Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of Multidideoxynucleoside Resistance-Conferring Mutations in Human Immunodeficiency Virus Type 1 Reverse Transcriptase on Polymerase Fidelity and Error Specificity

ABSTRACT Variants of human immunodeficiency virus type 1 (HIV-1) that are highly resistant to a number of nucleoside analog drugs have been shown to develop in some patients receiving 2′,3′-dideoxy-3′-azidothymidine therapy in combination with 2′,3′-dideoxycytidine or 2′,3′-dideoxyinosine. The appearance, in the reverse transcriptase (RT), of the Q151M mutation in such variants precedes the sequential appearance of three or four additional mutations, resulting in a highly resistant virus. Three of the affected residues are proposed to lie in the vicinity of the template-primer in the three-dimensional structure of the HIV-1 RT–double-stranded DNA complex. The amino acid residue Q151 is thought to be very near the templating base. The nucleoside analog resistance mutations in the β9-β10 (M184V) and the β5a (E89G) strands of HIV-1 RT were previously shown to increase the fidelity of deoxynucleoside triphosphate insertion. Therefore, we have examined wild-type HIV-1BH10 RT and two nucleoside analog-resistant variants, the Q151M and A62V/V75I/F77L/F116Y/Q151M (VILYM) RTs, for their overall forward mutation rates in an M13 gapped-duplex assay that utilizeslacZα as a reporter. The overall error rates for the wild-type, the Q151M, and the VILYM RTs were 4.5 × 10−5, 4.0 × 10−5, and 2.3 × 10−5 per nucleotide, respectively. Although the mutant RTs displayed minimal decreases in the overall error rates compared to wild-type RT, the error specificities of both mutant RTs were altered. The Q151M RT mutant generated new hot spots, which were not observed for wild-type HIV-1 RT previously. The VILYM RT showed a marked reduction in error rate at two of the predominant mutational hot spots that have been observed for wild-type HIV-1 RT.
The Good‐Genes and Compatible‐Genes Benefits of Mate Choice

Genetic benefits from mate choice could be attained by choosing mates with high heritable quality (“good genes”) and that are genetically compatible (“compatible genes”). We clarify the conceptual and empirical framework for estimating genetic benefits of mate choice, stressing that benefits must be measured from offspring fitness because there are no unequivocal surrogates for genetic quality of individuals or for compatibility of parents. We detail the relationship between genetic benefits and additive and nonadditive genetic variance in fitness, showing that the benefits have been overestimated in previous verbal treatments. We point out that additive benefits readily arise from nonadditive gene action and that the idea of “heritable nonadditive benefits” is a misconception. We review the empirical evidence of the magnitude of benefits of good genes and compatible genes in animal populations, and we outline the most promising future directions for empirical research on the genetic benefits of mate choice.
MEK kinase activity is not necessary for Raf‐1 function

Raf‐1 protein kinase has been identified as an integral component of the Ras/Raf/MEK/ERK signalling pathway in mammals. Activation of Raf‐1 is achieved by Ras.GTP binding and other events at the plasma membrane including tyrosine phosphorylation at residues 340/341. We have used gene targeting to generate a ‘knockout’ of the raf‐1 gene in mice as well as a rafFF mutant version of endogenous Raf‐1 with Y340FY341F mutations. Raf‐1−/− mice die in embryogenesis and show vascular defects in the yolk sac and placenta as well as increased apoptosis of embryonic tissues. Cell proliferation is not affected. Raf‐1 from cells derived from raf‐1FF/FF mice has no detectable activity towards MEK in vitro, and yet raf‐1FF/FF mice survive to adulthood, are fertile and have an apparently normal phenotype. In cells derived from both the raf‐1−/− and raf‐1FF/FF mice, ERK activation is normal. These results strongly argue that MEK kinase activity of Raf‐1 is not essential for normal mouse development and that Raf‐1 plays a key role in preventing apoptosis.
Classification of Acute Myelogenous Leukemia using Multilevel Wavelet Transform and Neural Network for Bio-Medical Applications

Image segmentation is considered the most critical step in image processing and helps to analyze, infer and make decisions especially in the medical field. Analyzing digital microscope images for earlier Acute Myelogenous leukemia (AML) diagnosis and treatment require sophisticated software and hardware systems. The need for automation of leukemia detection arises since current methods involve manual examination of the blood smear as the first step toward diagnosis. In this paper presents selected mathematical methods used for image segmentation and application of wavelet transform for the following segments classification by multi resolution decomposition of segments blood cell images. The Haar wavelets transform and Daubechies wavelet transform approach has been adopted here and used for feature extraction allowing its use for image denoising and resolution enhancement as well. Feature classification is then achieved by self-organizing neural networks. A proposed method has been verified for simulated structures and then gives the better segmentation accuracy and Precision for analysis of microscopic images.
Pbx1-dependent control of VMC differentiation kinetics underlies gross renal vascular patterning

The architecture of an organ's vascular bed subserves its physiological function and metabolic demands. However, the mechanisms underlying gross vascular patterning remain elusive. Using intravital dye labeling and 3D imaging, we discovered that systems-level vascular patterning in the kidney is dependent on the kinetics of vascular mural cell (VMC) differentiation. Conditional ablation of the TALE transcription factor Pbx1 in renal VMC progenitors in the mouse led to the premature upregulation of PDGFRβ, a master initiator of VMC-blood vessel association. This precocious VMC differentiation resulted in nonproductive angiogenesis, abnormal renal arterial tree patterning and neonatal death consistent with kidney dysfunction. Notably, we establish that Pbx1 directly represses Pdgfrb, and demonstrate that decreased Pdgfrb dosage in conditional Pbx1 mutants substantially rescues vascular patterning defects and neonatal survival. These findings identify, for the first time, an in vivo transcriptional regulator of PDGFRβ, and reveal a previously unappreciated role for VMCs in systems-level vascular patterning. Summary: Intravital dye labeling and 3D imaging reveal that Pbx1-mediated vascular mural cell differentiation is required for the repression of PDGFRβ signaling and functional renal vascularization in mice.
Evaluation of constrained application protocol for wireless sensor networks

IPv6 over Low power Wireless Personal Area Networks (6LoWPAN) and IPv6 Routing Protocol for Low-power and Lossy networks (RPL) have accelerated the integration of Wireless Sensor Networks (WSNs) and smart objects with the Internet. At the same time, the development of the Constrained Application Protocol (CoAP) has made it possible to provide resource constrained devices with web service functionalities. CoAP is an HTTP like web transfer protocol able to extend the REpresentational State Transfer (REST) architecture to LoWPANs. The major difference between CoAP and HTTP is the different transport layer protocol (UDP instead of TCP) and the header compression which makes the packet size significantly smaller. This work provides an evaluation of CoAP compared to HTTP. The performance is evaluated in terms of mote's energy consumption and response time. The aim of the paper is to demonstrate, with a quantitative and qualitative analysis, that CoAP is more suited to REST based WSNs compared to HTTP. The results have been obtained by means of simulation as well as tests on real sensor motes.
mHealth: Blood donation application using android smartphone

mHealth is new horizons for health that offers healthcare services by utilizing the mobile devices and communication technologies. In health care services, blood donation is a complex process and consumes time to find some donor who has the compatibility of blood group with the patient. We developed android based blood donation application as mHealth solutions to establish a connection between the requester and donor at anytime and anywhere. The objective of this application is to provide the information about the requested blood and number of available donors around those localities. It assists the requester to broadcast the message across the maintained volunteer blood donor network by our application and update the requester at the same time who is willing to donate the requested blood. To evaluate our application, we created requester-donor profiles and analysed that it will help to improve the timely access of the information and rapid response in emergency situation.
An Extension of PEEC Method for Magnetic Materials Modeling in Frequency Domain

An extension of the partial element equivalent circuit (PEEC) method for magnetic materials modeling in the frequency domain applied on toroidal magnetic inductors with rectangular cross section is presented in this paper. The extension is performed by coupling the PEEC method and the boundary element method (BEM). The influence of magnetic material is modeled by distributions of “fictitious magnetic currents and charges” existing on the surface of a magnetic body. To verify the developed 3-D PEEC model, calculated and measured impedances are compared for two winding arrangements employing a ferrite T38 core. A good agreement between the PEEC simulation and measurements is presented up to the first resonant frequency. The described PEEC modeling approach enables 3-D electromagnetic simulations with much less computational effort than given for existing finite element method (FEM) simulators.
Soluble IL-6 Receptor and IL-27 Subunit p28 Protein Complex Mediate the Antiviral Response through the Type III IFN Pathway

Previously, we demonstrated that the soluble IL-6R (sIL-6R) plays an important role in the host antiviral response through induction of type I IFN and sIL-6R–mediated antiviral action via the IL-27 subunit p28; however, the mechanism that underlies sIL-6R and p28 antiviral action and whether type III IFN is involved remain unknown. In this study, we constructed a sIL-6R and p28 fusion protein (sIL-6R/p28 FP) and demonstrated that the fusion protein has stronger antiviral activity than sIL-6R alone. Consequently, knockout of sIL-6R inhibited virus-triggered IFN-λ1 expression. In addition, sIL-6R/p28 FP associated with mitochondrial antiviral signaling protein and TNFR-associated factor 6, the retinoic acid–inducible gene I adapter complex, and the antiviral activity mediated by sIL-6R/p28 FP was dependent on mitochondrial antiviral signaling protein. Furthermore, significantly reduced binding of p50/p65 and IFN regulatory factor 3 to the IFN-λ1 promoter was observed in sIL-6R knockout cells compared with the control cells. Interestingly, a novel heterodimer of c-Fos and activating transcription factor 1 was identified as a crucial transcriptional activator of IFN-λ1. The sIL-6R/p28 FP upregulated IFN-λ1 expression by increasing the binding abilities of c-Fos and activating transcription factor 1 to the IFN-λ1 promoter via the p38 MAPK signaling pathway. In conclusion, these results demonstrate the important role of sIL-6R/p28 FP in mediating virus-induced type III IFN production.
An operator-theoretic viewpoint to non-smooth dynamical systems: Koopman analysis of a hybrid pendulum

We apply an operator-theoretic viewpoint to a class of non-smooth dynamical systems that are exposed to event-triggered state resets. The considered benchmark problem is that of a pendulum which receives a downward kick at certain fixed angles. The pendulum is modeled as a hybrid automaton and is analyzed from both a geometric perspective and the formalism of Koopman operator theory. A connection is drawn between these two interpretations of a dynamical system by establishing a link between the spectral properties of the Koopman operator and the geometric properties in the state-space.
Discriminant analysis of promoter regions in Escherichia coli sequences

We have previously developed a general method based on the statistical technique of discriminant analysis to predict splice junctions in eukaryotic mRNA sequences [Nakata, K. , Kanehisa, M. and DeLisi, C. (1985) Nucleic Acids Res., 13, 5327-5340]. In order to evaluate further applicability of this method, we now analyze the promoter region of Escherichia coli sequences. The attributes used for discrimination include the accuracy of consensus sequence patterns measured by the perceptron algorithm, the thermal stability map, the base composition and the Calladine-Dickerson rules for helical twist angle, roll angle, torsion angle and propeller twist angle. When applied to selected E. coli sequences in the GenBank database, the method correctly identifies 75% of the true promoter regions.
Preliminary evaluation of a kinetic parameter estimator with application to direct parametric reconstruction

We present a ML-EM estimator for kinetic parameters from list-mode and histogram mode (hist-mode) dynamic PET data, based upon the observation that emissions originating from each contributing exponential mode in the compartment model are identically and independently distributed samples drawn from an inhomogeneous Poisson distribution. An approximation formula for the covariance of the estimator is developed based on the Cramer-Rao bound, validated for 1- and 2-compartment models, and compared with multiple noise realizations. 1D experimental data were simulated using various count levels and rate constants typical of metastatic colorectal cancer and glioma FDG uptake. We conclude that estimation of kinetic parameters from list-mode data is theoretically achievable and that estimate covariance can be usefully approximated from a single realization
Involvement of the Leader Sequence in Sendai Virus Pathogenesis Revealed by Recovery of a Pathogenic Field Isolate from cDNA

ABSTRACT We previously demonstrated that a systematic passage of a pathogenic field isolate of Sendai virus (SeV), the Hamamatsu strain, in embryonated eggs caused attenuation of virulence to mice, and we isolated viral clones of distinct virulence (K. Kiyotani et al. Arch. Virol. 146:893-908, 2001). One of the clones, E15cl2, which was obtained from the virus at the 15th egg passage of E0, the parental Hamamatsu clone for egg passage, had 165-fold-attenuated virulence to mice and possessed only four mutations in the entire 15,384-base genome: in an antigenomic sense, U to A at position 20 (U20A) and U to A at position 24 (U24A) in the leader sequence, the promoter for transcription and replication, and A to G at position 9346 (silent) and A to U at position 12174 (Ser to Cys) in the L gene. To examine the possibility that leader mutations affect virus pathogenesis, we recovered live viruses from cDNA derived from the Hamamatsu strain. A mutant virus possessing either a mutation of U20A or U24A in the leader sequence showed a slightly lower pathogenicity than that of the parental virus, whereas a double mutant virus possessing both of the mutations showed 25-fold-attenuated virulence, accompanying a significantly lower virus replication in the mouse lung. Replications of the leader mutant viruses were also impaired in a primary culture of mouse pulmonary epithelial cells but not in chicken embryo fibroblasts. These findings suggest that leader mutations of SeV affect virus pathogenesis by altering virus replication in a host-dependent manner.
Decolorization of diazo‐dye Reactive Blue 172 by Pseudomonas aeruginosa NBAR12

A novel bacterial strain capable of decolorizing textile dyes was isolated from dye contaminated soil obtained from industrial estate of Ahmedabad, Gujarat, India. The bacterial isolate Pseudomonas aeruginosa NBAR12 was capable of decolorizing 12 different dyes tested with decolorization efficiency varying in the range of 80 to 95%. Maximum extent as well as rate of Reactive Blue 172 (RB 172) decolorization was observed when glucose (2 g · l–1) and yeast extract (2.5 g · l–1) were supplemented in the medium. The optimum dye pH and temperature for dye decolorization was found to be 7 and 40 °C, respectively. The decolorizing activity was found to increase with increasing the dye concentration from 50 to 400 mg · l–1. The dye decolorization was strongly inhibited at 500 mg dye l–1 in the medium. High performance thin layer chromatography analysis indicated that dye decolorization occurred due to the breakdown of dye molecules into colorless end products. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Fault tolerant control using evolving fuzzy modeling

This paper proposes a fault-tolerant control (FTC) approach using evolving fuzzy modeling. FTC is performed in two steps: fault detection and fault accommodation. Fault accommodation uses evolving Takagi-Sugeno fuzzy models, and fault detection uses a model-based approach also based on fuzzy models. Information from fault detection is used for fault accommodation in a model predictive control (MPC) scheme. The evolving fuzzy modeling approach increases the control performance when the process is with faults. The proposed approach continuously evaluate the control performance and perform on-line clustering, if it is necessary. Evolving FTC is used to accommodate two simulated faults in a distillation column process. The considered faults are the load process fault (variation in feed composition) and the change in heating (variation of re-boiler temperature). The fault tolerant control using evolving fuzzy modeling was able to accommodate the simulated faults.
Extending Coordination Theory to the Field of Distributed Group Multiple Criteria Decision-Making

Distributed group decision-making becomes prevalent in networked and informationbased organizations today. In addition to providing GDSS with modelling tools such as MCDM techniques to effectively support distributed group decision-making tasks, coordination is deemed to be critical to the success of such complicated processes. Current coordination theory in the field of distributed group decision-making does not explicitly deal with process using MCDM techniques, although a few studies have adapted organizational coordination theory in the field of general GDSS research. This paper aims to provide theoretical view of coordination in the field of group MCDM processes based on existing organizational theory and its extensions in GDSS. We propose such a theoretical extension by formulating parallel and sequential coordination methods in the context of distributed group MCDM, which represent the loosest and tightest task interdependence. We then present an implementation of these coordination methods in a GDSS environment with respect to system design and group decisionmaking procedures. The proposed coordination methods may provide guidelines for GDSS designers and practitioners in coordinating and structuring distributed group MCDM processes.
Flue-gas-influenced heavy metal bioaccumulation by the indigenous microalgae Desmodesmus communis LUCC 002

Desmodesmus communis LUCC 002 was cultivated using flue gas originating from a coal-fired power plant as a carbon dioxide (CO2) source. The flue gas contains various heavy metals. For investigating the fate of flue-gas-introduced metals on the cultivation system, bioaccumulation was measured in the microalgal biomass and milieu. The accumulated biomass was found to contain eight heavy metals: arsenic, chromium, barium, lead, selenium, silver, cadmium, and mercury. High heavy metal accumulations were also found in the control group of algae grown without the addition of flue gas at the same location. Further testing revealed that some of the heavy metals originated from well water used in the cultivation. The flue-gas-influenced bioaccumulation pattern of different heavy metals was observed. The responses of individual heavy metals and the influence of well water microbial flora on the algal growth were investigated, this study showed that hormesis was developed by the D. communis LUCC 002.
Reducing misses to external memory accesses in task-level pipelining

Recently, researchers have shown an increased interest in using task-level pipelining to accelerate the overall execution of applications mainly consisting of producer-consumer tasks. This paper proposes optimization techniques for enhancing our approach to pipeline the execution of producer-consumer tasks in FPGA-based multicore architectures with reductions in the number of accesses to external memory. Our approach is able to speedup the overall execution of successive, data-dependent tasks, by using multiple cores and specific customization features provided by FPGAs. We evaluate the impact in the performance of task-level pipelining when using different hash functions and optimization schemes in the inter stage buffer (ISB). The optimizations proposed in this paper were evaluated with FPGA implementations. The experimental results show the efficiency of a simple scheme to reduce external memory accesses and the suitability of the hash function being used. Furthermore, the results reveal noticeable performance improvements for the set of benchmarks being used.
Prosody modeling of spontaneous mandarin speech and its application to automatic speech recognition

A prosody-assisted ASR approach for spontaneous Mandarin speech is proposed. It employs the joint prosody labeling and modeling algorithm proposed previously to construct a hierarchical prosodic model (HPM) and uses it in two-stage speech recognition. A word lattice is first generated by the HMM method using tri-phone AM and bigram LM. Then, the lattice is extended by replacing LM to a trigram model. A rescoring process is applied in the second stage to sequentially add factor POS and PM LMs, and the HPM. The method is evaluated on the MCDC database comprising 8 dialogues of 16 speakers with length of 9.09 hours. Error rates of syllable/character/word were reduced from 35.6/40.2/45.1% by the baseline trigram HMM method to 32.4/36.5/41.8% by the proposed method. The improvement is reasonably good as considering the WER upper-bound of 13.4% for the word lattice owing to the high OOV rate of the database. By error analysis, we find that many tone recognition errors and word segmentation errors were corrected. Besides, some information of the testing utterance was also obtained by the ASR, including POS of word, PM, tone of syllable, break type of syllable juncture, and prosodic state of syllable.
Constrained attitude control of agile spacecraft using CMGs

This paper investigates rest-to-rest attitude reorientation problem for an agile spacecraft in the presence of attitude-constrained zones. Since agile spacecraft require an attitude control system that provides rapid rotational maneuverability and tracking capability, control moment gyro (CMG) is often considered as ideal torque-generating actuators. Specifically, based on a quadratic potential function, a nonlinear attitude controller is developed to avoid the undesired celestial objects autonomously while achieving asymptotic attitude stabilization. Then, general singular robust (GSR) steering logic is employed to determine the CMG gimbal rate commands that can generate the commanded spacecraft control torques from attitude controller. The proposed attitude control scheme has simple structure, which is of great interest for aerospace industry when onboard computing power is limited. Finally, simulation results for a CMG-based spacecraft are presented to show the effectiveness of the proposed attitude control systems.