of ICGs, which occurs without acidification of the RER cisternae, is therefore a sorting event involving the cocondensation of a complete set of secretory enzymes and proenzymes, which for brevity we refer to collectively as the zymogens. With the exception of approximately 50% of the RNase, the zymogens in ICGs are covalently cross-linked by intermolecular disulphide bonds. The synthesis of all three resident ER cisternal proteins--PDI, GRP 78/BiP, and GRP 94--with the carboxy-terminal sequence KDEL, is induced in response to the accumulation of massive amounts of misfolded secretory protein in the ICGs in the lumen of the RER. After injection of rats with large doses of parachlorophenylalanine-methylester, crystals form in the lumen of the RER. We show that these crystals appear to be a lattice of amylase with the other zymogens incorporated between the layers. Both GRP 78/BiP and PDI are excluded from these crystals. The formation of these amylase crystals within the RER and the inclusion of other zymogens is, therefore, also a sorting event. These data establish that in exocrine pancreatic cells zymogens can cocondense in the RER into either amorphous aggregates or crystals that exclude other soluble RER proteins. This demonstrates that cocondensation is a mechanism capable of sorting zymogens within the secretory pathway.
Understanding the Nature of Social Mobile Instant Messaging in Cellular Networks

Social mobile instant messaging (MIM) applications, running on portable devices such as smartphones and tablets, have become increasingly popular around the world, and have generated significant traffic demands on cellular networks. Despite its huge user base and popularity, little work has been done to characterize the traffic patterns of MIM. Compared with traditional cellular network service, MIM traffic embodies several specific attributes such as non-Poisson arrivals, keep-alive (KA) mechanism and heavy-tailed message length, which consumes even small amount of core network bandwidth but considerable radio resources of mobile access network. This letter investigates user behavior patterns and traffic characteristics of MIM applications, based on real traffic measurements within a large-scale cellular network covering 7 million subscribers. Moreover, we propose a joint ON/OFF model to describe the traffic characteristics of MIM, and evaluate the performance of cellular network running MIM service in various scenarios. Comparing with the MIM service models of 3GPP, our results are more realistic to estimate the networks performance.
Making Sense of Partial

We address the challenging task of processing partial multimodal utterances in a mixed-initiative dialogue system for multiple applications such as information seeking, device control etc. Based on four dieren t types of expectations computed by our action planner (aka dialog manager), we distinguish between expected utterances, various degrees of unexpected but plausible utterances, and uninterpretable utterances. We include a description of the backbone architecture and the representation formalisms used.
Classification of Words Based on Affix Evidence

Category of a word, as may be indicated in a lexicon, is a useful piece of information for most linguistic exercises. Hence determination of categories of words in a natural language is an important task. There has been much work in Part-of-Speech tagging of words in texts, where the tagset is usually pre-determined and provided to the system. In this work we attempt to determine the categories of the root words of a language by considering the usage of suffixes in a corpus of a (highly) inflectional language. This information can be used in a lexicon. Instead of using a pre-defined list of word categories, we first identify the underlying word categories by using a set-theoretic representation of the information on suffix usage available from the input corpus.
A Multilevel Model to Estimate the Within- and the Between-Center Components of the Exposure/Disease Association in the EPIC Study

In a multicenter study, the overall relationship between exposure and the risk of cancer can be broken down into a within-center component, which reflects the individual level association, and a between-center relationship, which captures the association at the aggregate level. A piecewise exponential proportional hazards model with random effects was used to evaluate the association between dietary fiber intake and colorectal cancer (CRC) risk in the EPIC study. During an average follow-up of 11.0 years, 4,517 CRC events occurred among study participants recruited in 28 centers from ten European countries. Models were adjusted by relevant confounding factors. Heterogeneity among centers was modelled with random effects. Linear regression calibration was used to account for errors in dietary questionnaire (DQ) measurements. Risk ratio estimates for a 10 g/day increment in dietary fiber were equal to 0.90 (95%CI: 0.85, 0.96) and 0.85 (0.64, 1.14), at the individual and aggregate levels, respectively, while calibrated estimates were 0.85 (0.76, 0.94), and 0.87 (0.65, 1.15), respectively. In multicenter studies, over a straightforward ecological analysis, random effects models allow information at the individual and ecologic levels to be captured, while controlling for confounding at both levels of evidence.
A Novel User Interface Approach For Managing Large Character Set on Small Mobile Screen

The constrained nature of Mobile devices imposes great challenges on effective user interfaces for game playability. This paper addresses the issue controlling large set of characters on small screens with constrained mobile keys. To this effect we implemented the a mobile version of the Mauritian Domino ( MomoDomino) game consisting of 27 dominoes to test our novel interface design for the control of large character on small screens using the same mobile keys. We investigated on various display layout and their corresponding algorithm and complexity before choosing an optimal layout. In addition, we investigated on an intuitive and seamless game play interface, the novelty being the ability to select and play dominoes using the same key-inputs. Game design methodologies and game mechanics were included for enhanced user-immersion in the game. The results of our design proved to be very intuitive and hence conclusive in terms of game playability. In addition, an optimized display strategy of game components was achieved, hence maximizing space usage on small screens. Our game was tested with excellent feedback by university students. The results obtained can therefore provide a useful guidance for future interface design on small display devices.
Increasing Affinity of Interferon-γ Receptor 1 to Interferon-γ by Computer-Aided Design

We describe a computer-based protocol to design protein mutations increasing binding affinity between ligand and its receptor. The method was applied to mutate interferon-γ receptor 1 (IFN-γ-Rx) to increase its affinity to natural ligand IFN-γ, protein important for innate immunity. We analyzed all four available crystal structures of the IFN-γ-Rx/IFN-γ complex to identify 40 receptor residues forming the interface with IFN-γ. For these 40 residues, we performed computational mutation analysis by substituting each of the interface receptor residues by the remaining standard amino acids. The corresponding changes of the free energy were calculated by a protocol consisting of FoldX and molecular dynamics calculations. Based on the computed changes of the free energy and on sequence conservation criteria obtained by the analysis of 32 receptor sequences from 19 different species, we selected 14 receptor variants predicted to increase the receptor affinity to IFN-γ. These variants were expressed as recombinant proteins in Escherichia coli, and their affinities to IFN-γ were determined experimentally by surface plasmon resonance (SPR). The SPR measurements showed that the simple computational protocol succeeded in finding two receptor variants with affinity to IFN-γ increased about fivefold compared to the wild-type receptor.
Digital Right Management for IP Protection

The Digital Rights Management (DRM) principle is generally well known for the exchange of files (music, video), or software management. Specialized solutions concerning vprofessional software are behind a business called "Software License Managemen". The concept of DRM can be transposed to other areas, in particular to the design of hardware devices. Although the concept of DRM is allowed and widely used in the field of software, this is not the case for Integrated Circuit design (no industrial solutions to date are actually proposed). We propose into this paper a new approach based on a original way to extract Physically Unclonable Function which is at the heart of the DRM proposal.
The Influence of Flexible Bending on the Electrodynamic Characteristics of RFID Tags

In this paper, we study the effect of the bending effect on the electrodynamic characteristics of the RFID tag. The simulation of RFID tags with a more complex topology was carried out. An antenna based on a circular meander line was taken as the basis of the tag and its reduced model was presented. The results of the study allow us to see the negative changes in the electrodynamic characteristics during flexible deformations. This will allow to take into account during design and production the features of the behavior of RFID tags during operation (transportation, wear, etc.) in order to increase the likelihood of reading tags under adverse operating conditions.
Quantifying levels of animal activity using camera trap data

Activity level (the proportion of time that animals spend active) is a behavioural and ecological metric that can provide an indicator of energetics, foraging effort and exposure to risk. However, activity level is poorly known for free‐living animals because it is difficult to quantify activity in the field in a consistent, cost‐effective and non‐invasive way. This article presents a new method to estimate activity level with time‐of‐detection data from camera traps (or more generally any remote sensors), fitting a flexible circular distribution to these data to describe the underlying activity schedule, and calculating overall proportion of time active from this. Using simulations and a case study for a range of small‐ to medium‐sized mammal species, we find that activity level can reliably be estimated using the new method. The method depends on the key assumption that all individuals in the sampled population are active at the peak of the daily activity cycle. We provide theoretical and empirical evidence suggesting that this assumption is likely to be met for many species, but may be less likely met in large predators, or in high‐latitude winters. Further research is needed to establish stronger evidence on the validity of this assumption in specific cases; however, the approach has the potential to provide an effective, non‐invasive alternative to existing methods for quantifying population activity levels.
The Fastest Arbitrary k-space Trajectories

Introduction: We present a method to compute the fastest possible gradient waveforms for a given k-space trajectory. In our design, we exploit the fact that each gradient set has its own limitation. This is an extension of our previous method described in [1]. In that solution, the worst-case magnitude gradient and slew constraints were considered. This has the advantage of resulting in waveforms that are invariant to any rotation of the trajectory, at the expense of sub-utilizing the hardware. Here, we present an improvement of the algorithm. We constraint the waveforms for each gradient set separately, while still requiring that the trajectory follows the desired kspace path. This produces the fastest waveforms. A redesign is needed when the trajectory is rotated, as the solution depends on the orientation of the curve. Our algorithm is fast and non-iterative and can compute waveforms on-the-fly.
The Dynamics Of Cultural Change In An Enterprise Systems Implementation

Enterprise systems (ES) are important cross-business software that can be difficult to implement. A key factor impacting ES implementation lies with the influence of organisational culture which may enable or hinder such implementations. Existing research has focused on culture as being a stable, homogenous variable and little consideration has been given to the dynamics of cultural and organisational change during ES implementations. This study addresses such gaps with an in-depth case study that examined an enhancement of an ERP system. The results identified three dimensions where there was evidence of a cultural conflict between the organisation and the ES implementation, and that different subcultures within the organisation operated in different ways to facilitate or impede the adoption of the system for these groups. The evidence also showed that the implementation resulted in cultural changes within the organisation to reflect the values embedded in the ES. This research therefore provides valuable insights into cultural effects of large-scale implementations at an organisational level and shows that such effects are not necessarily homogenous and may vary due to the cultural values of subgroups involved.
Synthesis of Duplexers With the Common Port Matched at All Frequencies

In this paper, we present a novel approach to the synthesis of duplexers with the antenna port matched at all frequencies without the use of 90° hybrids. The design is based on the synthesis of a three-port prototype network composed of coupled resonators, which models the duplexer in a normalized low-pass frequency domain. The polynomials characterizing this network are derived under the lossless assumption and imposing a particular condition on the polynomial determinant of the scattering matrix. Based on these polynomials, the synthesis of the canonical transversal prototype is performed. A new algorithm based on rotations of the coupling matrix is then introduced for the generation of new topologies, potentially more advantageous for the practical implementation. The proposed design approach is illustrated with several examples and by means of a test device, which has been designed and fabricated. The measurements have shown to be in excellent agreement with the expectations.
The Effectiveness of Simple Decision Heuristics : A Case Study of Experts ’ Forecasts of the Commercial Success of Early-Stage R & D Projects

ast that early-s evaluate 37 by examining cast. We use a eparately and of the experts' correct forecasts. We then compare predictions derived from the conjunctive model, analysts' ns. The 82.6%, out-of-time tests. Results indicate that simple decision heuristics perform better than ABSTRACT We investigate the decision heuristic used by experts to forec stage R&D projects are subsequently commercialized. Expert project characteristics and subjectively combine data on all cues both critical flaws as well as positive factors to arrive at a fore conjunctive model that sums " good " and " bad " cue counts s achieve a 94.1% classification accuracy forecasts and a statistical model with future project commercializatio conjunctive model correctly predicts 86.0%, experts correctly predict while a statistical model correctly predicts 78.6% in out-of-sample, statistically derived decision rules in a real setting.
Social Graph Generation & Forecasting Using Social Network Mining

Considering the noticeable attraction of users to social networking sites, lots of research has been carried out to take advantage of the users’ information available in these sites. Knowledge mining techniques have been developed in order to extract valuable pieces of information from the users’ activities. This paper deals with a methodology to generate a social graph of users’ actions and predict the future social activities of the users based upon the existing relationships. This graph is updated dynamically based on the changes in the selected social network. The forecasting performed is based upon some predefined rules applied on the graph.
What is the carrying capacity for fish in the ocean? A meta-analysis of population dynamics of North Atlantic cod

Population and community data in one study are usually analyzed in isolation from other data. Here, we in- troduce statistical methods that allow many data sets to be analyzed simultaneously such that different studies may "borrow strength" from each other. In the simplest case, we simultaneously model 21 Atlanic cod (Gadus morhua) stocks in the North Atlantic assuming that the maximum reproductive rate and the carrying capacity per unit area are random variables. This method uses a nonlinear mixed model and is a natural approach to investigate how carrying ca- pacity varies among populations. We used empirical Bayes techniques to estimate the maximum reproductive rate and carrying capacity of each stock. In all cases, the empirical Bayes estimates were biologically reasonable, whereas a stock by stock analysis occasionally yielded nonsensical parameter estimates (e.g., infinite values). Our analysis showed that the carrying capacity per unit area varied by more than 20-fold among populations and that much of this variation was related to temperature. That is, the carrying capacity per square kilometre declines as temperature increases. Resume : Les donnees provenant d'etudes demographiques ou biocenotiques sont habituellement analysees separement les unes des autres. On trouvera ici des methodes statistiques qui permettent l'analyse simultanee de plusieurs series de donnees de facon a ce que les differentes etudes se renforcent mutuellement. Le cas le plus simple consiste en une mo- delisation simultanee de 21 stocks de morues franches (Gadus morhua) de l'Atlantique nord qui presume que le taux maximal de reproduction et la capacite limite par unite de surface sont des variables aleatoires. La methode utilise un modele mixte non-lineaire et elle se revele etre une strategie naturelle pour l'etude de la variation de la capacite limite chez les populations. Des techniques empiriques bayesiennes ont servi a estimer le taux maximal de reproduction et la capacite limite de chaque stock. Dans tous les cas, les estimes obtenus sont biologiquement vraisemblables; en re- vanche, des analyses faites stock par stock generent a l'occasion des estimations absurdes (e.g., des valeurs infinies). Nos analyses montrent que la capacite limite par unite de surface varie d'un facteur de plus de 20 d'une population a une autre et qu'une partie importante de cette variation est reliee a la temperature. En effet, la capacite limite par kilo- metre carre decline a mesure que la temperature augmente.