Miracle-dz/UniFAR-FTUs huggingface dataset:
The cAMP-PKA Signaling Pathway Regulates Pathogenicity, Hyphal Growth, Appressorial Formation, Conidiation, and Stress Tolerance in Colletotrichum higginsianum

Colletotrichum higginsianum is an economically important pathogen that causes anthracnose disease in a wide range of cruciferous crops. Understanding the mechanisms of the cruciferous plant–C. higginsianum interactions will be important in facilitating efficient control of anthracnose diseases. The cAMP-PKA signaling pathway plays important roles in diverse physiological processes of multiple pathogens. C. higginsianum contains two genes, ChPKA1 and ChPKA2, that encode the catalytic subunits of cyclic AMP (cAMP)-dependent protein kinase A (PKA). To analyze the role of cAMP signaling pathway in pathogenicity and development in C. higginsianum, we characterized ChPKA1 and ChPKA2 genes, and adenylate cyclase (ChAC) gene. The ChPKA1 and ChAC deletion mutants were unable to cause disease and significantly reduced in hyphal growth, tolerance to cell wall inhibitors, conidiation, and appressorial formation with abnormal germ tubes, but they had an increased tolerance to elevated temperatures and exogenous H2O2. In contrast, the ChPKA2 mutant had no detectable alteration of phenotypes, suggesting that ChPKA1 contributes mainly to PKA activities in C. higginsianum. Moreover, we failed to generate ΔChPKA1ChPKA2 double mutant, indicating that deletion of both PKA catalytic subunits is lethal in C. higginsianum and the two catalytic subunits possibly have overlapping functions. These results indicated that ChPKA1 is the major PKA catalytic subunit in cAMP-PKA signaling pathway and plays significant roles in hyphal growth, pathogenicity, appressorial formation, conidiation, and stress tolerance in C. higginsianum.
An improved prefixspan algorithm research for sequential pattern mining

PrefixSpan, the classic sequential patterns mining algorithm, has the problem of large expenses in constructing projected databases. A Sequential Patterns Mining based on Improved PrefixSpan (SPMIP) algorithm is proposed on the basic of the defects above. This algorithm can reduce the scale of projected databases and the time of scanning projected databases through adding the pruning step and reducing the scanning of certain specific sequential patterns production. In this way, algorithm efficiency can be raised, and the sequential patterns needed are obtained. The experiment results show that the SPMIP algorithm is more efficient than the PrefixSpan algorithm while the sequential patterns obtained are not affected.
Preprocessing of color retinal fundus images

Preprocessing is a primary step in many systems for retinal image segmentation and analysis. It improves segmentation and localization of anatomical structures of the image. In this paper, a new automatic method for preprocessing of digital color fundus images is proposed. First, a binary mask is generated using Gaussian filter to define the region of interest. Then intensity information is extracted from both red and green channels to obtain a modified intensity channel component. The performance of the proposed method has been evaluated using 241 images from three publicly available datasets. Experimental results show a visual enhancement of the retinal images with emphasis on the optic disc boundary.
CS 6180 Lecture 25 – Event Logic , Computer Security , and Unguessable Atoms

The constructive/intuitionistic type theory we have been studying in this course and which is implemented by the Nuprl proof assistant has many novel features introduced by the Cornell researchers who designed and implemented the theory, starting in 1980 [3] presented in the 1986 book Implementing Mathematics [6] and continuing for thirty seven years with lively innovative work in Ithaca and abroad [5]. One of the special features of the implementation is that it supports distributed computation on its library of definitions, theorems, and tactics. In this lecture we will continue our discussion of distributed protocols with a brief comparison of the easy to understand 2/3 consensus protocol [12] and the widely used Paxos protocol invented by Leslie Lamport [9, 10]. It is not easy to understand and even harder to verify, but it has been verified in Nuprl using the logic of events in the hands of dedicated experts such as Mark Bickford, Vincent Rahli, and Robbert van Renesse with help from Dan Arnon [2] when he was working at the EMC Corporation, now part of Dell. We will only discuss the highlights of this major effort to illustrate the expressive power of constructive type theory. This research also provides further evidence that the Church/Turing thesis about computability is applicable only to limited to a subset of what we now understood to be computable processes. We will also look at the type of Atoms and how it is used in computer security and distributed systems. This is a fascinating type not found in other type theories. The type has the characteristic that it is not enumerable, yet it is not uncountable. There are two fundamental articles on this topic. One is by Stuart Allen who invented the type and gave a supervaluation semantics in the article “An Abstract Semantics for Atoms in Nuprl” [1]. Another key article is by Mark Bickford entitled “Unguessable Atoms: A Logical Foundation for Security” [4] in which Mark shows how to use atoms in security protocols. We will not examine the applications, but the type is very interesting in its own right. 1 Distributed Protocols We have briefly discussed the 2/3 consensus protocol. It is easy to understand and reason about. We have proven it correct [12]. Industry uses the more complex but more efficient Paxos protocol [9, 10] for which Lamport won the Turing Award. We have also proved this protocol correct based on ideas from Van Renesse [13]. We will not have time to go into details of this protocol and its subtle correctness proof. However, we have a number of interesting and revealing stories about our efforts and our work with industry on this protocol.
Elimination of Harmonics in a Multi-Level Inverter with Unequal DC Sources Using the Homotopy Algorithm

This paper focuses on elimination of harmonics in a multi-level voltage-source inverter with unequal DC sources. The main objective of harmonic elimination is to reduce the total harmonic distortion (THD) in the output voltage waveform. The basic concept of this reduction is to eliminate specific harmonics, which are generally the lowest orders, with an appropriate choice of switching angles. Homotopy algorithm is used to solve the transcendental equations for finding the switching angles. This algorithm can be used for any number of voltage levels without complex analytical calculations. Simulation results verify the validity and effectiveness of the proposed algorithm.
Microcalibrator System for Chemical Signature and Reagent Delivery

Networked systems of low-cost, small, integrable chemical sensors will enable monitoring of Nonproliferation and Materials Control targets and chemical weapons threats. Sandia-designed prototype chemical sensor systems are undergoing extended field testing supported by DOE and other government agencies. A required surety component will be verification of microanalytical system performance, which can be achieved by providing a programmable source of chemical signature(s) for autonomous calibration of analytical systems. In addition, such a controlled chemical source could be used to dispense microaliquots of derivatization reagents, extending the analysis capability of chemical sensors to a wider range of targets. We have developed a microfabricated system for controlled release of selected compounds (calibrants) into the analytical stream of microsensor systems. To minimize pumping and valve requirements of microfluidic systems, and to avoid degradation issues associated with storage of dilute solutions, we have utilized thermally labile organic salts as solid-phase reservoir materials. Reproducible deposition of tetrapropyl ammonium hydroxide onto arrays of microfabricated heating elements can provide a pair of calibration marker compounds (one fast and one slow-eluting compound) for GC analyses. The use of this microaliquot gas source array for hydrogen generation is currently under further development. The goal of the latter effort will be more » to provide a source of high-pressure, low viscosity GC carrier gas for Sandia's next-generation microfabricated gas-phase chemical analysis systems. « less
Real time depth measurement using FPGA

In this work, the proposed method is real-time object depth measurement using FPGA. It based on the distance between the corners of the object. Depth measurements are generated in the Corner Detected image. In the proposed method, the corner detected from the input received from the camera is used as a template. The distance between the detected corners is calculated and the depth is measured. A real-time system that is implemented on Xilinx Virtex5 XC5LVX330 Field Programmable Gate Array (FPGA) hardware. Architecture is designed using Verilog hardware description language (Verilog HDL). FPGA receives the VGA (640×480) image from the camera using the STC-MC33CL and transmits the corresponding depth image to the monitor using the HDMI interface in real time.
Adaptive deadlock-free worm-hole routing in hypercubes

Two new algorithms for worm-hole routing in the hypercube are presented. The first hypercube algorithm is adaptive, but non-minimal in the sense that some derouting is permitted. Then another deadlock-free adaptive worm-hole based routing algorithm for the hypercube interconnection is presented which is minimal. Finally some well-known worm-hole algorithms for the hypercube were evaluated together with the new ones on a hypercube of 2/sup 10/ nodes. One oblivious algorithm, the Dimension-Order, or E-Cube routing algorithm (W. Dally, C. Seitz, 1987) was tried. In addition, three partially adaptive algorithms were considered: the Hanging algorithm (Y. Birk, P. Gibbons, D. Soroker, J. Sanz, 1989 and S. Konstantinidou, 1990), the Zenith algorithm (S. Konstantinidou, 1990), and the Hanging-Order algorithm (G.-M. Chia, S. Chalasani, C.S. Raghavendra, 1991). Finally, a fully adaptive minimal algorithm presented independently by L. Gravano, G. Pifarre, S.A. Felperin and J. Sanz (1991) and J. Duato was tried. This algorithm allows each message to choose adaptively among all the shortest paths from its source to its destination. Only four virtual channels per physical link are needed to achieve this. This technique is referred to as Fully. The results obtained show that the two new algorithms are good candidates as a choice for worm-hole routing in the hypercube network. <<ETX>>
Antecedents and consequences of supply chain information integration: a resource-based view

Purpose This paper aims to investigate the antecedents of supply chain information integration (SCII) and their consequences on company performance from the perspective of resource-based view (RBV). Design/methodology/approach Based on empirical survey data collected from 202 Australian manufacturers, this study examines the effects of strategic supply chain relationship (SCR) and supply chain technology (SCT) internalization on external and internal information integration (II) and the effects of external and internal II on operational (operational efficiency and service quality) and financial performance. Structural equation modeling and the maximum-likelihood estimation methods are used to test the proposed relationships. Findings The results indicate that both strategic SCR and SCT internalization are positively related to external and internal II. Moreover, strategic SCR has a stronger positive relationship with external II than with internal II, and SCT internalization has a stronger positive relationship with internal II than with external II. Internal II is positively related only to service quality, and external II is positively related only to operational efficiency. Both operational efficiency and service quality are positively related to financial performance. Originality/value This study contributes to the SCII literature and provides significant managerial implications for manufacturers to leverage their supply chain resources and capabilities by establishing a resources-capabilities-performance framework for the antecedents and consequences of SCII.
A Low-Complexity Joint Time Synchronization and Channel Estimation Scheme for Orthogonal Frequency Division Multiplexing Systems

In this paper, a novel training sequence structure along with a joint time synchronization and channel estimation scheme for orthogonal frequency division multiplexing (OFDM) systems is proposed. The proposed training sequence structure is composed of an orthogonal sequence attached by cyclic prefix and cyclic postfix. Both the lengths of the cyclic extensions attached are chosen to be longer than the maximum delay spread of the wireless channel. Based on the unique structure of the training sequence, we present a low-complexity joint time synchronization and channel estimation scheme. Unlike conventional methods, which require either discrete Fourier transform (DFT) operations or matrix inversions to acquire channel impulse response (CIR) information, the proposed scheme requires only a correlator and a comparator. At the expense of the same training sequence overheads, computer simulation results show that the proposed joint scheme outperforms conventional time synchronization methods by orders. Furthermore, the overall bit error rate (BER) performance of the proposed joint scheme is shown to be close to the ultimate bound characterized by perfect synchronization and channel estimation. The proposed joint scheme also provides significant BER performance gain as compared to a scheme that properly combines a conventional synchronization method with a DFT-based channel estimation method.
Identifying Sox2 interaction partners in the developing lung

Lung development is determined by the coordinated expression of several key genes, and previously, we and others have shown the importance the SRY (sex determining region Y)-box 2 (Sox2) gene in lung development. Transgenic expression of Sox2 during lung development resulted in cystic airways and here we show that modulating the timing of ectopic Sox2 expression in the branching regions of the developing lung results in variable cystic lesions resembling the spectrum of the human congenital disorder Congenital Cystic Adenomatoid Malformation (CCAM). Sox2 dominantly differentiated naïve epithelial cells into the proximal lineage, irrespective of the presence of Fgf10. Sox2 directly induced the expression of Trp63, the master switch towards the basal cell lineage. In addition, Sox2 induced the expression of Gata6, a factor involved in the emergence of bronchioalveolar stem cells. In addition, we showed that SOX2 and TRP63 are co-expressed in the lungs of human CCAM type II patients. The combination of premature differentiation towards the proximal cell lineage and the induction of proliferation finally resulted in the cyst-like structures. Thus, we show that Sox2 is directly responsible for the emergence of two lung progenitor cells, basal cells by regulating the master gene Trp63, and bronchoalveolar stem cells by regulating Gata6.
Lack of Adherence of Clinical Isolates ofPseudomonas aeruginosa to Asialo-GM1 on Epithelial Cells

ABSTRACT Numerous studies have reported that asialo-GM1, gangliotetraosylceramide, or moieties serve as epithelial cell receptors for Pseudomonas aeruginosa. Usually this interaction is confirmed with antibodies to asialo-GM1. However, few, if any, of these reports have evaluated the binding of fresh clinical isolates of P. aeruginosa to asialo-GM1 or the specificity of the antibodies for the asialo-GM1 antigen. We confirmed that asialo-GM1 dissolved in dimethyl sulfoxide could be added to the apical membrane of Madin-Darby canine kidney cells growing as a polarized epithelium on Transwell membranes (J. C. Comolli, L. L. Waite, K. E. Mostov, and J. N. Engel, Infect. Immun. 67:3207–3214, 1999) and that such treatment enhanced the binding of P. aeruginosa strain PA103. However, no otherP. aeruginosa strain, including eight different clinical isolates, exhibited enhanced binding to asialo-GM1-treated cells. Studies with commercially available antibodies to asialo-GM1 showed that these preparations had high titers of antibody to P. aeruginosa antigens, including whole cells, purified lipopolysaccharide (LPS), and pili. Inhibition studies showed that adsorption of an antiserum to asialo-GM1 withP. aeruginosa cells could remove the reactivity of antibodies to asialo-GM1, and adsorption of this serum with asialo-GM1 removed antibody binding to P. aeruginosa LPS. Antibodies in sera raised to asialo-GM1 were observed to bind to P. aeruginosa cells by immunoelectron microscopy. Antibodies to asialo-GM1 inhibited formation of a biofilm by P. aeruginosa in the absence of mammalian cells, indicating a direct inhibition of bacterial cell-cell interactions. These findings demonstrate that asialo-GM1 is not a major cellular receptor for clinical isolates of P. aeruginosa and that commercially available antibodies raised to this antigen contain high titers of antibody to multiple P. aeruginosa antigens, which do not interfere with the binding of P. aeruginosa to mammalian cells but possibly interfere with the binding of P. aeruginosa cells to each other.
Relocation, the restructuring of the labour process and job quality

Organizations restructure their activities and relocate work to other subsidiaries and companies, both in their own countries and across borders. The key question of this chapter is whether work is transformed when it is moved and with what effect. Do companies simply duplicate the processes at the destination or are the activities restructured along the way, leading to changes in the division of labour? And what is the impact of such changes on job quality?
A comparison of total hip and knee replacement in specialty and general hospitals.

BACKGROUND The emergence of specialty orthopaedic hospitals has generated widespread controversy, but little is known about the quality of care they deliver. Our objective was to compare the characteristics and outcomes of patients undergoing major joint replacement in specialty orthopaedic and general hospitals. METHODS We conducted a retrospective cohort study of 51,788 Medicare beneficiaries who underwent total hip replacement and 99,765 who underwent total knee replacement in thirty-eight specialty orthopaedic hospitals and 517 general hospitals between 1999 and 2003. We compared demographic data, rates of comorbid illness, and socioeconomic status of patients treated in specialty and general hospitals. Logistic regression was used to calculate the odds of an adverse outcome (death or selected surgical complications) after adjustment for patient characteristics and hospital procedural volume. RESULTS The demographic data and the ratio of primary to revision arthroplasties were similar, but patients who received care in specialty hospitals had less comorbidity and resided in more affluent zip codes than their counterparts in general hospitals in 2003. Specialty hospitals had significantly greater mean procedural volumes in 2003 than did general hospitals for both total hip replacement (thirty-three compared with twenty procedures; p = 0.05) and total knee replacement (seventy-five compared with forty procedures; p = 0.006). The unadjusted rate of adverse outcomes was lower in specialty hospitals than in general hospitals for total hip replacement (3.0% compared with 6.9%; p < 0.001) and total knee replacement (2.1% compared with 3.9%; p < 0.001). After adjusting for patient characteristics and procedural volume, the odds of adverse outcomes occurring were significantly lower for patients in specialty hospitals than for those in general hospitals for both primary joint replacement (odds ratio, 0.64; 95% confidence interval, 0.56 to 0.75; p < 0.001) and revision joint replacement (odds ratio, 0.49; 95% confidence interval, 0.36 to 0.66; p < 0.001). CONCLUSIONS After adjustment for patient characteristics and hospital volume, the specialty orthopaedic hospitals had better patient outcomes, as measured by Medicare administrative data, than did the general hospitals.
Future scenarios in UK apparel supply chains: a disaggregative Delphi study

Purpose: The purpose of the paper is to explore the issues of strategic and supply chain alignment in the apparel supply chain now, and to establish future scenarios for the development of the apparel supply chain in the context of emerging retail strategy and a changing trading environment. Approach: The approach adopted is a Disaggregative Delphi study based on interviews with experts from across the UK apparel supply chain, a survey ranking variables as important now and in 5 years’ time and development of three future scenarios from which emerging supply chain configurations are presented. Findings: The findings reveal a gap between retail strategy and supply chain practice, with cost and design integrity dominating supply chain decisions. Three future supply chain configurations are developed that illustrate varying tendencies towards enhanced standardisation and cost efficiency; proximity supported flexibility; and responsiveness to niche market demands, respectively. Research implications and limitations: There is a lingering gap between theory and practice in the apparel supply chain, with a persistent focus on cost, limited adoption of fast fashion and an emerging emphasis on standardisation downstream. The supply chain configurations revealed reflect the difference between upstream and downstream practices which impacts on theory, as most extant research is retail centric. The research is limited to the apparel industry, but there is opportunity to generalise to other low-cost, fast moving consumer sectors. Practical implications: The findings illustrate the opportunity for innovation in the apparel supply chain in response to growing multi-channel distribution and delays in product development, to align the supply chain with retail strategy. The lingering focus on cost, slow uptake of new technologies and deterioration in relationships is challenged. Originality and value: Empirical evidence in the apparel supply chain is dominated by single case approaches and the retail perspective. This paper is unique in that it explores the whole apparel supply chain from multiple expert perspectives, while also developing scenarios to inform future research and practice. It introduces the concept of the Dissaggregative Delphi to supply chain ‘futures’ studies, reflecting the lack of a one-size-fits-all solution. The research explores the supply chain response to shifting retail strategy and reveals the emerging importance of downstream standardisation in future supply chain configurations – at the expense of responsiveness elsewhere in the supply chain.