Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays.
Application of Tissue Engineering Techniques for Rotator Cuff Regeneration Using a Chitosan-Based Hyaluronan Hybrid Fiber Scaffold

Background The current surgical procedures for irreparable rotator cuff tears have considerable limitations. Tissue engineering techniques using novel scaffold materials offer potential alternatives for managing these conditions. Hypothesis A chitosan-based hyaluronan hybrid scaffold could enhance type I collagen products with seeded fibroblasts and thereby increase the mechanical strength of regenerated tendon in vivo. Study Design Controlled laboratory study. Methods The scaffolds were created from chitosan-based hyaluronan hybrid polymer fibers. Forty-eight rabbit infraspinatus tendons and their humeral insertions were removed to create defects. Each defect was covered with a fibroblast-seeded scaffold (n = 16) or a non-fibroblast-seeded scaffold (n = 16). In the other 16 shoulders, the rotator cuff defect was left free as the control. At 4 and 12 weeks after surgery, the engineered tendons were assessed by histological, immunohistochemical (n = 2), and biomechanical (n = 6) analyses. Results Type I collagen was only seen in the fibroblast-seeded scaffold and increased in the regenerated tissue. The tensile strength and tangent modulus in the fibroblast-seeded scaffold were significantly improved from 4 to 12 weeks postoperatively. The fibroblast-seeded scaffold had a significantly greater tangent modulus than did the non-fibroblast-seeded scaffold and the control at 12 weeks. Conclusion This scaffold material enhanced the production of type I collagen and led to improved mechanical strength in the regenerated tissues of the rotator cuff in vivo. Clinical Relevance Rotator cuff regeneration is feasible using this tissue engineering technique.
A Database Interface for Complex Objects

We describe a formal design for a logical query language using psi-terms as data structures to interact effectively and efficiently with a relational database. The structure of psi-terms provides an adequate representation for so-called complex objects. They generalize conventional terms used in logic programming: they are typed attributed structures, ordered thanks to a subtype ordering. Unification of psi-terms is an effective means for integrating multiple inheritance and partial information into a deduction process. We define a compact database representation for psi-terms, representing part of the subtyping relation in the database as well. We describe a retrieval algorithm based on an abstract interpretation of the psi-term unification process and prove its formal correctness. This algorithm is efficient in that it incrementally retrieves only additional facts that are actually needed by a query, and never retrieves the same fact twice.
A unified approach to configuration-based dynamic analysis of quadcopters for optimal stability

A special type of rotary-wing Unmanned Aerial Vehicles (UAV), called Quadcopter have prevailed to the civilian use for the past decade. They have gained significant amount of attention within the UAV community for their redundancy and ease of control, despite the fact that they fall under an under-actuated system category. They come in a variety of configurations. The “+” and “x” configurations were introduced first. Literature pertinent to these two configurations is vast. However, in this paper, we define 6 additional possible configurations for a Quadcopter that can be built under either “+” or “x” setup. These configurations can be achieved by changing the angle that the axis of rotation for rotors make with the main body, i.e., fuselage. This would also change the location of the COM with respect to the propellers which can add to the overall stability. A comprehensive dynamic model for all these configurations is developed for the first time. The overall stability for these configurations are addressed. In particular, it is shown that one configuration can lead to the most statically-stable platform by adopting damping motion in Roll/Pitch/Yaw, which is described for the first time to the best of our knowledge.
A novel NPC inverter for harmonics elimination and reactive power compensation

A three-phase two-leg NPC inverter is presented for power quality compensator. Eight power switches instead of twelve power switches used in the conventional three-level inverter are adopted in the adopted inverter. The voltage stress of power semiconductors is equal to half dc bus voltage instead of full dc bus voltage in the conventional two-level inverter. In this paper, the proposed inverter is operated as a power quality compensator to supply the active power for the dc or ac load and to eliminate harmonics and reactive power drawn from the nonlinear loads. Therefore, the balanced and sinusoidal line currents are drawn from the ac system. To derive the necessary active power and maintain the constant dc bus voltage, a dc bus voltage control in the outer low-bandwidth control system is used. A carrier-based current control in the inner high-bandwidth control system is used to track the line current commands. The mathematical model of the proposed converter is derived and the control algorithm is provided. Simulation and Experiments based on a laboratory prototype are presented to verify the effectiveness of the proposed control scheme.
Automatic Statistical Object Detection for Visual Surveillance

Detection and tracking of foreground objects in a video scene requires a robust technique for background modeling. The modeling issues such as noise robustness, adaptation and model accuracy must be addressed while allowing for the automatic choice of relevant parameters. In this paper three major contributions are presented. First, the representative background model is a general multivariate kernel density estimation to address the model accuracy issue as well as capturing color dependencies without any knowledge about the underlying probability density of the pixel colors. Second, a single-class classifier is trained adaptively and independently for each pixel, using its estimated densities during the training stage. Finally, noise robustness is achieved by enforcing spatial consistency of the background model
Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface‐ and solution‐based biophysical methods

The binding interactions of small molecules with carbonic anhydrase II were used as model systems to compare the reaction constants determined from surface‐ and solution‐based biophysical methods. Interaction data were collected for two arylsulfonamide compounds, 4‐carboxybenzenesulfonamide (CBS) and 5‐dimethyl‐amino‐1‐naphthalene‐sulfonamide (DNSA), binding to the enzyme using surface plasmon resonance, isothermal titration calorimetry, and stopped‐flow fluorescence. We demonstrate that when the surface plasmon resonance biosensor experiments are performed with care, the equilibrium, thermodynamic, and kinetic constants determined from this surface‐based technique match those acquired in solution. These results validate the use of biosensor technology to collect reliable data on small molecules binding to immobilized macromolecular targets. Binding kinetics were shown to provide more detailed information about complex formation than equilibrium constants alone. For example, although carbonic anhydrase II bound DNSA with twofold higher affinity than CBS, kinetic analysis revealed that CBS had a fourfold slower dissociation rate. Analysis of the binding and transition state thermodynamics also revealed significant differences in the enthalpy and entropy of complex formation. The lack of labeling requirements, high information content, and high throughput of surface plasmon resonance biosensors will make this technology an important tool for characterizing the interactions of small molecules with enzymes and receptors.
N-gram adaptation using Dirichlet class language model based on part-of-speech for speech recognition

Language model plays an important role in automatic speech recognition (ASR) systems. Performance of this model depends on its adaptation to the linguistic features. Accordingly, adaptation methods endeavour to apply syntactic and semantic characteristics of the language for language modeling. The previous adaptation methods such as family of Dirichlet class language model (DCLM) extract class of history words. These methods due to lake of syntactic information are not suitable for high morphology languages such as Farsi. This work proposes an idea for using syntactic information such as part-of-speech (POS) in DCLM for combining with an n-gram language model. In our proposed approach, word clustering is based on POS of previous words and history words. The performance of language models are evaluated on BijanKhan corpus using a hidden Markov model based ASR system. Our experiments show that using POS information along with history words and class of history words improves language model, and decreases the perplexity on our corpus. Exploiting POS information along with DCLM, the word error rate of the ASR system decreases by 1% in comparison to DCLM.
Study on a Pneumatic Artificial Muscle Actuator

Pneumatic artificial actuator had been designed and was used as power driven. A 3-DOF Pneumatic artificial actuator was described as a micro-robot flexible actuator, the mechanical model and dynamic characteristics were studied for high accurate control. The control system was designed and the actuator characteristics were tested in experiments. Results prove the pneumatic artificial actuator has good performances and can be controlled in high speed and high accuracy by computer system with PWM (Pulse Width Modulation: PWM).
Molecular architecture of a multifunctional MCM complex

DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase–primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPγS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus.
Augmentation of organ-associated natural killer activity by biological response modifiers. Isolation and characterization of large granular lymphocytes from the liver

Natural killer (NK) activity in the rat and human has been attributed to cells having the morphology of large granular lymphocytes (LGL). However, this association has been less clear in the mouse, largely because of difficulties in obtaining highly enriched populations of LGL from normal spleen and blood. We have previously observed that the administration of the biological response modifier (BRM) maleic anhydride divinyl ether (MVE-2) strongly augmented NK activity in lung and liver, and the augmented NK activity coincided with increased resistance to the formation of experimental metastases in these organs. The degree of NK augmentation was most striking in the liver, an unexpected and previously unreported observation. In the present study, both MVE-2 or Corynebacterium parvum induced a dramatic augmentation of liver NK activity, which reached maximum levels 3-5 d after treatment. This augmentation of NK activity in the liver coincided with a large increase in the number of lymphoid cells with the morphological characteristics of LGL that could be isolated from enzymatically digested suspensions of perfused liver. The yield of LGL per liver following BRM treatment corresponded to a 10-50-fold increase as compared to normal mice. LGL were purified from these enzymatically digested suspensions of perfused liver by depletion of adherent cells on nylon wool columns and subsequent enrichment for low-density lymphoid cells by fractionation on Percoll density gradients. The enrichment of LGL correlated with greatly increased NK activity against YAC-1. Conversely, the higher-density fractions were depleted of both LGL and NK activity. This increase in NK activity in the liver was suppressed by in vivo treatment with anti-asialo GM1 (asGM1) serum. This treatment also resulted in a corresponding reduction in both the total number and percentage of LGL. By flow cytometry analysis, the phenotype of the majority of these highly cytolytic LGL isolated from the livers of BRM-treated mice were asGM1+, Thy-1+, Ly-5+, Qa-5+, Mac- 1+, and Gma-1+, whereas these LGL were Ly-1-, Lyt-2-, L3T4-, and surface Ig-. We conclude that the livers of BRM-treated mice can provide a rich source of highly active mouse LGL that could be used for further characterization of this lymphocyte subset. Further, these studies imply a potential for BRM therapy of neoplastic or viral diseases through augmentation of organ-associated immune responses.
Differences in the Distribution of CD4+ and CD8+ T Cells in Emphysematous Lungs

Background: Recent studies have shown that T cells are the predominant cells infiltrating the alveolar wall of patients with emphysema. Since CD4+ and CD8+ cells have dissimilar function, they may have different distributions in emphysematous lungs. Objectives: The aim of this study was to investigate whether CD4+ and CD8+ are differently distributed in the lungs of patients with emphysema. Methods: We evaluated CD4+ and CD8+ cell infiltration in lung tissue sections obtained from smokers with pulmonary emphysema who had undergone lung volume reduction surgery (n = 10). Paraffin-embedded lung tissue sections were immunostained using antibodies against CD4+ or CD8+, and distributions of CD4+ and CD8+ cells were evaluated using a morphometric analysis. We determined the degree of emphysema using the area fraction of the alveolar wall (AA,aw) and examined its relation to the number of cells per unit area of the alveolar wall (NA). Results: The majority of CD4+ cells were located in the lung parenchyma of severe emphysematous lesions characterized by the lowest alveolar wall fraction (AA,aw). In contrast, more CD8+ cells were located in mild emphysematous lesions than in severe lesions. Conclusions: These results suggest that CD4+ and CD8+ cells are differently distributed according to the severity of emphysema. CD4+ T cells are located preferentially in severe emphysematous lesions whereas CD8+ T cells occur preferentially in mild emphysematous lesions.
An Analysis of Wireless Network Coding for Unicast Sessions: The Case for Coding-Aware Routing

A recent approach, COPE, for improving the throughput of unicast traffic in wireless multi-hop networks exploits the broadcast nature of the wireless medium through opportunistic network coding. In this paper, we analyze throughput improvements obtained by COPE-type network coding in wireless networks from a theoretical perspective. We make two key contributions. First, we obtain a theoretical formulation for computing the throughput of network coding on any wireless network topology and any pattern of concurrent unicast traffic sessions. Second, we advocate that routing be made aware of network coding opportunities rather than, as in COPE, being oblivious to it. More importantly, our work studies the tradeoff between routing flows "close to each other" for utilizing coding opportunities and "away from each other" for avoiding wireless interference. Our theoretical formulation provides a method for computing source-destination routes and utilizing the best coding opportunities from available ones so as to maximize the throughput. We handle scheduling of broadcast transmissions subject to wireless transmit/receive diversity and link interference in our optimization framework. Using our formulations, we compare the performance of traditional unicast routing and network coding with coding-oblivious and coding-aware routing on a variety of mesh network topologies, including some derived from contemporary mesh network testbeds. Our evaluations show that a route selection strategy that is aware of network coding opportunities leads to higher end-to-end throughput when compared to coding-oblivious routing strategies.
The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri)1[OPEN]

Adaptation of seagrass to the marine environment involves modification and loss of conserved plant genes. Seagrasses are marine angiosperms that evolved from land plants but returned to the sea around 140 million years ago during the early evolution of monocotyledonous plants. They successfully adapted to abiotic stresses associated with growth in the marine environment, and today, seagrasses are distributed in coastal waters worldwide. Seagrass meadows are an important oceanic carbon sink and provide food and breeding grounds for diverse marine species. Here, we report the assembly and characterization of the Zostera muelleri genome, a southern hemisphere temperate species. Multiple genes were lost or modified in Z. muelleri compared with terrestrial or floating aquatic plants that are associated with their adaptation to life in the ocean. These include genes for hormone biosynthesis and signaling and cell wall catabolism. There is evidence of whole-genome duplication in Z. muelleri; however, an ancient pan-commelinid duplication event is absent, highlighting the early divergence of this species from the main monocot lineages.
Moment-Method Analysis of Volume Dielectric Scatterers. Four Independent Entire-Domain Solutions: Is Entire-Domain Philosophy a Luxury or Necessity in the Method of Moments?

Four independent methods are presented for entire-domain (large-domain) moment-method analysis of lossy, inhomogeneous dielectric scatterers. They share two basic steps in solving volume integral equations: (1) the approximation of the scatterer geometry by large trilinear hexahedrons; and (2) the approximation of the unknown vector function in the hexahedrons by three-dimensional polynomials. The results are compared among themselves and with those obtained by subdomain (the only existing) methods, demonstrating great superiority of the entire-domain approach in solving three-dimensional scattering and interaction problems. 0 1996 John Wiley & Sons, Inc.
Nitrogen changes in the leaves and accumulation of some minerals in the seeds of red, white and chitti beans ('Phaseolus vulgaris') under water deficit conditions

Field studies were carried out using split-plot experiments in randomized complete block design with four replications. The objective of the studies was to determine the nitrogen (N) contents in the leaves and seeds in addition with some other mineral nutrients in the seeds of common bean (Phaseolus vulgaris L.) genotypes grown under contrasting water regimes. Two levels of irrigation (irrigation after 55-60 and 100-110 mm evaporation from class A pan as normal and water stress conditions, respectively) and eight genotypes of beans including Chitti (COS16, KS21486, and MCD4011), red (Akhtar, AND1007, and D81083) and white (WA4502-1 and WA4531-17) were investigated in main- and sub-plots, respectively. Total N content of leaves at two growth stages (pre-flowering and seed filling period) and total contents of seed iron (Fe), zinc (Zn), phosphorous (P), nitrogen and protein were measured at harvesting. Analysis of variance indicated significant differences between genotypes in the studied traits. Irrigation regimes had significant effect on all traits except to seed N and protein contents. The results indicated that white beans had lower leaf N and seed protein contents than red and Chitti beans under both irrigation regimes. Under drought condition, AND1007 and COS16 showed significantly (p≤0.05) higher levels of leaf N (1.88 and 1.83 in vegetative stage and 0.72 and 0.73 in R8 stage, respectively). Also, seed protein in water stressed plants was higher in Chitti beans. Water deficit reduced the mean leaf N by 19% and mean grain yield by 52.7% in all genotypes. Water deficiency significantly reduced seed Fe, Zn, and P contents, but the impact of drought on Fe and P contents was more than on Zn and N contents. Under stress condition, Chitti beans showed the lowest decrease (16.5%) in their seeds iron contents. Genotypes AND1007, COS16, MCD4011 and WA4502-1 were classified as efficient water users based on grain yield efficiency index (GYEI). Overall, genotypes that produce high grain yield under stress conditions and respond well to irrigation are the most desirable because they are able to express their high yield potential in a wide range of water availability.
A Case Study of Joint Online Truck Scheduling and Inventory Management for Multiple Warehouses

For a real-world problem---transporting pallets between warehouses to guarantee sufficient supply for known and additional stochastic demand---we propose a solution approach via convex relaxation of an integer programming formulation, suitable for online optimization. The essential new element linking routing and inventory management is a convex piecewise-linear cost function that is based on minimizing the expected number of pallets that still need transportation. For speed, the convex relaxation is solved approximately by a bundle approach yielding an online schedule in five to 12 minutes for up to three warehouses and 40,000 articles; in contrast, computation times of state-of-the-art LP solvers are prohibitive for online application. In extensive numerical experiments on a real-world data stream, the approximate solutions exhibit negligible loss in quality; in long-term simulations the proposed method reduces the average number of pallets needing transportation due to short-term demand to less than half the number observed in the data stream.