Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a keratinase activity assay using recombinant chicken feather keratin substrates

Poultry feathers consist mainly of the protein keratin, which is rich in β-pleated sheets and consequently resistant to proteolysis. Although many keratinases have been identified, the reasons for their substrate specificity towards β-keratin remain unclear due to difficulties in preparing a soluble feather keratin substrate for use in activity assays. In the present study, we overexpressed Gallus gallus chromosomes 2 and 27 β-keratin-encoding genes in Escherichia coli, purified denatured recombinant proteins by Ni2+ affinity chromatography, and refolded by stepwise dialysis to yield soluble keratins. To assess the keratinolytic activity, we compared the proteolytic activity of crude extracts from the feather- degrading bacterium Fervidobacterium islandicum AW-1 with proteinase K, trypsin, and papain using purified recombinant keratin and casein as substrates. All tested proteases showed strong proteolytic activities for casein, whereas only F. islandicum AW-1 crude extracts and proteinase K exhibited pronounced keratinolytic activity for the recombinant keratin. Moreover, LC-MS/MS analysis of keratin hydrolysates allowed us to predict the P1 sites of keratinolytic enzymes in the F. islandicum AW-1 extracts, thereby qualifying and quantifying the extent of keratinolysis. The soluble keratin-based assay has clear therapeutic and industrial potential for the development of a high-throughput screening system for proteases hydrolyzing disease-related protein aggregates, as well as mechanically resilient keratin-based polymers.
A Novel Clusterer Ensemble Algorithm Based on Dynamic Cooperation

As the better generalization ability of clusterer ensemble methods, they are widely applied to diverse domains. But now many challenges still exist. One of the drawbacks of the ensemble is, ignoring the valuable information contained in the process of training component clusterers. This paper explores a new ensemble method for cluster analysis based on dynamic cooperation, and this method adjusts the centroids using the information provided by all component clusterers. The basic idea is to make training information fully sharable in the ensemble method. We apply the proposed ensemble method to the UCI benchmark data sets and the experimental results show that the approach provides a practical solution.
The Process of Knowledge Discovery in Databases: A First Sketch

The general idea of discovering knowledge in large amounts of data is both appealing and intuitive. Typically we focus our attention on learning algorithms, which provide the core capability of generalizing from large numbers of small, very specific facts to useful high-level rules; these learning technique's seem to hold the most excitement and perhaps the most substantive scientific content in the knowledge discovery in databases (KDD) enterprise. However, when we engage in real-world discovery tasks, we find that they can be extremely complex, and that induction of rules is only one small part of the overall process. While others have written overviews of the concept of KDD, and even provided block diagrams for "knowledge discovery systems," no one has begun to identify all of the building blocks in a realistic KDD process. This is what we attempt to do here. Besides bringing into the discussion several parts of the process that have received inadequate attention in the KDD community, a careful elucidation of the steps in a realistic knowledge discovery process can provide a framework for comparison of different technologies and tools that are almost impossible to compare without a clean model.
Parallel efficient implementation of hierarchical algorithms for module placement of large chips

The PROUD module placement algorithm mainly uses a hierarchical decomposition technique and the solution of sparse linear systems based on a resistive network analogy. It has been shown that the PROUD algorithm can achieve a comparable design of the placement problems for very large circuits with the best placement algorithm based on simulated annealing, but with several order of magnitude faster. The modified PROUD, namely MPROUD algorithm by perturbing the coefficient matrices performs much faster that the original PROUD algorithm. Due to the instability and unguaranteed convergence of MPROUD algorithm we have proposed a new convergent and numerically stable PROUD, namely Improved PROUD algorithm, denoted as IPROUD with attractive computational costs to solve the module placement problems by making use of the MINRES method based on Lanczos process. In this paper, we subsequently propose parallel versions of the original, modified and improved PROUD algorithms that combine both fine and coarse grain parallelism to obtain another order of magnitude improvement in the runtime without loss of the quality of the layout. Experimental results using Message Passing Interface (MPI) on various multiprocessor systems are reported showing its advantages for a variety of large layout benchmark circuits.
A New Semantic Web Approach for Constructing, Searching and Modifying Ontology Dynamically

Semantic web is the next generation web, which concerns the meaning of web documents It has the immense power to pull out the most relevant information from the web pages, which is also meaningful to any user, using software agents. In today's world, agent communication is not possible if concerned ontology is changed a little. We have pointed out this very problem and developed an Ontology Purification System to help agent communication. In our system you can send queries and view the search results. If it can't meet the criteria then it finds out the mismatched elements. Modification is done within a second and you can see the difference. That's why we emphasis on the word dynamic. When Administrator is updating the system, at the same time that updation is visible to the user.
Plasmid-homologous sequences in the chromosome of plasmidless Coxiella burnetii Scurry Q217

Chromosomal DNA from Coxiella burnetii Scurry Q217 was screened for the presence of plasmid-homologous sequences. Total DNA from Scurry Q217 was digested with NotI, and the resulting DNA fragments were separated by contour-clamped homogeneous electric field pulsed-field gel electrophoresis (CHEF-PFGE). Following hybridization with biotin-labeled QpH1 plasmid as a probe, two DNA fragments of 40 and 170 kb were identified as targets. These fragments were cloned, and subclones containing QpH1-homologous sequences were completely sequenced. The physical mapping of DNA fragments was achieved by PCR with primers derived from adjacent fragments, and a total of 18,360 bp was sequenced. Within the QpH1-homologous region spanning 16,624 bp, homology was as high as 99%. Deletions were identified within EcoRI fragments A(H)-C(H)-K(H)-B(H) (13,490 bp) and J(H)-G(H)-E(H)-L+-D(H) (6,509 bp) and in fragment A(H) alone (619 bp). An insertion of 744 bp was identified within the JDc region of Scurry Q217. A search for putative coding regions identified a total of 17 open reading frames (ORFs). Compared to plasmid QpH1, 6 ORFs were identical, 5 ORFs were different in size, 6 ORFs were newly generated, and 25 ORFs were lost. It was found that plasmid-homologous sequences in Scurry Q217 were of chromosomal origin.
Architecture for comparing alternative designs of a tactical naval Command and Control system using discrete-event simulation

Research was conducted recently at Naval Postgraduate School focusing on the development of a system architecture for a tactical naval Command and Control (C2) system. The system architecture methodology started with describing an operational concept, moved to the co-development of the functional architecture and the physical architecture, and concluded with the development of a notional operational architecture. A portion of the contact prosecution process for a Surface Action Group (SAG) involved in securing local sea control was modeled in the discrete-event simulation software Arena®, and this effort is the focus of this paper. Simulations for both potential alternative designs were conducted. Finally, a comparison of the simulation results demonstrated the feasibility of the developed architecture framework to compare alternative designs of the C2 system.
Automatic pupillometry from digital images

Determination of two-dimensional characteristics of the anterior surface of the eye is becoming increasingly important in modern optometry and ophthalmology practice. In particular, accurate estimation of the pupil size and centration is crucial in customized refractive surgery, corneal transplantation, and advanced contact lens fitting. The pupil parameters change under different lighting conditions so they often need to be related to some fixed reference such as the limbus outline. However, current commercial pupillometers do not estimate limbus position. We present a novel algorithm for automatic extraction of pupil parameters from digital images that takes the relative limbus information into account. The algorithm utilizes several customized image processing techniques that form a robust procedure which performs well for a wide range of clinical images. We apply the developed algorithm to images obtained by a standard digital camera, and specialized ophthalmic instruments such as a wavefront sensor and a high-speed imaging system.
A Novel Expectation-Maximization Framework for Speech Enhancement in Non-Stationary Noise Environments

Voiced speeches have a quasi-periodic nature that allows them to be compactly represented in the cepstral domain. It is a distinctive feature compared with noises. Recently, the temporal cepstrum smoothing (TCS) algorithm was proposed and was shown to be effective for speech enhancement in non-stationary noise environments. However, the missing of an automatic parameter updating mechanism limits its adaptability to noisy speeches with abrupt changes in SNR across time frames or frequency components. In this paper, an improved speech enhancement algorithm based on a novel expectation-maximization (EM) framework is proposed. The new algorithm starts with the traditional TCS method which gives the initial guess of the periodogram of the clean speech. It is then applied to an L1 norm regularizer in the M-step of the EM framework to estimate the true power spectrum of the original speech. It in turn enables the estimation of the a-priori SNR and is used in the E-step, which is indeed a logmmse gain function, to refine the estimation of the clean speech periodogram. The M-step and E-step iterate alternately until converged. A notable improvement of the proposed algorithm over the traditional TCS method is its adaptability to the changes (even abrupt changes) in SNR of the noisy speech. Performance of the proposed algorithm is evaluated using standard measures based on a large set of speech and noise signals. Evaluation results show that a significant improvement is achieved compared to conventional approaches especially in non-stationary noise environment where most conventional algorithms fail to perform.
A museum guide robot: Dealing with multiple participants in the real-world

Using video-recordings from a real-world eld trial of a mu-seum guide robot, we show how a robot's gaze influences the visitors' state of participation in group constellations. Then, we compare the robot's conduct to a human tour guide's gaze strategies. We argue that a robot system, to deal with real-world everyday situations, needs to be equipped with knowledge about interactional coordination, incremental processing and strategies for pro-actively shaping the users' conduct.
Deregulation of the CEACAM Expression Pattern Causes Undifferentiated Cell Growth in Human Lung Adenocarcinoma Cells

CEACAM1, CEA/CEACAM5, and CEACAM6 are cell adhesion molecules (CAMs) of the carcinoembryonic antigen (CEA) family that have been shown to be deregulated in lung cancer and in up to 50% of all human cancers. However, little is known about the functional impact of these molecules on undifferentiated cell growth and tumor progression. Here we demonstrate that cell surface expression of CEACAM1 on confluent A549 human lung adenocarcinoma cells plays a critical role in differentiated, contact-inhibited cell growth. Interestingly, CEACAM1-L, but not CEACAM1-S, negatively regulates proliferation via its ITIM domain, while in proliferating cells no CEACAM expression is detectable. Furthermore, we show for the first time that CEACAM6 acts as an inducer of cellular proliferation in A549 cells, likely by interfering with the contact-inhibiting signal triggered by CEACAM1-4L, leading to undifferentiated anchorage-independent cell growth. We also found that A549 cells expressed significant amounts of non-membrane anchored variants of CEACAM5 and CEACAM6, representing a putative source for the increased CEACAM5/6 serum levels frequently found in lung cancer patients. Taken together, our data suggest that post-confluent contact inhibition is established and maintained by CEACAM1-4L, but disturbances of CEACAM1 signalling by CEACAM1-4S and other CEACAMs lead to undifferentiated cell growth and malignant transformation.
SuperPatchMatch: An Algorithm for Robust Correspondences Using Superpixel Patches

Superpixels have become very popular in many computer vision applications. Nevertheless, they remain underexploited, since the superpixel decomposition may produce irregular and nonstable segmentation results due to the dependency to the image content. In this paper, we first introduce a novel structure, a superpixel-based patch, called SuperPatch. The proposed structure, based on superpixel neighborhood, leads to a robust descriptor, since spatial information is naturally included. The generalization of the PatchMatch method to SuperPatches, named SuperPatchMatch, is introduced. Finally, we propose a framework to perform fast segmentation and labeling from an image database, and demonstrate the potential of our approach, since we outperform, in terms of computational cost and accuracy, the results of state-of-the-art methods on both face labeling and medical image segmentation.
Natural frames and interacting particles in three dimensions

Motivated by the problem of formation control for vehicles moving at unit speed in three-dimensional space, we are led to models of gyroscopically interacting particles, which require the machinery of curves and frames to describe and analyze. A Lie group formulation arises naturally, and we discuss the general problem of determining (relative) equilibria for arbitrary G-invariant controls (where G = SE(3) is a symmetry group for the control law). We then present global convergence (and non-collision) results for specific two-vehicle interaction laws in three dimensions, which lead to specific formations (i.e., relative equilibria). Generalizations of the interaction laws to n vehicles is also discussed, and simulation results presented.
99mTc-Labeled HYNIC-DAPI Causes Plasmid DNA Damage with High Efficiency

99mTc is the standard radionuclide used for nuclear medicine imaging. In addition to gamma irradiation, 99mTc emits low-energy Auger and conversion electrons that deposit their energy within nanometers of the decay site. To study the potential for DNA damage, direct DNA binding is required. Plasmid DNA enables the investigation of the unprotected interactions between molecules and DNA that result in single-strand breaks (SSBs) or double-strand breaks (DSBs); the resulting DNA fragments can be separated by gel electrophoresis and quantified by fluorescent staining. This study aimed to compare the plasmid DNA damage potential of a 99mTc-labeled HYNIC-DAPI compound with that of 99mTc pertechnetate (99mTcO4 −). pUC19 plasmid DNA was irradiated for 2 or 24 hours. Direct and radical-induced DNA damage were evaluated in the presence or absence of the radical scavenger DMSO. For both compounds, an increase in applied activity enhanced plasmid DNA damage, which was evidenced by an increase in the open circular and linear DNA fractions and a reduction in the supercoiled DNA fraction. The number of SSBs elicited by 99mTc-HYNIC-DAPI (1.03) was twice that caused by 99mTcO4 − (0.51), and the number of DSBs increased fivefold in the 99mTc-HYNIC-DAPI-treated sample compared with the 99mTcO4 − treated sample (0.02 to 0.10). In the presence of DMSO, the numbers of SSBs and DSBs decreased to 0.03 and 0.00, respectively, in the 99mTcO4 – treated samples, whereas the numbers of SSBs and DSBs were slightly reduced to 0.95 and 0.06, respectively, in the 99mTc-HYNIC-DAPI-treated samples. These results indicated that 99mTc-HYNIC-DAPI induced SSBs and DSBs via a direct interaction of the 99mTc-labeled compound with DNA. In contrast to these results, 99mTcO4 − induced SSBs via radical formation, and DSBs were formed by two nearby SSBs. The biological effectiveness of 99mTc-HYNIC-DAPI increased by approximately 4-fold in terms of inducing SSBs and by approximately 10-fold in terms of inducing DSBs.
Adaptive Travel Time Path Selection in Hierarchical Index Road Network

It is the truth that spending life on the road is not fun. Therefore, every driver is searching for the "shortest path" for their traveling. Since the real objective is the smallest time frame that the driver spends on the road before arriving at the required destination. Various methods have been proposed to solve the problem of this shortest path under the hierarchical index road network. Unfortunately that none of them has considered the situation of traveling in the congestion traffic mode. This paper presents a solution, called an adaptive travel-time path selection algorithm, to obtain the shortest path where the shortest travel-time has been achieved. The experiment had shown that the selected path obtaining from the proposed algorithm has less time complexity than the previous existing methods.
Spectral-Efficiency Analysis of Massive MIMO Systems in Centralized and Distributed Schemes

This paper analyzes the spectral efficiency of massive multiple-input multiple-output (MIMO) systems in both centralized and distributed configurations, referred to as C-MIMO and D-MIMO, respectively. By accounting for real environmental parameters and antenna characteristics, namely, path loss, shadowing effect, multipath fading, and antenna correlation, a novel comprehensive channel model is first proposed in closed-form, which is applicable to both types of MIMO schemes. Then, based on the proposed model, the asymptotic behavior of the spectral efficiency of the MIMO channel, under both the centralized and distributed configurations is analyzed and compared in exact forms, by exploiting the theory of very long random vectors. Afterwards, a case study is performed by applying the obtained results into MIMO networks with circular coverage. In such a case, it is attested that for the D-MIMO of cell radius rc and circular antenna array of radius ra, the optimal value of ra that maximizes the average spectral efficiency is accurately established by raopt = rc/1.31. Monte Carlo simulation results corroborate the developed spectral-efficiency analysis.
A Cooperative User-System Approach for Optimizing Performance in Content Distribution/Delivery Networks

Recently, the demand for content delivery in wired/wireless heterogeneous networks is increasing at a rapid pace. Content Distribution/Delivery Networks (CDNs) are considered to be one of the best solutions for dealing with this increasing demand. In this paper, we point out that the performance of a CDN typically degrades in such heterogeneous environments due to the changes in not only user demand but also wireless mobility, which triggers unexpected fluctuations in traffic. Wireless users, roaming between different access networks, may contribute to sudden and unexpected demand spikes in certain parts of the content delivery system. To address this issue, we develop a cooperative server selection scheme, which is designed to maximize robustness to such changes with the cooperation between the content delivery system and its users. The performance of our proposal is evaluated by extensive computer simulations. The evaluation results demonstrate that our proposed scheme effectively makes the considered content delivery system resilient against request fluctuations while minimizing system overloading.
Spoken Language Derived Measures for Detecting Mild Cognitive Impairment

Spoken responses produced by subjects during neuropsychological exams can provide diagnostic markers beyond exam performance. In particular, characteristics of the spoken language itself can discriminate between subject groups. We present results on the utility of such markers in discriminating between healthy elderly subjects and subjects with mild cognitive impairment (MCI). Given the audio and transcript of a spoken narrative recall task, a range of markers are automatically derived. These markers include speech features such as pause frequency and duration, and many linguistic complexity measures. We examine measures calculated from manually annotated time alignments (of the transcript with the audio) and syntactic parse trees, as well as the same measures calculated from automatic (forced) time alignments and automatic parses. We show statistically significant differences between clinical subject groups for a number of measures. These differences are largely preserved with automation. We then present classification results, and demonstrate a statistically significant improvement in the area under the ROC curve (AUC) when using automatic spoken language derived features in addition to the neuropsychological test scores. Our results indicate that using multiple, complementary measures can aid in automatic detection of MCI.
Simvastatin protects against the development of endometriosis in a nude mouse model.

CONTEXT Endometriosis is a common condition associated with infertility and pelvic pain in women. Recent in vitro studies have shown that statins decrease proliferation of endometrial stroma (ES) and inhibit angiogenesis. OBJECTIVE The aim was to evaluate effects of simvastatin on development of endometriosis in a nude mouse model. METHODS Proliferative phase human endometrial biopsies were obtained from healthy donors and established as organ cultures or used to isolate ES cells. To establish endometriosis in the nude mouse, endometrial tissues were maintained in 1 nm estradiol (E) for 24 h and subsequently injected into ovariectomized nude mice. Mice (n = 37) were treated with E (8 mg, SILASTIC capsule implants; made in author laboratory) alone or with E plus simvastatin (5 or 25 mg/kg x d) for 10 d beginning 1 d after tissue injection (from three donors). Mice were killed and examined for disease. Effects of simvastatin on matrix metalloproteinase-3 (MMP-3) were evaluated in cultures of ES cells. PRIMARY OUTCOME The number and size of endometriotic implants were measured. RESULTS Simvastatin induced a dose-dependent decrease of the number and size of endometrial implants in mice. At the highest dose of simvastatin, the number of endometrial implants decreased by 87%, and the volume by 98%. Simvastatin also induced a concentration-dependent decrease in MMP-3 in the absence and presence of inflammatory challenge (using IL-1alpha). CONCLUSIONS Simvastatin exerted a potent inhibitory effect on the development of endometriosis in the nude mouse. Mechanisms of action of simvastatin may include inhibition of MMP-3. The present findings may lead to the development of novel treatments of endometriosis involving statins.