Miracle-dz/UniFAR-FTUs huggingface dataset:
Salt stress–induced changes in antioxidative defense system and proteome profiles of salt-tolerant and sensitive Frankia strains

ABSTRACT An appreciation of comparative microbial survival is most easily done while evaluating their adaptive strategies during stress. In the present experiment, antioxidative and whole cell proteome variations based on spectrophotometric analysis and SDS-PAGE and 2-dimensional gel electrophoresis have been analysed among salt-tolerant and salt-sensitive Frankia strains. This is the first report of proteomic basis underlying salt tolerance in these newly isolated Frankia strains from Hippophae salicifolia D. Don. Salt-tolerant strain HsIi10 shows higher increment in the contents of superoxide dismutase, catalase and ascorbate peroxidase as compared to salt-sensitive strain HsIi8. Differential 2-DGE profile has revealed differential profiles for salt-tolerant and salt-sensitive strains. Proteomic confirmation of salt tolerance in the strains with inbuilt efficiency of thriving in nitrogen-deficient locales is a definite advantage for these microbes. This would be equally beneficial for improvement of soil nitrogen status. Efficient protein regulation in HsIi10 suggests further exploration for its potential use as biofertilizer in saline soils.
BGN: A novel scatternet formation algorithm for bluetooth-based sensor networks

To address the unreliability and inefficiency of the existing algorithms for Bluetooth scatternet formation, this paper proposes a new efficient algorithm, Bluetooth Growing Network (BGN) algorithm, which constructs Bluetooth scatternet by adding reserve links among its branch nodes so that the resulting scatternet can maintain a high degree of connectivity while avoiding exccessive redundant links. Extensive simulation results demonstrate that the scatternet constructed by BGN algorithm is efficient in terms of the number of bridge nodes, average data transmission distance, network reliablity and overall network traffic.
Effect of Dominant-Negative Epidermal Growth Factor Receptors on Cardiomyocyte Hypertrophy

Angiotensin II (AngII) induces heart growth via cardiomyocyte hypertrophy, and central to this is the capacity of the type 1 AngII receptor (AT1R) to “transactivate” epidermal growth factor receptors (EGFRs)—a family with four main subtypes (HER1-4)—although the exact molecular mechanism remains unresolved. In this study, the pharmacological inhibition of AngII-stimulated ERK1/2 activation and cardiomyocyte hypertrophy by increasing concentrations of an EGFR inhibitor, AG1478, indicated that other EGFR subtypes, in addition to HER1, may be involved. We constructed expression vectors and adenoviruses expressing truncated mutant versions of HER1, HER2, and HER4 and determined their capacity to act as dominant-negative inhibitors when co-transfected with full-length EGFRs. It is surprising that adenoviral-mediated expression of these truncated EGFRs in cardiomyocytes led to paradoxical, ligand-independent increases in cardiomyocyte hypertrophy and unusual morphological changes. These results challenge our perception of AT1R-mediated EGFR transactivation and imply that truncated EGFRs may affect cell function through unconventional mechanisms.
On the Graph Fourier Transform for Directed Graphs

The analysis of signals defined over a graph is relevant in many applications, such as social and economic networks, big data or biological networks, and so on. A key tool for analyzing these signals is the so-called graph Fourier transform (GFT). Alternative definitions of GFT have been suggested in the literature, based on the eigen-decomposition of either the graph Laplacian or adjacency matrix. In this paper, we address the general case of directed graphs and we propose an alternative approach that builds the graph Fourier basis as the set of orthonormal vectors that minimize a continuous extension of the graph cut size, known as the Lovász extension. To cope with the nonconvexity of the problem, we propose two alternative iterative optimization methods, properly devised for handling orthogonality constraints. Finally, we extend the method to minimize a continuous relaxation of the balanced cut size. The formulated problem is again nonconvex, and we propose an efficient solution method based on an explicit–implicit gradient algorithm.
CaFE: a tool for binding affinity prediction using end-point free energy methods

UNLABELLED Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. AVAILABILITY AND IMPLEMENTATION CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. CONTACT tingjunhou@zju.edu. cn.
A fast and precise circuit simulation method for switching power converters using a mixture of circuits and behavioral models

We propose a fast and precise simulation method for replicating the transient responses and frequency characteristics of switching power converters using a mixture of real circuits and behavioral models. The method used a behavioral simulation tool (Verilog-A), which was supported by an analog simulator such as SPECTRE®. The time-step became variable, however, the nonlinear operation of the circuit was considered and state-space equations were formulated by applying the hybrid-dynamical-system control scheme in behavioral modeling [1]. Each macro block can have either the real schematic and behavioral model. The transient simulation operates in such a way that the analog simulator advances the simulation step by step while obtaining results from behavioral blocks. Further application of the periodic steady state (PSS) and periodic stability (PSTB) analyses, allowed us to obtain the frequency characteristics in short time. For verification, we simulated the circuits of the current-mode buck DC-DC converter IC, which was previously fabricated using a 0.18-um CMOS process. When we chose blocks of a buffer, the switching and output circuits and RS-FF real transistor circuits, while the rest behavioral models, we achieved transient response and frequency characteristics that were 13 and 75 times faster, respectively, than the analog simulator alone, while keeping less than 3.9% and 2.5% of errors compared with IC's evaluation results.
Investigation of Low-Temperature Hydrogen Plasma-Etching Processes for Silicon Wafer Solar Cell Surface Passivation in an Industrial Inductively Coupled Plasma Deposition Tool

A hydrofluoric-acid (HF)-free hydrogen plasma dry etching process prior to the deposition of intrinsic amorphous silicon onto thin n-type planar Czochralski silicon wafers is developed. The influence of substrate temperature, hydrogen flow rate, and power density on the passivation quality is investigated. Advanced characterization using spectroscopic ellipsometry and transmission electron microscopy shows the impact of the etching conditions, especially the temperature and gas flow rates, on the surface quality and interface properties. It is found that the native oxide can only be removed effectively when wafers are subjected to higher temperature or lower hydrogen flow rate. The hydrogen, oxygen, and carbon concentration profiles at the a-Si/c-Si interface of the plasma-etched samples are studied and compared with the traditionally HF cleaned interface to gain a better understanding of the reasons for the superior passivation quality.
Ours NetVLAD Ours NetVLAD Ours NetVLAD Query Image Reweighting Mask Ours NetVLAD Ours NetVLAD Ours

We qualitatively show how feature weights change adaptively based on the context in the proposed image representation as detailed in Section 2 (Fig. 1 and Fig. 2). Additionally, we show examples of retrieval results on the San Francisco dataset [2] (Section 3), and retrieval results on the Oxford Buildings 105k dataset [4] (Section 4) that were not included in the paper due to space constraints.
The Impact Non-Factor.

A t the Annual Meeting of the American Society of Cell Biology in San Francisco held in December, 2012, a group of editors and publishers of medical and scientific journals crafted the San Francisco Declaration on Research Assessment (DORA), subsequently published in May, 2013. The DORA document was created as a result of the group’s consensus concern that a journal’s Impact Factor does not accurately represent the quality or scientific value of the content of the journal. Also of concern to the group was the increasing trend to citation of review articles or other secondary sources, as opposed to primary research sources, in biomedical publications. The first general recommendation in DORA was: “Do not use journal-based metrics, such as journal Impact Factors, as a surrogate measure of the quality of individual research articles, to assess an individual scientist’s contributions, or in hiring, promotion, or funding decisions. ” The document went on to make a further 17 specific recommendations, aimed at funding agencies, institutions, publishers, organizations that supply metrics, and investigators. Since the initial publication of the DORA document, more than 12,700 individuals (including the undersigned authors) and more than 850 organizations have signed on in support of DORA. In July, 2016, the American Society for Microbiology (ASM) – responsible for 8 different biomedical journals – stated: “Despite widespread condemnation of journal Impact Factors to assess the significance of published work, these numbers continue to be widely misused in publication, hiring, funding, and promotion decisions. ” The ASM leadership and Editors of ASM journals made the decision to remove reference to the Impact Factor from all ASM journals, and from related informational or promotional materials. They further noted: “The relentless pursuit of high Impact Factor publications has been detrimental for science. ” TheMay, 2017 issues of the Journal of Clinical Pharmacology andClinical Pharmacology in Drug Development – two scientific journals owned by the American College of Clinical Pharmacology (ACCP) and published by Wiley – contained simultaneous editorials stating that reference to the Impact Factor would be removed from the journals and their web sites, and from any informational material made available from the ACCP. How did we get here? The late Eugene E. Garfield passed away in February, 2017, at the age of 91. He was a prodigious intellect and a pioneering innovator in the field of citation science. His 1955 article in Science proposed the concepts of a citation index for science, and an Impact Factor for journals. The journal Impact Factor was actually anticipated to assist libraries in the selection of journals to which they would subscribe. Garfield went on to found the Institute for Scientific Information, and was behind the founding of Current
Integrated Care and Leprosy in India:A Role for Indian Systems of Medicine and Traditional Health Practice in the Eradication of Leprosy

The benefits of an integrated approach in the future of leprosy control in India are discussed, by involving professionals from different systems of medicine and coordinated by dermatologists working in the field of community dermatology. The low level of education amongst traditional healers has led to misdiagnosis and inappropriate treatment, thus emphasizing the importance of health education for patients, families and local practitioners to enable prompt and appropriate treatment. The Indian systems of medicine though supportive do not have the required rehabilitation services. Traditional health practitioners demonstrated an improved knowledge of leprosy on completion of training, and were able to detect and refer suspect cases with only early signs of disease.
A new pipelined binary search architecture for IP address lookup

Efficient hardware implementation of address lookup is one of the most important design issues of Internet routers. Address lookup significantly impacts router performance since routers need to process tens-to-hundred millions of packets per second in real time. In this paper, we propose a practical IP address lookup structure based on the binary tree of prefixes of different lengths. The proposed structure produces multiple balanced trees, and hence it solves the issues of the unbalanced binary prefix tree of the existing scheme. The proposed structure is implemented using pipelined binary search combined with a small size TCAM. Performance evaluation results show that the proposed architecture requires a 2000-entry TCAM and total 250-kbyte SRAM to store about 30000 prefix samples from MAE-WEST router, and an address lookup is achieved by one memory access. The proposed scheme scales very well with both large databases and longer addresses as in IPv6.
Frugal IV alternatives to identify the parameter for an endogenous regressor

A review of the econometric literature on instrumental variables (IV) estimation shows that the performance of traditional IV estimation relies critically on the quality of the instruments. We discuss three different approaches that do not require the availability of observed instrumental variables: the ‘Higher Moments’ (HM) estimator, the ‘Identification trough Heteroscedasticity’ (IH) estimator, and the ‘Latent Instrumental Variable’ (LIV) approach. These methods attempt to identify the regression parameters not through observed instruments but by using other information that enables identifiability. The performance of these methods is illustrated on simulated and empirical data. Copyright © 2009 John Wiley & Sons, Ltd.
Optimal experimental design for mechanistic nonlinear dynamic models using multisine inputs: Application to a Diesel engine

For many applications first-principles nonlinear dynamic models are preferred by practitioners. Parameter estimation for these models is often a non-trivial and time consuming task. The use of optimally designed dynamic inputs can reduce the experimental burden and increase the accuracy of the estimated parameters. Traditionally, piecewise polynomial input sequences are exploited for this purpose. In contrast, this paper proposes optimal experiment design with the use of random phase multisine inputs, which are typically used for black box model identification. The main motivations are (i) the practical requirement that the inputs have to be concentrated around an operating point, and (ii) the fact that fast dynamics have to be included in the input profile without introducing a large number of discretization parameters. Moreover, multisines can be designed to excite exclusively a specific frequency band of interest. As an illustration, optimal inputs are designed and validated experimentally for estimating the parameters important for the dynamical behaviour of a Diesel engine air path model.
Relational WordNet model for semantic search in Holy Quran

The Holy Quran, due to its unique style and allegorical nature, needs special attention about searching and information retrieval issues. The legacy keyword searching techniques are incapable of retrieving semantically relevant verses. In this paper, we address the deficiencies of key word based searching and the issues related to semantic search in the Holy Quran, and propose a model that is capable of performing semantic search. The model exploits WordNet relationships in relational database model. The implementation of this model has been carried out in latest tools and Surah Al-Baqrah, the largest chapter of the Holy Quran, has been taken as sample text. The precision of our model's prototype implementation is far better than simple key word searching.
A fast and efficient heuristic algorithm for the delay- and delay variation bound multicast tree problem

More and more multicast communications are becoming real-time. In real-time communications, messages must be transmitted to their destination nodes within a certain amount of time; otherwise the messages will be rendered futile. To support real-time multicast communications, computer networks have to guarantee an upper bound on the end-to-end delay from the source node to each of the destination nodes. This is known as the multicast end-to-end delay problem. On the other hand, if the same message fails to arrive at each destination node at the same time, there will probably arise inconsistency or unfairness problem among users. This is related to the multicast delay variation problem. Our research subject is concerned with the minimization of multicast delay variation under the multicast end-to-end delay constraint. The problem has been proved to be NP-complete and a heuristic algorithm for it called DVMA (delay variation multicast algorithm) has been proposed. In this paper we find that in spite of DVMA's smart performance in terms of multicast delay variations, its time complexity is as high as O(klmn/sup 4/). It is strongly believed that such a high time complexity does not fit in a modern high-speed computer network environment. Therefore, we present an alternative heuristic algorithm with a much lower time complexity O(mn/sup 2/) and with a satisfactory performance. Computer simulations also testify that our algorithm is both fast and efficient.
Low power VLSI circuit implementation using mixed static CMOS and domino logic with delay elements

The advent of dynamic CMOS logic, more precisely domino logic, made them widely used for the implementation of low power VLSI circuits. However, the main drawback of this logic is the non implementation of inverted logic. To implement the inverted logic, it is required to duplicate the logic circuit up to that part with inverted inputs. This obviously results the increase in area, delay as well as the power dissipation of the circuit. On the other hand, it is very simple to realize the circuit with both the inverted and non-inverted logic using static CMOS implementation. In this paper, this problem is addressed with the realization of the circuit which requires the implementation of inverted logic using mixed static and domino logic. To show the efficiency of the proposed model, a simple example like implementation of high fan-in NAND gate cascaded with AND gate is considered. With the comparison of all the three logics with a fixed fan-in of 7, 8 and 9 for both the gates, on an average 69.7% improvement is achieved in Power Delay Product (PDP), 11.4% improvement in area in terms of transistors using mixed logic implementation over static logic implementation and 68.64% improvement in PDP and 28.4% improvement in area over dynamic CMOS implementation when designed in 180nm technology.
Myelodysplastic syndrome with isolated 5q deletion (5q- syndrome). A clonal stem cell disorder characterized by defective ribosome biogenesis

The 5q- syndrome was first described by van den Berghe and co-workers in 1974. In this perspective article, Dr. Cazzola discusses its clonal nature and examines recent findings indicating that haploinsufficiency of genes mapping to chromosome 5q31–q32 leads to aberrant ribosome biogenesis. Dr. Cazzola also discusses the current uncertainties on the use of lenalidomide for treatment of myelodysplastic syndrome with deletion 5q. See related articles on pages 994 and 1001.
Time trends in primary HIV-1 drug resistance among recently infected persons.

CONTEXT Transmission of multiclass drug-resistant human immunodeficiency virus type 1 (HIV-1) may increase with wider use of antiretroviral therapy. OBJECTIVE To determine trends in prevalence of HIV-1 drug resistance among recently infected individuals in a geographic area with a high penetration of antiviral treatment. DESIGN, SETTING, AND PATIENTS Consecutive case series of 225 patients referred to a San Francisco, Calif, hospital with recent HIV-1 infection from June 1996 through June 2001. MAIN OUTCOME MEASURE Time trends in the prevalence of genotypic and phenotypic primary drug resistance. RESULTS Mutations associated with resistance to nonnucleoside reverse transcriptase inhibitors (NNRTIs) steadily increased from 0% in 1996-1997 to 12 (13.2%) in 2000-2001 (P =.01). There was 1 mutation associated with protease inhibitor resistance in 1996-1997 (2.5%) and there were 7 (7.7%) in 2000-2001 (P =.25). Genotypic resistance to nucleoside reverse transcriptase inhibitors (NRTIs) initially decreased and then returned to prior levels (P =.007 for test of homogeneity). Genotypic resistance to 2 or more classes of drugs increased from 1 (2.5%) to 12 (13.2%) (P =.004), but only 1 infection (1.2%) in the latter period was resistant to all 3 classes of agents (P =.58). Primary phenotypic resistance decreased for NRTIs from 21% to 6.2% (P =.03) and increased for NNRTIs from 0 to 8 (9.9%) (P =.02). Phenotypic resistance increased for protease inhibitors from 2.6% to 6.2% (P =.32). Median time to virologic suppression (<500 copies/mL) during therapy was 12 weeks for patients with genotypic evidence of resistance compared with 5 weeks for patients with drug-sensitive infections (P =.02). CONCLUSIONS The frequency of primary resistance to NNRTIs is increasing, although resistance to all available classes of antiretroviral therapy remains rare. Genotypic resistance testing in recently infected persons predicts time to viral suppression during therapy.
Respiratory effects in the aftermath of a major fire in a chemical waste depot.

OBJECTIVES The aim of this study was to investigate respiratory effects among emergency services first responders and residents with exposure to combustion products in the aftermath of a chemical waste depot fire. METHODS The study population comprised 138 individuals who were present in the area downwind of an accidental fire. Identified by telephone interview six years later, subjects with persistent respiratory symptoms were suspected as having Reactive Airways Dysfunction Syndrome (RADS). Medical tests were performed. For bronchial responsiveness, a cut-off point of PD (20)<2.39 mg histamine was taken and a dose-response slope (DRS) was calculated. Suspected RADS cases were compared with healthy controls for exposure to combustion products, lung function, and bronchial responsiveness. RESULTS The 25 suspected RADS cases were more frequently exposed than the 99 controls; the crude odds ratio for high versus low exposure was 6.5 [95% confidence interval (95% CI) 2.4-18.0]. Suspected cases showed a lower ratio of forced expiratory volume in one second to forced vital capacity (FEV(1)/FVC; P=0.028). Overall, suspected cases had higher DRS than controls. The difference was significant for males only (P=0.006), and non-smoking males (P=0.014). Highly exposed subjects had higher DRS than low exposed subjects (P=0.056). These differences were significant when restricted to non-smokers (P=0.034) and to males (P=0.019). Differences between cases and controls were stronger when the population was restricted to current non-smokers. CONCLUSIONS Persistent respiratory symptoms and bronchial responsiveness were associated with exposure to combustion products of a chemical waste depot fire which occurred more than six years earlier. Authorities and emergency services are recommended to take this into consideration when managing incidents in order to limit possible exposure to airway irritants.