Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconstructing Genome-Wide Protein–Protein Interaction Networks Using Multiple Strategies with Homologous Mapping

Background One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein–protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been proposed for predicting PPIs from the known PPIs of source organisms. Results Here, we propose a multiple-strategy scoring method to identify reliable PPIs for reconstructing the mouse PPI network from two well-known organisms: human and fly. We firstly identified the PPI candidates of target organisms based on homologous PPIs, sharing significant sequence similarities (joint E-value ≤ 1 × 10−40), from source organisms using generalized interolog mapping. These PPI candidates were evaluated by our multiple-strategy scoring method, combining sequence similarities, normalized ranks, and conservation scores across multiple organisms. According to 106,825 PPI candidates in yeast derived from human and fly, our scoring method can achieve high prediction accuracy and outperform generalized interolog mapping. Experiment results show that our multiple-strategy score can avoid the influence of the protein family size and length to significantly improve PPI prediction accuracy and reflect the biological functions. In addition, the top-ranked and conserved PPIs are often orthologous/essential interactions and share the functional similarity. Based on these reliable predicted PPIs, we reconstructed a comprehensive mouse PPI network, which is a scale-free network and can reflect the biological functions and high connectivity of 292 KEGG modules, including 216 pathways and 76 structural complexes. Conclusions Experimental results show that our scoring method can improve the predicting accuracy based on the normalized rank and evolutionary conservation from multiple organisms. Our predicted PPIs share similar biological processes and cellular components, and the reconstructed genome-wide PPI network can reflect network topology and modularity. We believe that our method is useful for inferring reliable PPIs and reconstructing a comprehensive PPI network of an interesting organism.
Sparse Projections over Graph

Recent study has shown that canonical algorithms such as Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) can be obtained from graph based dimensionality reduction framework. However, these algorithms yield projective maps which are linear combination of all the original features. The results are difficult to be interpreted psychologically and physiologically. This paper presents a novel technique for learning a sparse projection over graphs. The data in the reduced subspace is represented as a linear combination of a subset of the most relevant features. Comparing to PCA and LDA, the results obtained by sparse projection are often easier to be interpreted. Our algorithm is based on a graph embedding model, which encodes the discriminating and geometrical structure in terms of the data affinity. Once the embedding results are obtained, we then apply regularized regression for learning a set of sparse basis functions. Specifically, by using L1-norm regularizer (e.g. lasso), the sparse projections can be efficiently computed. Experimental results on two document databases demonstrate the effectiveness of our method.
Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

Next-generation sequencing technologies can be used to analyse genetically heterogeneous samples at unprecedented detail. The high coverage achievable with these methods enables the detection of many low-frequency variants. However, sequencing errors complicate the analysis of mixed populations and result in inflated estimates of genetic diversity. We developed a probabilistic Bayesian approach to minimize the effect of errors on the detection of minority variants. We applied it to pyrosequencing data obtained from a 1.5-kb-fragment of the HIV-1 gag/pol gene in two control and two clinical samples. The effect of PCR amplification was analysed. Error correction resulted in a two- and five-fold decrease of the pyrosequencing base substitution rate, from 0.05% to 0.03% and from 0.25% to 0.05% in the non-PCR and PCR-amplified samples, respectively. We were able to detect viral clones as rare as 0.1% with perfect sequence reconstruction. Probabilistic haplotype inference outperforms the counting-based calling method in both precision and recall. Genetic diversity observed within and between two clinical samples resulted in various patterns of phenotypic drug resistance and suggests a close epidemiological link. We conclude that pyrosequencing can be used to investigate genetically diverse samples with high accuracy if technical errors are properly treated.
Shape-based interpolation of binary 3-D images using morphological skeletonization

In this paper, the morphological skeleton interpolation (MSI) algorithm is presented. It is an efficient shape-based interpolation method used for interpolating slices between successive slices of a 3D object. It is based on the well known mathematical morphology procedure of morphological skeletonization, that is used as a representation of an object. The proposed morphological skeleton matching process provides translation, rotation and scaling information at the same time. The interpolated slices preserve the shape of the original object slices, when the slices have similar shapes. It can also modify the shape of an object when the successive slices have not got similar shapes. Applications on artificial and real data are also presented.
Assessing Users' Attachment to Their Mobile Devices

Mobile devices are often described as very personal objects and users are said to develop deep relationships with them. Motivated by such recurring statements, this paper introduces user-device attachment as a concept describing the relationship between users and their mobile devices. By drawing on literature from marketing, HCI, and sociology, the domain and dimensions of user-device attachment are described. Three dimensions: symbolism, aesthetics, and perceived necessity are conceptualized to represent elements of user-device attachment. An initial instrument for measurement is developed and assessed with exploratory and confirmatory factor analyses. Corresponding with the conceptualized dimensions, a three-factor solution was found and confirmed using data gathered in two surveys (n1=130, n2=323). The resulting instrument provides a basis for future discussions and conceptual and empirical work on the phenomenon of user-device attachment in mobile user behavior. Possible benefits of applying the construct to areas like mobile advertising and mobile service development are identified.
First investigation of feasibility of contact-less non-destructive optical sensors to detect, acquire and digitally process forensic handwriting based on pressure information

Both in biometric and forensic sciences, handwriting modality plays an important role. While in biometrics, the sub-discipline of online analysis utilises recordings of the actual writing process, offline analysis has a close link to handwriting forensics. In the later domain, goals comprise for example writer identification or uncover indented writing of found writing traces on documents. In this paper we study the general feasibility of a new approach to handwriting forensics by means of three contact-less non-destructive 2D/3D optical sensors providing high resolution images in the nanometer range which have already shown great potential for the digitised crime scene forensics e.g for fingerprints or gun cartridges. We perform a three-step concept: First, in a general sensor review we identify one sensor which appears most appropriate for our initial use cases, along with appropriate parametrization. Secondly, we propose a first test setup for the acquisition of handwriting traces on paper. The corresponding data is captured from the first and second layer of a five sheets paper stack. Thirdly, we present and discuss our first results of digital image pre-processing based on topographic information representing the pen pressure during the writing process. Our pre-processing approach is focused on segmenting the writing trace in topographical data. For segmentation of the trace we apply different linear filter like mean or binomial as well as non-linear filter like median.
Dealing with acoustic mismatch for training multilingual subspace Gaussian mixture models for speech recognition

The subspace Gaussian mixture model (SGMM) has been recently proposed as an acoustic modeling technique suitable for configuring multilingual speech recognition systems. It is attractive for this purpose since its parametrization allows its “shared” model parameters to be trained with data from multiple languages [1]. In this work, we report on the results of an experimental study carried out with the goal of improving native Spanish language speech recognition performance using an existing telephone speech corpus of English spoken by speakers of Spanish origin. Compensation for sources of acoustic variability between Spanish and English language data sets was found to be important in obtaining good multilingual ASR performance. We conclude with a discussion about the notion of acoustic similarity between the state dependent parameters of the SGMM, and its possible use in effectively modelling pronunciation variation.
Multiple Phosphorylation of SacY, a Bacillus subtilisTranscriptional Antiterminator Negatively Controlled by the Phosphotransferase System*

The Bacillus subtilis SacY transcriptional antiterminator is a regulator involved in sucrose-promoted induction of the sacB gene. SacY activity is negatively controlled by enzyme I and HPr, the general energy coupling proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PTS), and by SacX, a membranal protein homologous to SacP, theB. subtilis sucrose-specific PTS-permease. Previous studies suggested that the negative control exerted by the PTS on bacterial antiterminators of the SacY family involves phosphoenolpyruvate-dependent phosphorylation by the sugar-specific PTS-permeases. However, data reported herein show direct phosphorylation of SacY by HPr(His∼P) with no requirement for SacX. Experiments were carried out to determine the phosphorylatable residues in SacY. In silico analyses of SacY and its homologues revealed the modular structure of these proteins as well as four conserved histidines within two homologous domains (here designated P1 and P2), present in 14 distinct mRNA- and DNA-binding bacterial transcriptional regulators. Single or multiple substitutions of these histidyl residues were introduced in SacY by site-directed mutagenesis, and their effects on phosphorylation and antitermination activity were examined. In vitro phosphorylation experiments showed that SacY was phosphorylated on three of the conserved histidines. Nevertheless, in vivo studies using cells bearing asacB′-lacZ reporter fusion, as well as SacY mutants lacking the phosphorylatable histidyls, revealed that only His-99 is directly involved in regulation of SacY antitermination activity.
A parameter identification algorithm for the METANET model with a limited number of loop detectors

This paper analyzes the parameter identification of the macroscopic traffic flow model METANET. In previous papers, this calibration has been done by minimizing numerically the difference between the data and the prediction of the model. Results indicate that this optimization usually falls in quite suboptimal local minima, especially when there are sensors only available in some segments. The authors propose an identification procedure where the calibration is done in 3 main steps: Firstly, the parameters of the fundamental diagram for each segment with data available are found. Subsequently, the parameters of the speed equation are computed using an optimization procedure considering the values of the fundamental diagram as known. Lastly, a global optimization is run in order to improve the final identification. Moreover, a new mathematical definition of the fundamental diagram is proposed. The identification algorithm was tested over a section of the I-210 West in Southern California, using several days of loop detector data collected during the morning rush-hour period. The results shows a good estimation of both densities and speeds with a mean error of 10.95% and 11.35%, respectively.
Pathogenic Lysosomal Depletion in Parkinson's Disease

Mounting evidence suggests a role for autophagy dysregulation in Parkinson's disease (PD). The bulk degradation of cytoplasmic proteins (including α-synuclein) and organelles (such as mitochondria) is mediated by macroautophagy, which involves the sequestration of cytosolic components into autophagosomes (AP) and its delivery to lysosomes. Accumulation of AP occurs in postmortem brain samples from PD patients, which has been widely attributed to an induction of autophagy. However, the cause and pathogenic significance of these changes remain unknown. Here we found in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine mouse model of PD that AP accumulation and dopaminergic cell death are preceded by a marked decrease in the amount of lysosomes within dopaminergic neurons. Lysosomal depletion was secondary to the abnormal permeabilization of lysosomal membranes induced by increased mitochondrial-derived reactive oxygen species. Lysosomal permeabilization resulted in a defective clearance and subsequent accumulation of undegraded AP and contributed directly to neurodegeneration by the ectopic release of lysosomal proteases into the cytosol. Lysosomal breakdown and AP accumulation also occurred in PD brain samples, where Lewy bodies were strongly immunoreactive for AP markers. Induction of lysosomal biogenesis by genetic or pharmacological activation of lysosomal transcription factor EB restored lysosomal levels, increased AP clearance and attenuated 1-methyl-4-phenylpyridinium-induced cell death. Similarly, the autophagy-enhancer compound rapamycin attenuated PD-related dopaminergic neurodegeneration, both in vitro and in vivo, by restoring lysosomal levels. Our results indicate that AP accumulation in PD results from defective lysosomal-mediated AP clearance secondary to lysosomal depletion. Restoration of lysosomal levels and function may thus represent a novel neuroprotective strategy in PD.
Scalable on-demand media streaming with packet loss recovery

Inspired by recent techniques for reliable bulk data distribution, this paper develops scalable protocols for reliable on-demand delivery of streaming media. Models are developed that quantify the best possible scalability for given client characteristics. The results of the models are used to guide the design and assess the performance of the proposed streaming techniques. The new protocols, RPB and RBS, are relatively simple to implement and achieve nearly the best possible scalability and efficiency for a given set of client characteristics and desirable/feasible media quality.
Isolation, Culture, and Transfection of Melanocytes

Located in the basal epidermis and hair follicles, melanocytes of the integument are responsible for its coloration through production of melanin pigments. Melanin is produced in lysosomal‐like organelles called melanosomes. In humans, this skin pigmentation acts as an ultraviolet radiation filter. Abnormalities in the division of melanocytes are quite common, with potentially oncogenic growth usually followed by cell senescence producing benign naevi (moles), or occasionally melanoma. Therefore, melanocytes are a useful model for studying melanoma, as well as pigmentation and organelle transport and the diseases affecting these mechanisms. This chapter focuses on the isolation, culture, and transfection of human and murine melanocytes. The first basic protocol describes the primary culture of melanocytes from human skin and the maintenance of growing cultures. The second basic protocol details the subculture and preparation of mouse keratinocyte feeder cells. The primary culture of melanocytes from mouse skin is described in the third basic protocol, and, lastly, the fourth basic protocol outlines a technique for transfecting melanocytes and melanoma cells. Curr. Protoc. Cell Biol. 63:1.8. 1‐1.8. 20. © 2014 by John Wiley & Sons, Inc.
Professional Practice and Innovation: Level of Agreement between Coding Sources of Percentage Total Body Surface Area Burnt (%TBSA)

The percentage of total body surface area burnt (%TBSA) is a critical measure of burn injury severity and a key predictor of burn injury outcome. This study evaluated the level of agreement between four sources of %TBSA using 120 cases identified through the Victorian State Trauma Registry. Expert clinician, ICD-10-AM, Abbreviated Injury Scale, and burns registry coding were compared using measures of agreement. There was near-perfect agreement (weighted Kappa statistic 0.81–1) between all sources of data, suggesting that ICD-10-AM is a valid source of %TBSA and use of ICD-10-AM codes could reduce the resource used by trauma and burns registries capturing this information.
Resolving social conflict among females without overt aggression

Members of animal societies compete over resources and reproduction, but the extent to which such conflicts of interest are resolved peacefully (without recourse to costly or wasteful acts of aggression) varies widely. Here, we describe two theoretical mechanisms that can help to understand variation in the incidence of overt behavioural conflict: (i) destruction competition and (ii) the use of threats. The two mechanisms make different assumptions about the degree to which competitors are socially sensitive (responsive to real-time changes in the behaviour of their social partners). In each case, we discuss how the model assumptions relate to biological reality and highlight the genetic, ecological and informational factors that are likely to promote peaceful conflict resolution, drawing on empirical examples. We suggest that, relative to males, reproductive conflict among females may be more frequently resolved peacefully through threats of punishment, rather than overt acts of punishment, because (i) offspring are more costly to produce for females and (ii) reproduction is more difficult to conceal. The main need now is for empirical work to test whether the mechanisms described here can indeed explain how social conflict can be resolved without overt aggression.
Finite volume schemes for the biharmonic problem on general meshes

Finite volume schemes for the approximation of a biharmonic problem with Dirichlet boundary conditions are constructed and analyzed, first on grids which satisfy an orthogonality condition, and then on general, possibly non conforming meshes. In both cases, the piece-wise constant approximate solution is shown to converge in L2 () to the exact solution; similar results are shown for the discrete approximate of the gradient and the discrete approximate of the Laplacian of the exact solution. Error estimates are also derived. These results are confirmed by numerical results.
Dichloridobis(2-chlorobenzyl-κC)[5,6-diphenyl-3-(2-pyridyl)-1,2,4-triazine-κ2 N 2,N 3]tin(IV)

The asymmetric unit of the crystal structure of the title compound, [Sn(C7H6Cl)2Cl2(C20H14N4)], contains two independent molecules. Each SnIV atom is chelated by the bipyridine-like N-heterocycle and exists in a distorted trans-C2SnCl2N2 octahedral coordination environment. One chlorobenzyl substituent is disordered in each molecule in 0.5:0.5 and 0.778 (2):0.222 (2) ratios.
Joining Cognitive Capabilities in 3D Media Spaces

A non-destructive method of electro-coating a preselected pattern of electrically insulating or conducting material onto a semiconductor device which includes a photoresponsive junction. The method includes the step of illuminating the semiconductor device prior to initiating the flowing of electro-coating current therethrough. The method has particular utility in providing electroplated grid patterns and connections on large area photovoltaic cells. Also disclosed is the use of current generated by a photovoltaic cell to effect the electro-coating thereof.
Burst optical deflection routing protocol for wavelength routing WDM networks

Given the significant progress made and the continuing advances expected in the optical networking technology, it becomes attractive to build a future Optical Internet that natively supports bursty IP datagrams. Burst switching WDM optical networks are touted as suitable network architectures for future Optical Internet backbones. However, the lack of optical processing capabilities results in increased burst blocking probability, which in turn leads to very limited network performance. Efficient contention resolution method is therefore necessary. Based on discussions of the state of the art of recent optical technologies, a burst optical deflection routing protocol is proposed. The idea of this approach is to use idle optical links as fiber delay lines for contention resolution. Simulation results show that the proposed protocol is available solution for effectively reducing the blocking probability and increasing the performance of burst switching WDM optical networks.
Building an Anti-phishing Game to Enhance Network Security Literacy Learning

Internet phishing attack is increasing and causing enormous economic loss in recent years. The network security literacy learning for educating students to defense phishing attack becomes more important. However, with the growing of attacking tricks, the anti-phishing knowledge is continuously increasing. The traditional learning platform with antiphishing technical documents is not sufficient for students to prevent the phishing attacks. To transform the continuously increasing anti-phishing knowledge to learning materials, the Bloom's taxonomy of cognitive domain was used to classify anti-phishing knowledge into different levels of learning skills. Since traditional anti-phishing documents are difficult to read for students, the Anti-phishing Education Game was developed to provide an interactive narrative learning environment for learning by doing. Thus, the game missions can be adaptively provided to students based on their learning achievements and engage students' attention. The experimental result shows that students have significant progress in identifying phishing page and high learning motivation by using our approach.