Miracle-dz/UniFAR-FTUs huggingface dataset:
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application

UNLABELLED uMelt(SM) is a flexible web-based tool for predicting DNA melting curves and denaturation profiles of PCR products. The user defines an amplicon sequence and chooses a set of thermodynamic and experimental parameters that include nearest neighbor stacking energies, loop entropy effects, cation (monovalent and Mg(++)) concentrations and a temperature range. Using an accelerated partition function algorithm along with chosen parameter values, uMelt interactively calculates and visualizes the mean helicity and the dissociation probability at each sequence position at temperatures within the temperature range. Predicted curves display the mean helicity as a function of temperature or as derivative plots. Predicted profiles display stability as a function of sequence position either as 50% helicity temperatures or as the helicity probability at specific temperatures. The loss of helicity associated with increasing temperature may be viewed dynamically to visualize domain formation within the molecule. Results from fluorescent high-resolution melting experiments match the number of predicted melting domains and their relative temperatures. However, the absolute melting temperatures vary with the selected thermodynamic parameters and current libraries do not account for the rapid melting rates and helix stabilizing dyes used in fluorescent melting experiments. uMelt provides a convenient platform for simulation and design of high-resolution melting assays. AVAILABILITY AND IMPLEMENTATION The application was developed in Actionscript and can be found online at http://www.dna. utah.edu/umelt/umelt.html. Adobe Flash is required to run in all browsers.
A Stochastic Model of DNA Fragments Rejoining

When cells are exposed to ionizing radiation, DNA damages in the form of single strand breaks (SSBs), double strand breaks (DSBs), base damage or their combinations are frequent events. It is known that the complexity and severity of DNA damage depends on the quality of radiation, and the microscopic dose deposited in small segments of DNA, which is often related to the linear transfer energy (LET) of the radiation. Experimental studies have suggested that under the same dose, high LET radiation induces more small DNA fragments than low-LET radiation, which affects Ku efficiently binding with DNA end and might be a main reason for high-LET radiation induced RBE [1] since DNA DSB is a major cause for radiation-induced cell death. In this work, we proposed a mathematical model of DNA fragments rejoining according to non-homologous end joining (NHEJ) mechanism. By conducting Gillespie's stochastic simulation, we found several factors that impact the efficiency of DNA fragments rejoining. Our results demonstrated that aberrant DNA damage repair can result predominantly from the occurrence of a spatial distribution of DSBs leading to short DNA fragments. Because of the low efficiency that short DNA fragments recruit repair protein and release the protein residue after fragments rejoining, Ku-dependent NHEJ is significantly interfered with short fragments. Overall, our work suggests that inhibiting the Ku-dependent NHEJ may significantly contribute to the increased efficiency for cell death and mutation observed for high LET radiation.
Salient Region Detection in Video Using Spatiotemporal Visual Attention Model

Salient region detection is very useful in video analysis. A salient region detection method based on spatiotemporal visual attention model is proposed in this paper. Visual attention mechanism is used to generate saliency map of the image sequence. Spatial saliency map is computed in accordance with some predefined features including intensity, color and orientation. Temporal visual saliency of each pixel is calculated using motion feature. Both spatial saliency map and temporal saliency map are combined to obtain the overall visual saliency map. Then salient regions are detected based on the visual saliency map. The proposed salient region detection method has been tested on many videos. The experiment results show that the presented method is valid and effective. The detection results are consistent with human visual system.
Quantitative Structure-Activity Relationship Study on Phthalimide Derivatives as HIV-1 Reverse Transcriptase Inhibitors

Quantitative structure-activity relationships (QSAR) was performed to correlate the physicochemical properties, ie, electronic, hydrophobic, and steric properties with the HIV-1 reverse transcriptase inhibitory activity of phthalimide derivatives. Multiple linear regression (MLR) analysis was used for the study. The best QSAR model was obtained with correlation coefficient (r) of 0.974 and crossvalidated r (q) of 0.785. This model indicates that the inhibitory activity correlated to the electronic properties, ie, partial atomic charge at carbon 2, the highest occupied molecular orbital (HOMO), and the dipole moment. This activity also correlated to the steric property, ie, molecular volume (MV) and the hydrophobic property, log P.
A Revocable Backup System

We present a system which enables a user to remove a file from both the file system and all the backup tapes on which the file is stored. The ability to remove files from all backup tapes is desirable in many cases. Our system erases information from the backup tape without actually writing on the tape. This is achieved by applying cryptography in a new way: a block cipher is used to enable the system to "forget" information rather than protect it. Our system is easy to install and is transparent to the end user. Further, it introduces no slowdown in system performance and little slowdown in the backup procedure.
Voltage- and current-controlled high CMRR instrumentation amplifier using CMOS current conveyors

A new approach to the design of an instrumentation amplifier using only 2 CMOS current-controlled conveyors and an active resistor is introduced. The new approach, which has no passive components, offers a wide bandwidth and a high common-mode rejection ratio (CMRR). Electronically controllable gain by voltage and current is also obtained by this new circuit. The circuit is simulated using the parameters of a 0.35-μ m TSMC CMOS technology. Theoretical analysis of the circuits was carried out, and the performance of the block circuit was confirmed through PSpice simulation results.
The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer

The heterochromatin protein 1 (HP1) family of proteins is involved in gene silencing via the formation of heterochromatic structures. They are composed of two related domains: an N‐terminal chromo domain and a C‐terminal shadow chromo domain. Present results suggest that chromo domains may function as protein interaction motifs, bringing together different proteins in multi‐protein complexes and locating them in heterochromatin. We have previously determined the structure of the chromo domain from the mouse HP1β protein, MOD1. We show here that, in contrast to the chromo domain, the shadow chromo domain is a homodimer. The intact HP1β protein is also dimeric, where the interaction is mediated by the shadow chromo domain, with the chromo domains moving independently of each other at the end of flexible linkers. Mapping studies, with fragments of the CAF1 and TIF1β proteins, show that an intact, dimeric, shadow chromo domain structure is required for complex formation.
Energy-efficient and high-performance software architecture for storage class memory

Recently, interest in incorporating Storage Class Memory (SCM), which blurs the distinction between memory and storage, into mainstream computing has been increasing rapidly. In this paper, we address the emerging questions regarding the use of SCM. Based on an embedded platform that employs FeRAM, a type of SCM, we present our findings. In summary, by introducing SCM, power efficiency improves while performance is degraded. We also show that such performance degradations may be removed with operating system level schemes that fully exploit the characteristics of SCM. Finally, we present permanent computing that supports lightweight system on/off capabilities by using SCM.
Quantum Tunneling in DNA

DNA contains all of the genetic information necessary to grow and sustain life and it is designed in such a way as to be remarkably stable despite it’s complexities. This paper discusses the inherent quantum mechanical nature of the hydrogen bonds in DNA nucleotides, specically the occurrence of proton tunneling within the hydrogen bond and the implications this has on the integrity of DNA replication as a whole. This paper also touches upon the eect radiation has on the frequency of proton tunneling in hydrogen bonds and the deleterious results it has on DNA replication integrity.
Adaptive bubble router: a design to improve performance in torus networks

A router design for torus networks that significantly reduces message latency over traditional wormhole routers is presented in this paper. This new router implements virtual cut-through switching and fully-adaptive minimal routing. Packet deadlock is avoided by providing escape ways governed by Bubble flow control, a mechanism that guarantees enough free buffer space in the network to allow continuous packet movement. Both deterministic and adaptive Bubble routers have been designed in VLSI using VHDL synthesis tools. Adopting a fair quantitative comparison, we demonstrate that Bubble routers exhibit a reduction in base latency values over 40% with respect to the corresponding wormhole routers, without any penalty in network throughput. With much lower VLSI costs than adaptive wormhole routers, the adaptive Bubble router is even faster than deterministic wormhole routers based on virtual channels.
Relationship Between Search for and Presence of Meaning in Life in High School Students

Objective: To explore the relationship between search for and presence of meaning in life in Chinese high school students.Methods: The Meaning in Life Questionnaire was used in the cross-sectional study(N=1659) and the longitudinal study(N=84,three measurements). Results: There was positive relation between search for and presence of meaning in life only when the two dimensions were measured simultaneously.However,after controlling interference variables,the post-test presence of meaning was predicted only by the pre-test presence,but not significantly related to pre-test search.The post-test search for meaning was predicted only by the pre-test search,but not significantly related to pre-test presence.Conclusion: Search for meaning and presence of meaning are fairly stable over long periods of time.These two variables only affect their own development.Their change is independent of each other over time.
Flexible Design in Public Private Partnerships : A PFI case study in the National Health Service

The focus of this paper is improving individual Private Finance Initiative (PFI) projects to deliver better value for the benefit of the partners in PFI. Signing long term contracts of 20 to 30 years with the private sector typically enlarges demand risks in PFI. Subsequently, this report seeks a way to deliver more valuable PFI projects by the effective management of demand risks. Incorporation of flexibilities in design is found to be a promising solution to deal with greater demand risks. Flexibility can add a significant value to the project as it allows actively reacting to the unforeseen circumstances in the future. Consequently, it will enable to cut losses in downside scenarios and amplify gains in upside scenarios. In order to benefit from the use of flexibilities in PFI project, it is essential for the public sector to structure flexibilities into the contract at the start of the project. This paper proposes managerial ways of considering the flexibilities systematically and structurally by an illustrative process using matrices called “OUF Matrices”: Operational Matrix, Uncertain Event Matrix and Flexibility Matrix. The process is designed in a way to help the partners to consider a sufficient number of scenarios and to look at the possibility of using flexibility. This paper also makes a contribution to the financial valuation of flexibilities in design to deal with demand risks using a case study of a PFI development in National Health Service in the UK. The financial model built for the case study suggests that the incorporation of flexibilities can substantially increase the value of the project only for the public sector who is responsible for taking demand risks. However, the fact that the private sector owns the asset limits the public sector’s interests in adopting flexibilities. It is thus desirable to develop a way of sharing the added value of flexibility in order to motivate the private sector to create and exercise flexibilities in the project. An approach by introducing the “option fee” in the contract is suggested in this paper, which the public sector pays to the private sector in terms of an additional unitary payment over the concession period. In this way, both partners in PFI can take advantages from incorporating flexibilities in the project.
Design of low power and high speed configurable booth multiplier

A configurable multiplier optimized for low power and high speed operations and which can be configured either for single 16-bit multiplication operation, single 8-bit multiplication or twin parallel 8-bit multiplication is designed. The output product can be truncated to further decrease power consumption and increase speed by sacrificing a bit of output precision. Furthermore, the proposed multiplier maintains an acceptable output quality with enough accuracy when truncation is performed. Thus it provides a flexible arithmetic capacity and a tradeoff between output precision and power consumption. The approach also dynamically detects the input range of multipliers and disables the switching operation of the non effective ranges. Thus the ineffective circuitry can be efficiently deactivated, thereby reducing power consumption and increasing the speed of operation. Thus the proposed multiplier outperforms the conventional multiplier in terms of power and speed efficiencies.
Variability of Stand Structures and Development in Old-Growth Forests in the Pacific Northwest, USA

The forest stand structure class “old-growth” has previously been qualitatively described as having several distinct “sub-structures. ” Species composition, diameter distribution, and other structural features commonly associated with old-growth in the Pacific Northwest are quite variable. We determined which quantitative stand structure variables are commonly found together using the Spearman correlation and non-metric multidimensional analysis. Some features were more commonly found together than others, indicating different old-growth stand types, or sub-structures. Cluster analysis classified the old-growth forests into four groups: Douglas-fir dominance, shade tolerant species dominance, and intermediate groups. The intermediate groups were split by the density of large logs and large shade tolerant trees. The old-growth sub-structures appear to change from one to another as the old forest develops.
Privacy-Preserving Access to Big Data in the Cloud

Cloud storage can simplify data management and reduce data maintenance costs. However, many users and companies hesitate to move their data to cloud storage because of security and privacy concerns about third-party cloud service providers. Oblivious RAM (ORAM) aims to enable privacy-preserving access to data stored in the cloud. This article offers a tutorial on ORAM and surveys recent literature. The authors also study the access load-balancing problem when applying ORAM to big data in the cloud. They propose heuristic algorithms to achieve access load balancing in both static and dynamic deployments.
Directed selection of influenza virus produces antigenic variants that match circulating human virus isolates and escape from vaccine‐mediated immune protection

Influenza vaccination does not provide 100% protection from infection, partly due to antigenic drift of the haemagglutinin (HA) protein. Low serum antibody titres increase the risk of infection. To determine whether there were additional correlates of risk, we examined the relationship between human serum immunity and antigenic variation in seasonal H3N2 influenza viruses. Seasonal H3N2 vaccine strains grown in the presence of heterogeneous human or mono‐specific ferret antisera selected variants with mutations in the HA antigenic sites. Surprisingly, circulating strains infecting human subjects in the same seasons displayed mutations in the same positions, although only in one case did the change correspond to the same amino acid. Serum antibody titres were lower against both the in vitro selected and clinical isolates compared with the vaccine strains, suggesting that the mutations are relevant to vaccine failure. Antibody titres were also significantly lower in sera from infected subjects than in non‐infected subjects, suggesting relatively poor responses to vaccination in the infected subjects. Collectively, the data suggest that risk from influenza infection is a result of poor response to vaccination, as well as encounter with drifted seasonal influenza virus antigenic variants. The results also show that directed selection under human immune pressure could reveal antigenic variants relevant to real‐world drifted viruses, helping in annual vaccine re‐formulation.
Inversion of long-lived trace gas emissions using combined Eulerian and Lagrangian chemical transport models

We present a method for estimating emissions of long-lived trace gases from a sparse global network of high-frequency observatories, using both a global Eulerian chemical transport model and Lagrangian particle dispersion model. Emissions are derived in a single step after determin- ing sensitivities of the observations to initial conditions, the high-resolution emissions field close to observation points, and larger regions further from the measurements. This method has the several advantages over inversions using one type of model alone, in that: high-resolution simulations can be carried out in limited domains close to the measurement sites, with lower resolution being used further from them; the influence of errors due to aggregation of emissions close to the measurement sites can be minimized; assumptions about boundary conditions to the Lagrangian model do not need to be made, since the entire emissions field is estimated; any combination of appropriate models can be used, with no code modification. Because the sensitivity to the entire emissions field is derived, the estimation can be carried out using tradi- tional statistical methods without the need for multiple steps in the inversion. We demonstrate the utility of this approach by determining global SF6 emissions using measurements from the Advanced Global Atmospheric Gases Experiment (AGAGE) between 2007 and 2009. The global total and large-scale patterns of the derived emissions agree well with previous studies, whilst allowing emissions to be determined at higher resolution than has previously been possible, and improving the agreement between the modeled and observed mole fractions at some sites.
The supermassive black hole in Centaurus A: a benchmark for gas kinematical measurements

We present new HST Space Telescope Imaging Spectrograph observations of the nearby radio galaxy NGC 5128 (Centaurus A). The bright emission line with longest wavelength accessible from HST, [S III]λ9533 A, was used to study the kinematics of the ionized gas in the nuclear region with a 0.
Comparative Activity of Ciprofloxacin, Levofloxacin and Moxifloxacin against Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia Assessed by Minimum Inhibitory Concentrations and Time-Kill Studies

The aim of this study was to compare the in vitro susceptibility of Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia to three fluoroquinolones. The minimum inhibitory concentrations (MICs) to ciprofloxacin, levofloxacin and moxifloxacin were examined by E-test® for a total of 40 K. pneumoniae strains, 40 S. maltophilia strains and 40 P. aeruginosa strains. Then, the bactericidal activity of these fluoroquinolones was investigated on five strains of each bacterial species by means of time-kill curves. For K. pneumoniae and P. aeruginosa, the distance of the measured MIC from the clinical break-point is a good indicator of the bactericidal activity for ciprofloxacin and levofloxacin as obtained in our experiments. The lower the MIC, the better the bactericidal activity in term of CFU Log decreases. If MIC of ciprofloxacin and levofloxacin against the considered bacteria are far from clinical breakpoint, these two antibiotics are equivalent. According to our MIC50 and modal MIC, the breakpoints of both ciprofloxacin and levofloxacin seem to be somewhat high and data suggest reducing them. On S. maltophilia, none of the tested antibiotics showed a satisfactory activity.
VOLITION SUPPORT DESIGN MODEL

The purpose of this paper is to introduce a design model for supporting student volition. First, the construct of volition is explained and the importance of volition is further described in the context of goal attainment. Next, the theoretical basis of the model is described. Last, implications of the model are discussed for the design of learning environments as well as teacher education.
Robust Loop Closing Over Time

Long term autonomy in robots requires the ability to reconsider previously taken decisions when new evidence becomes available. Loop closing links generated by a place recognition system may become inconsistent as additional evidence arrives. This paper is concerned with the detection and exclusion of such contradictory information from the map being built, in order to recover the correct map estimate. We propose a novel consistency based method to extract the loop closure regions that agree both among themselves and with the robot trajectory over time. We also assume that the contradictory loop closures are inconsistent among themselves and with the robot trajectory. We support our proposal, the RRR algorithm, on well-known odometry systems, e.g. visual or laser, using the very efficient graph optimization framework g2o as back-end. We back our claims with several experiments carried out on real data.
Exploiting Trust in Bad Faith

Trust has been researched from various perspectives, focusing mainly on interpersonal trust in a traditional world of face-to-face interaction. Nowadays, technology has changed the ways people interact with each other, and thus the way trust is established or destroyed. Increasingly often we interact with rep-resentations of others mediated through technology rather than with people or organizations themselves. This changes the en-vironmental cues we rely on when assigning trust to others. In the current state of affairs, there is a mismatch between how we assign trust in technical environments on the one hand and how we should reasonably assign trust on the other hand, considering how technology works or fails to work. This mismatch is exploited in semantic attacks. This paper examines four brief case studies of such semantic attacks.