Miracle-dz/UniFAR-FTUs huggingface dataset:
The Effects of α-Helical Structure and Cyanylated Cysteine on Each Other

β-Thiocyanatoalanine, or cyanylated cysteine, is an artificial amino acid that can be introduced at solvent-exposed cysteine residues in proteins via chemical modification. Its facile post-translational synthesis means that it may find broad use in large protein systems as a probe of site-specific structure and dynamics. The C≡N stretching vibration of this artificial side chain provides an isolated infrared chromophore. To test both the perturbative effect of this side chain on local secondary structure and its sensitivity to structural changes, three variants of a model water-soluble alanine-repeat helix were synthesized containing cyanylated cysteine at different sites. The cyanylated cysteine side chain is shown to destabilize, but not completely disrupt, the helical structure of the folded peptide when substituted for alanine. In addition, the C≡N stretching bandwidth of the artificial side chain is sensitive to the helix−coil structural transition. These model system results indicate that cyanylated cysteine can be placed into protein sequences with a native helical propensity without destroying the helix, and further that the CN probe may be able to report local helix formation events even when it is water-exposed in both the ordered and disordered conformational states. These results indicate that cyanylated cysteine could be a widely useful probe of structure-forming events in proteins with large in vitro structural distributions.
Purification and characterization of an extreme halothermophilic protease from a halophilic bacterium Chromohalobacter sp. TVSP101

An extreme halophilic bacterium was isolated from solar saltern samples and identified based on biochemical tests and 16S r RNA sequencing as Chromohalobacter sp. strain TVSP101. The halophilic protease was purified using ultrafiltration, ethanol precipitation, hydrophobic interaction column chromatography and gel permeation chromatography to 180 fold with 22% yield. The molecular mass of the protease determined by SDS PAGE was 66 kDa. The purified enzyme was salt dependent for its activity and stability with an optimum of 4.5 M NaCl. The optimum temperature for maximum protease activity was 75ºC. The protease was optimally active at pH 8 and retained more than 80% of its activity in the range of pH 7-10. Sucrose and glycine at 10% (w/v) were the most effective osmolytes, retained 100% activity in the absence of NaCl. The activity was completely inhibited by ZnCl2 (2 mM), 0.1% SDS and PMSF (1mM). The enzyme was not inhibited by 1mM of pepstatin, EDTA and PCMB. The protease was active and retained 100% it activity in 10% (v/v) DMSO, DMF, ethanol and acetone.
A survey on effective way of detecting denial-of-service attack using multivariate correlation analysis

In today's era of communication we continuously come across well-organized interconnected systems like net servers, database files servers, cloud computing servers etc. These servers continuously handle in/out data queries and reply them considering each query as honest call. But these servers are under the danger of Denial of Service also known as (DOS) attack. DOS attack hampers the working efficiency of these systems tremendously, it is really essential to identify and cease these attacks from happening. This paper provides an effective and efficient DOS detection methodology which is based on feature normalization as well as Triangle area map generation in combination with multi-variant co-relational analysis approach. This (MCA) dependent detection approach employs rules of anomaly based detection technology thus making our system capable of identifying unfamiliar or familiar kinds of DOS attack. Additionally the TAM approach fastens MCA process and it's working accuracy improves due to its ability to understand and remember the pattern of valid and invalid route traffic.
Price Formation of Pledgeable Securities

I derive the equilibrium price function of securities that can be pledged as collateral, in an economy where rational investors receive heterogeneous information. Although the distribution of borrowers' and lenders' payoffs is truncated, the linear equilibrium price is in closed form. That allows to investigate the impact of pledgeability on informational efficiency. The margin premium depends on the price of liquidity and yields a "pledgeability bias", which increases the conditional volatility of the price function. The impact of pledgeability on prices contributes to explain excessive comovement and seemingly violations of the law of one price.
Incorporating Value-at-Risk in Portfolio Selection: An Evolutionary Approach

The mean-variance framework for portfolio selection should be revised when investor’s concern is the downside risk. This is especially true when the asset returns are not normal. In this paper, we incorporate value-at-risk (VaR) in portfolio selection and the mean-VaR framework is proposed. Due to the twoobjective optimization problem faced by the meanVaR framework, an evolutionary multi-objective approach is applied to construct the mean-VaR efficient frontier. In particular, the NSGA-II is considered here. From the empirical analysis it is found that the risk-averse investor might inefficiently allocate his wealth if his decision is based on the mean-variance framework.
Towards Fully Automated Motion Capture of Signs -- Development and Evaluation of a Key Word Signing Avatar

Motion capture of signs provides unique challenges in the field of multimodal data collection. The dense packaging of visual information requires high fidelity and high bandwidth of the captured data. Even though marker-based optical motion capture provides many desirable features such as high accuracy, global fitting, and the ability to record body and face simultaneously, it is not widely used to record finger motion, especially not for articulated and syntactic motion such as signs. Instead, most signing avatar projects use costly instrumented gloves, which require long calibration procedures. In this article, we evaluate the data quality obtained from optical motion capture of isolated signs from Swedish sign language with a large number of low-cost cameras. We also present a novel dual-sensor approach to combine the data with low-cost, five-sensor instrumented gloves to provide a recording method with low manual postprocessing. Finally, we evaluate the collected data and the dual-sensor approach as transferred to a highly stylized avatar. The application of the avatar is a game-based environment for training Key Word Signing (KWS) as augmented and alternative communication (AAC), intended for children with communication disabilities.
Could a dialog save your life?: analyzing the effects of speech interaction strategies while driving

We describe a controlled Wizard-of-Oz study using a medium-fidelity driving simulator investigating how a guided dialog strategy performs when compared to open dialog while driving, with respect to the cognitive loading these strategies impose on the driver. Through our analysis of driving performance logs, speech data, NASA-TLX questionnaires, and bio-signals (heart rate and EEG) we found the secondary speech task to have a measurable adverse effect on driving performance, and that guided dialog is less cognitively demanding in dual-task (driving plus speech interaction) conditions. The driving performance logs and heart rate variability information proved useful for identifying cognitively challenging situations while driving. These could provide important information to an in-car dialog management system that could take into account the driver's cognitive resources to provide safer speech-based interaction by adapting the dialog.
Application Mobility with HIP

Process migration, or application mobility as we call it, is the act of moving a process or an application between hosts during its execution. It enhances load management, fault resilience, and data access locality. Regardless of its impressive potential, it can’t be considered a commercial success due to its currently limited deployment. A reason for the failure is the complexity process migration creates in order to operate transparently from application’s perspective. Transparent network communication for migration capable operating systems has traditionally required either custom application or kernel implemented protocols, both breaking general interoperability. Perhaps surprisingly, mobility and multi-homing driven identifier/locator split architecture model provides an elegant solution for this classic problem. In this paper, we present an initial architecture for application mobility utilizing perhaps the most promising candidate for the identifier/locator split, Host Identity Protocol (HIP). Our novel use of the protocol introduces new requirements for HIP itself. The paper identifies these requirements and based on them introduces a protocol extension to enhance HIP’s suitability for application mobility.
Augmented chemical reactions: An augmented reality tool to support chemistry teaching

This demonstration shows an Augmented Reality tool to support teaching chemistry. The understanding of spacial relations in and between molecules is an essential part that has to be understood by students to learn chemistry As nowadays the techniques to show and simulate molecular behaviors get faster and better, 3D applications to show the molecules become more and more popular also in schools. Augmented Chemical Reactions is an application that shows the 3D spatial structure of molecules as well as the dynamics of the atoms in and between molecules. This application does not use the commonly used 3D user interface of mice and keyboards to move and rotate the virtual objects but it makes use of an intuitive 3D user interface. This 3D User interface is an direct manipulation user interface using the augmented reality technique. With this user interface it enables the users to better understand the spacial structure of the shown geometries.
High-performance language interoperability in multi-language runtimes

Programs often consist of parts that are written in different languages because sub-problems lend themselves to being implemented in a particular language. However, multi-language programs often suffer from poor performance, complex cross-language interfaces, or insufficient flexibility. We propose a novel approach for composing multiple language implementations in a seamless way. Foreign objects of one language can be used like regular objects in another language. Our interoperability mechanism targets language implementations that run on the same VM and have the same style of intermediate representation (IR), e.g., an abstract syntax tree (AST). For accessing foreign objects we generate foreign-language-specific IR patterns that we insert into the IR of the host application. Thus we avoid converting or marshalling foreign objects at the language border. Our mechanism also allows the just-in-time compiler of the host VM to inline and optimize across language borders.
In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia

Witches’ broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches’ broom disease.
How to exploit the device diversity and database interaction to propose a generic cost model?

Cost models have been following the life cycle of databases. In the first generation, they have been used by query optimizers, where the cost-based optimization paradigm has been developed and supported by most of important optimizers. The spectacular development of complex decision queries amplifies the interest of the physical design phase (PhD), where cost models are used to select the relevant optimization techniques such as indexes, materialized views, etc. Most of these cost models are usually developed for one storage device (usually disk) with a well identified storage model and ignore the interaction between the different components of databases: interaction between optimization techniques, interaction between queries, interaction between devices, etc. In this paper, we propose a generic cost model for the physical design that can be instantiated for each need. We contribute an ontology describing storage devices. Furthermore, we provide an instantiation of our meta model for two interdependent problems: query scheduling and buffer management. The evaluation results show the applicability of our model as well as its effectiveness.
Practical verifications for coverage and capacity predictions and simulations in real-world cellular UMTS networks

This paper presents verifications for UMTS coverage and capacity in a live network using planning and performance tools applied to a real-world operational UMTS network. Case study results are presented and followed by comparisons between coverage predictions, capacity simulations, field measurements and system statistics. Tuned propagation models based on area clutter, population profiles, digital height maps and base station (BS) engineering elements are taken into account to match the outputs of the planning tool to the practical drive-test and UMTS Terrestrial Radio Access Network (UTRAN) system Key Performance Indicators (KPIs) measurements. This work outcome addresses the importance of using planning tools for dimensioning coverage and capacity aspects in UMTS networks and draw some attention to network future optimization, load balancing and congestions relief in advance before system traffic statistics are being generated or afterwards as supplementary grounds for network optimization and maintenance that support statistics.
Lyapunov stability analysis of networks of scalar conservation laws

It is shown how an entropy-based Lyapunov function can be used for the stability analysis of equilibria in networks of scalar conservation laws. The analysis gives a sufficient stability condition which is weaker than the condition which was previously known in the literature. Various extensions and generalisations are briefly discussed. The approach is illustrated with an application to ramp-metering control of road traffic networks.
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data

SUMMARY MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2.0, for nucleosome positioning using MNase-Seq data or MNase- or sonicated- ChIP-Seq data combined with either single-end or paired-end sequencing. PING uses a model-based approach, which enables nucleosome predictions even in the presence of low read counts. We illustrate PING using two paired-end datasets from Saccharomyces cerevisiae and compare its performance with nucleR and ChIPseqR. AVAILABILITY PING 2.0 is available from the Bioconductor website at http://bioconductor.org. It can run on Linux, Mac and Windows.
Allocation of IT Decision Rights in Multibusiness Organizations: What Decisions, Who Makes Them, and when are They Taken?

Effective IT governance is an important requirement for strategic IT-based change. The extant literature focuses on which IT decisions should be governed and who is accountable for them. However, in multi-business organizations there is little theoretical guidance on which decisions should be made at the corporate and strategic business unit (SBU) levels, or when such decisions should be made as part of the corporate and SBU strategy processes. This paper draws on the strategic management literature to develop a theoretical framework for allocating IT decision rights between business and IT at the corporate and SBU levels. Importantly, the framework also unbundles corporate IT platform and SBU IT decision making across the corporate investment cycle. This is achieved by adopting a real options-based pricing investment model to reduce risk, uncertainty and complexity. The theoretical framework is illustrated with in-depth longitudinal case study and compared against existing normative IT governance prescriptions.
Effect of Short-Term Maximal Exercise on Biochemical Markers of Muscle Damage, Total Antioxidant Status, and Homocysteine Levels in Football Players

Purpose Prolonged physical exercise results in transient elevations of biochemical markers of muscular damage. This study examined the effect of short-term maximal exercise on these markers, homocysteine levels (Hcy), and total antioxidant status (TAS) in trained subjects. Methods Eighteen male football players participated in this study. Blood samples were collected 5-min before and 3-min after a 30-s Wingate test. Results The results indicated that plasma biochemical markers of muscle injury increased significantly after the Wingate test (P<0.05). Moreover, significant increase of white blood Cells and their main subpopulations (i.e. monocytes, neutrophiles, and lymphocytes) (P<0.001) has been observed. Likewise, uric acid, total bilirubin, and TAS increased significantly after exercise (P<0.05). However, Hcy levels were unaffected by the Wingate test (for 3-min post-exercise measurement). Conclusions Short-term maximal exercise (e.g. 30-s Wingate test) is of sufficient intensity and duration to increase markers of muscle damage, and TAS; but not Hcy levels. Increases in the selected enzymes probably come primarily from muscle damage, rather than liver damage. Moreover, increase of TAS confirms the Wingate test induced oxidative stress.
Stability properties and periodic evolutions of bilinear systems in input-output form

Bilinear systems in input-output form are introduced and represented by means of suitable rational functions in two indeterminates. Necessary and sufficient conditions for bounded-input/bounded-output (BIBO) stability are derived and compared with analogous results on two-dimensional systems stability. Several features of the output evolutions corresponding to finite support as well as to periodic input sequences are discussed and related to the polar structure of the rational functions describing the input-output maps.
Mining Explicit Features for Opinion Mining of Customer Reviews

Due to introduction of web 2.0 peoples are more familiar with internet. People buy the product and express their opinion in merchant website like amazon.com and epinion.com. There are various Web sites containing such opinions, e.g., consumer reviews of products, forums and blogs. Merchant website like amazon.com provides facility to give their opinion about the product. In this paper we purposed a new technique for explicit feature extraction. Datasets are crawled data from amazon.com of different modal of mobile. We use SVM and Naive Bayes classifier for our review documents. For SVM use SVM light , Weka tools for Naive Bayes. Our purposed method result shows that it is very valuable over existing system.
Targeting Batf2 for infectious diseases and cancer

The family members Batf, Batf2 and Batf3 belong to a class of transcription factors containing basic leucine zipper domains that regulate various immunological functions and control the development and differentiation of immune cells. Functional studies by others demonstrated a predominant role for Batf in controlling Th2 cell functions and lineage development of T lymphocytes as well as a critical role of Batf, Batf2 and Batf3 in CD8α+dendritic cell development. Moreover, Batf family member expression was measured in a vast collection of mouse and human cell types by cap analysis gene expression (CAGE), a recent developed sequencing technology, showing reasonable expression spectrum in immune cells consistent with previously published expression profiles. Batf and Batf3 were highly expressed in lymphocytes and the earlier moderately expressed in myeloid lineages. Batf2 was predominantly expressed in monocytes/macrophages. Functional studies in mice demonstrated that Batf2 has a central role in macrophage activation by regulating inflammatory responses during lipopolysaccharides stimulation and mycobacterial infection. Hence, Batf2 could be used as a biomarker and a potential host directed drug target in tuberculosis. Moreover, Batf2 act as a tumor suppressor gene and augmenting Batf2 in malignant cells might be an encouraging therapeutic treatment against cancer.
Genistein Induces Apoptosis in T Lymphoma Cells via Mitochondrial Damage

Abstract: The soy isoflavone genistein has been identified as having antiproliferative and apoptotic effects on various malignant cell types derived from solid tumors. Because little information regarding the effect of genistein on hematopoietic malignancies is available, we undertook this study of T-cell lymphomas. We tested the effect of genistein on murine T-cell lines derived from thymic lymphomas induced by an oncogenic murine leukemia virus. When T lymphoma cells were treated with genistein concentrations of 15 μM and greater, it was observed that the percentage of viable cells was significantly reduced in a dose- and time-dependent manner. The observed cell killing was found to be the result of apoptosis as detected by flow cytometric analysis of cells stained with annexin V and propidium iodide and assays for caspase-3 activation and DNA fragmentation. Cell staining with the mitochondrial specific dye JC-1 and detection of caspase-9 activation revealed that genistein produced mitochondrial depolarization as an early step in the induction of apoptosis. Bongkrekic acid inhibition of mitochondrial depolarization identified the mitochondria permeability transition pore (PTP) as a potential target of genistein activity. These results indicate that the induction of apoptosis by pharmacological concentrations of genistein in T lymphoma cells occurs via mitochondrial damage with the involvement of the PTP.