Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression Profile of Cytokines and Enzymes mRNA in Blood Leukocytes of Dogs with Leptospirosis and Its Associated Pulmonary Hemorrhage Syndrome

Background Dogs with leptospirosis show similar organ manifestations and disease course as human patients, including acute kidney injury and pulmonary hemorrhage, making this naturally-occurring infection a good animal model for human leptospirosis. Expression patterns of cytokines and enzymes have been correlated with disease manifestations and clinical outcome in humans and animals. The aim of this study was to describe mRNA expression of pro- and anti-inflammatory mediators in canine leptospirosis and to compare it with other renal diseases to identify patterns characterizing the disease and especially its pulmonary form. Methodology and Principal Findings The mRNA abundance of cytokines (IL-1α, IL-1β, IL-8, IL-10, TNF-α, TGF-β) and enzymes (5-LO, iNOS) was measured prospectively in blood leukocytes from 34 dogs with severe leptospirosis and acute kidney injury, including 22 dogs with leptospirosis-associated pulmonary hemorrhages. Dogs with leptospirosis were compared to 14 dogs with acute kidney injury of other origin than leptospirosis, 8 dogs with chronic kidney disease, and 10 healthy control dogs. Canine leptospirosis was characterized by high 5-LO and low TNF-α expression compared to other causes of acute kidney injury, although the decreased TNF-α expression was also seen in chronic kidney disease. Leptospirosis-associated pulmonary hemorrhage was not characterized by a specific pattern, with only mild changes noted, including increased IL-10 and decreased 5-LO expression on some days in affected dogs. Fatal outcome from pulmonary hemorrhages was associated with low TNF-α, high IL-1β, and high iNOS expression, a pattern possibly expressed also in dogs with other forms of acute kidney injury. Conclusion The patterns of cytokine and enzyme expression observed in the present study indicate a complex pro- and anti-inflammatory response to the infection with leptospires. The recognition of these signatures may be of diagnostic and prognostic relevance for affected individuals and they may indicate options for newer therapies targeting the identified pathways.
P2P MANET's - New Research Issues

MANETs are based on a network architecture that is quite different from the wired Internet architecture. In fact, a typical MANET architecture reminds us of the architectures introduced in the ‘80s to interconnect LANs, with level 2 routing which is based on MAC addresses. The MANET routing functionality is non-hierarchical on the level-2 and, thus, is several layers below the functionality offered by a P2P network. This implies that in a MANET the P2P concept will be implemented on top of level-2 routing. There is a definite need for overlay/P2P networking in a MANET, for the following reasons: (a) the MANET routing layer is often inadequate to provide the services needed by sophisticated mobile applications, and; (b) the unpredictability of the radio channel combined with the mobility of the users can pose major challenges to routing, requiring upper layer intervention. The leading strategy today is to keep MANET routing and transport protocols simple (mainly for ease of standardization), and; to complement them when necessary with upper layer functions via overlays and P2P networking.
Stability of RNA quadruplex in open reading frame determines proteolysis of human estrogen receptor α

mRNAs encodes not only information that determines amino acid sequences but also additional layers of information that regulate the translational processes. Notably, translational halt at specific position caused by rare codons or stable RNA structures is one of the potential factors regulating the protein expressions and structures. In this study, a quadruplex-forming potential (QFP) sequence derived from an open reading frame of human estrogen receptor α (hERα) mRNA was revealed to form parallel G-quadruplex and halt the translation elongation in vitro. Moreover, when the full-length hERα and variants containing synonymous mutations in the QFP sequence were expressed in cells, translation products cleaved at specific site were observed in quantities dependent on the thermodynamic stability of the G-quadruplexes. These results suggest that the G-quadruplex formation in the coding region of the hERα mRNA impacts folding and proteolysis of hERα protein by slowing down or temporarily stalling the translation elongation.
Effects of Shot-Peening on High Cycle Fretting Fatigue Behavior of Ti-6Al-4V

Abstract : Effects of Shot-peening on High Cycle Fretting Fatigue behavior of Ti-6Al-4V were investigated. Experiments were performed with 6.35 mm thick specimens which provided S/N curves. After the tests, it was observed that the specimens failed near the trailing edge of contact. Scanning Electron Microscopy showed that cracks initiated on the contact surface for 6.35 mm, and at the depth of specimen ranging from 200 to 300 microns for 3.81 mm thick specimens. Initial crack orientation was around 37 and 42 degrees respectively for 6.35 and 3.81 mm thicknesses. Finite Element Analysis (FEA) was conducted, and using FEA results, Smith-Watson-Topper, Findley, Shear Stress Range and Modified Shear Stress Range parameters were evaluated. Stress relaxation was observed after the failure of the specimens, and evaluations were repeated for different percentages of stress relaxation. Based on specific assumptions about stress relaxation. Modified Shear Stress range parameter was determined to be the only appropriate fatigue parameter that could meet all the required conditions for shot-peened fretting fatigue specimens. Also thickness effects on shot-peened specimens were investigated and discussed in this study.
An Improved Key Agreement Protocol Based on Key Association Set for Dynamic Peer Group

Secure group communication is a research hotspot. The Tree-based Group Diffie-Hellman Protocol is a fairly good key management scheme for dynamic peer group communications. Through analyzing TGDH protocol, the authors have found out that a deficiency exists with its communication mode. A lot of redundant messages are used to complete group re-keying so that more communication bandwidth will be consumed in TGDH. This paper aims to solve the deficiency and improve TGDH through designing a preparatory algorithm of finding a Key Association Set. A new re-keying protocol is also designed by using the algorithm. Theoretical analysis shows that our protocol effectively decreases the communication and storage overload of TGDH, with the communication bandwidth descending from O (nlogn) to O (n) and the key storage descending from O (n) to O (logn). The simulation result also shows the improved protocol has a better communication performance.
Novel Gram-Scale Production of Enantiopure R-Sulforaphane from Tuscan Black Kale Seeds

Dietary R-sulforaphane is a highly potent inducer of the Keap1/Nrf2/ARE pathway. Furthermore, sulforaphane is currently being used in clinical trials to assess its effects against different tumour processes. This study reports an efficient preparation of enantiopure R-sulforaphane based on the enzymatic hydrolysis of its natural precursor glucoraphanin. As an alternative to broccoli seeds, we have exploited Tuscan black kale seeds as a suitable source for gram-scale production of glucoraphanin. The defatted seed meal contained 5.1% (w/w) of glucoraphanin that was first isolated through an anion exchange chromatographic process, and then purified by gel filtration. The availability of glucoraphanin (purity ≈ 95%, weight basis) has allowed us to develop a novel simple hydrolytic process involving myrosinase (EC 3.2.1.147) in a biphasic system to directly produce R-sulforaphane. In a typical experiment, 1.09 g of enantiopure R-sulforaphane was obtained from 150 g of defatted Tuscan black kale seed meal.
Auction Design with Non-Convex Costs: An Experimental Approach

Bidders in procurement auctions often face avoidable fixed costs that give rise to complex preferences over both price and quantity supplied. We use experiments to study how enriching the bidding language (multi-part bids) and enriching market feedback (quantity-dependent prices) affect auction performance, relative to a uniform price benchmark. In combination, more expressive bidding and richer price feedback improve efficiency without changing procurement cost. On its own, more expressive bidding softens competition, but subjects consistently fail to identify and exploit even larger profit opportunities. In light of this, we discuss why subjects might handle certain types of complexity better than others.
Class-Specific Binary Correlograms for Object Recognition

This paper presents an efficient object-class recognition approach based on a new type of image descriptor: the Class-Specific Binary Correlogram (CSBC). In our representation, the image is described by a collection of CSBCs, where each one encodes the spatial distribution of class-specific features around a particular reference point. This representation is obtained by first performing an automatic selection of class-specific features from a vocabulary, and then extracting collections of binary correlograms that encode, at the same time, detected object parts and their spatial distribution around multiple points of the image. Our descriptors live in high-dimensional spaces (in the order of 10K dimensions), but they are very sparse. We show that efficient learning and matching procedures can be obtained for such a representation if we use, first, fast feature selection techniques specific for binary features, and then Boosting integrated with an appropriate Inverted File data organization. The proposed strategy works with weak supervision, outperforms state-of-the-art bag-of-feature methods, and it is more accurate and computationally more efficient than well-known geometrical-based methods, including our previous work on Generalized Correlograms (GCs) [1].
Modeling Huntington disease in yeast: Perspectives and future directions

Yeast have been extensively used to model aspects of protein folding diseases, yielding novel mechanistic insights and identifying promising candidate therapeutic targets. In particular, the neurodegenerative disorder Huntington disease (HD), which is caused by the abnormal expansion of a polyglutamine tract in the huntingtin (htt) protein, has been widely studied in yeast. This work has led to the identification of several promising therapeutic targets and compounds that have been validated in mammalian cells, Drosophila and rodent models of HD. Here we discuss the development of yeast models of mutant htt toxicity and misfolding, as well as the mechanistic insights gleaned from this simple model. The role of yeast prions in the toxicity/misfolding of mutant htt is also highlighted. Furthermore, we provide an overview of the application of HD yeast models in both genetic and chemical screens, and the fruitful results obtained from these approaches. Finally, we discuss the future of yeast in neurodegenerative research, in the context of HD and other diseases.
Toward an analytical approach to anonymous wireless networking

Communications in a wireless network are susceptible to unauthorized traffic analysis by eavesdroppers. Although cryptography can protect the contents of communication, the transmission times of packets alone can reveal significant networking information such as source- destination pairs and routes of traffic flow. This article focuses on analytical approaches to anonymous networking for the prevention of information retrieval through packet timing analysis. In particular, an analytical measure for route anonymity is proposed using information theoretic equivocation. Based on the metric, provably anonymous countermeasures are described for wireless ad hoc and sensor networks, where traffic is subjected to strict constraints on medium access and latency. A key objective is to bridge a long standing gap between the information theoretic approach to secrecy in communication, and a more pragmatic approach of Chaum mixing used in anonymous systems on the Internet. The efficacy of the proposed approach is demonstrated using an orthogonal transmitter directed signaling network.
Uniformly Convergent Interior Penalty Methods Using Multilinear Approximations for Problems in Elasticity

Interior penalty methods for linear elasticity, when used with bilinear elements, are effective in the context of compressible materials. However, they may produce poor approximations with these elements in the nearly incompressible regime. We propose a new general interior penalty formulation and prove that it is uniformly convergent with respect to the compressibility parameter for multilinear elements. The new formulation is a modification of well-known methods (nonsymmetric, incomplete, and symmetric interior penalty Galerkin) through underintegration of selected edge terms.
Parametric Maximum Flow Algorithms for Fast Total Variation Minimization

This report studies the global minimization of anisotropically discretized total variation (TV) energies with an $L^p$ (in particular, $L^1$ and $L^2$) fidelity term using parametric maximum flow algorithms to minimize $s$-$t$ cut representations of these energies. The TV/$L^2$ model, also known as the Rudin-Osher-Fatemi (ROF) model, is suitable for restoring images contaminated by Gaussian noise, while the TV/$L^1$ model is able to remove impulsive noise from grayscale images and perform multiscale decompositions of them. Preliminary numerical results on large-scale two-dimensional CT and three-dimensional brain MR images are presented to illustrate the effectiveness of these approaches.
Nonlinear transforms of ECG signals for digital QRS detection: a quantitative analysis

A class of algorithms has been developed which detects QRS complexes in the electrocardiogram (ECG). The algorithms employ nonlinear transforms derived from multiplication of backward differences (MOBD). The algorithms are evaluated with the American Heart Association ECG database, and comparisons are made with the algorithms reported by Okada (1979) and by Hamilton and Tompkins (1986). The MOBD algorithms provide a good performance tradeoff between accuracy and response time, making this type of algorithm desirable for real-time microprocessor-based implementation. <<ETX>>
Hierarchical network architecture for layered video streaming

We concern with the resources requirement of a hierarchical video-on-demand (VoD) system using layered videos in a heterogeneous environment such as Internet. An analytical model is developed to evaluate the performance of the system in terms of the blocking probability and the video quality. With the maximum cache hit (MCH) caching policy, if the customers can request different quality of the videos from the server, the blocking probability can be significantly reduced.
Laser cooling, friction and diffusion in a three-level cascade system.

A model is presented to calculate optical forces, friction, and diffusion for three-level atoms in a ladder configuration. This model is then applied to the 2 3 S1-2 3 P2-3 3 D3 cascade in metastable helium. It is demonstrated that metastable helium atoms can be decelerated within a much shorter distance using cascade excitation by overlapping traveling waves. The equilibrium temperature representing the final width of the velocity distribution is calculated as a function of laser detuning and intensity. This equilibrium temperature is also calculated for the situation of overlapping standing waves ~one-dimension! , and is found to be well above the Doppler limit for two-level 2 3 S1-2 3 P2 excitation. Numerical results are compared with existing experimental data. @S1050-2947~97! 03310-6#
An Implementation for Nested Relational Databases

Relational databases organize data in the First Normal Form, i.e., all values in a database are necessarily atomic (non-decomposable). Nested Relational Databases on the other hand are not constrained by this assumption; values of a nested relation can be either atomic values or nested relations themselves. This dissertation discusses the Indiana University prototype for nested relational databases, ANDA (Architecture for a Nested Database Applications). ANDA provides a mechanism for storing and manipulating nested relations and complex objects. All stages of query processing in ANDA are discussed. A query can be expressed in a graphical query language which is first translated to an access language and then optimized. Finally the access language interacts with the data structures of the system to evaluate the query. In ANDA, all tuples and objects are identified by a hierarchical, structured tuple-identifier (tuple-id). As tuple-ids have enough information to determine mutual relationships, extensive query processing is done by manipulating tuple-ids in main-memory. Query evaluation in ANDA is done by repeating the value $\to$ tuple-id $\to$ value cycle. The first phase involves extracting the required tuple-ids from the value-based indexing structure, VALTREE. In the second phase these tuple-ids are manipulated in the main-memory based CACHE. In the third phase, the tuple-ids from the CACHE are materialized using the RECLIST, which provides fast access to a value for a given tuple-id. An access language is designed to specify access plans. The access language abstracts the operations of the VALTREE, the RECLIST, and the CACHE. Access plans for ANDA are specified in the access language. A cost model has been proposed to provide a mechanism to compare alternative access plans. Other optimization strategies for optimizing access plans are also discussed. A graphical query language which allows direct manipulation of nested relational schemes has been designed to provide a user-friendly interface to ANDA.
Optical Proximity Communication With Passively Aligned Silicon Photonic Chips

We report high-fidelity 10-Gb/s optical-proximity-communication using reflecting mirrors micro-machined into silicon and co-integrated with low-loss silicon-on-insulator waveguides for packaged chip-to-chip communication. Device integration was carried out by dry etching a rib waveguide 8 mum wide that was tapered to a width of 13 mu m and subsequently truncated with a wet-etched, micro-mirror facet forming a 54deg angle with the (100) surface. Light in waveguides on a bottom chip can couple to waveguides on a top chip upon face-to-face positioning so that the reflecting mirrors form a coupled pair and complete an optical proximity hop. High-speed link measurements were accomplished with chips aligned with a six-axis nano-positioner stage and compared with results for a new precision alignment approach that packages silicon chips for proximity signaling. Our new packaging approach is based on the co-integration of pyramidal etch pits micro-machined into silicon that match a precision micro-sphere for accurate chip alignment. Assemblies of chips can self-align in the package using chip placement that is initially coarse. The final chip alignment accuracy of our new packaging approach is limited by photolithographic resolution. Additionally, multichip arrays can be aligned together with global positioning having similar precision. Nonreturn-to-zero data was fiber launched into the waveguides and transported across a package consisting of a three-chip assembly with two optical proximity hops for inter-chip communication. Continuous wave optical losses, eye diagrams, bit error rates, and power penalties were measured. A passively aligned chip-to-chip optical proximity hop in the package was measured to have optical coupling loss of 4.0 dB, which was 1 dB more than when measured with precision-aligned chips with a nano-positioning stage. RMS jitter and amplitude metrics for the eye quality are shown to be nearly identical (to within 1%) when OPxC hops associated with the package is inserted into 10-Gb/s links. This self-aligned mechanism enables chip packages for several classes of proximity communication.
A new method for detecting pipeline deformation by an inspection robot with a moving 2D laser rang finder

Buried pipelines would be deformed as a result of the loading of surface facilities and vehicles. If the deformation has gone beyond the critical level, it may cause serious consequences, such as the damage of the pipeline. Pipeline deformation is also applied to estimate the stress in the pipeline, and thus to keep the pipeline stress below the critical level. A new method for detecting pipeline deformation by an inspection robot with a laser range finder (LRF) is presented in this paper. The robot posture changes instantaneous when the robot is running in the pipeline, which makes the deformation detection difficult. To calculate the deformation rate of the pipeline, the moving frame of the robot, the base frame on the pipeline, and frame of the LRF are established and their transformation matrix are deduced with the posture angles of the robot detected real-time. After the range data collected by the LRF are transformed to the base frame, a least squares method is used to fit the ellipse function. With the fitted ellipse function, the ellipse can be drawn and the deformation rate can be calculated easily. Experiments by the inspection robot in real pipelines are carried out and the results show that the proposed method is useful and valid.
Fast FPGA placement using space-filling curve

In this paper, we propose a placement method for island-style FPGAs, based on recursive bi-partitioning followed by application of space-filling curves. Experimental results of our method show 55% improvement in cost, when compared to random initial placement of the popular tool VPR. The solutions thus obtained require 44.5% fewer moves during final iterative refinement by ultra-low temperature simulated annealing, whereas the quality of solution is on the average 0.1% better. This establishes the utility of the method for fast reconfiguration of FPGA based co-processors.
H2-forming N5, N10-methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum catalyzes a stereoselective hydride transfer as determined by two-dimensional NMR spectroscopy.

5,6,7,8-Tetrahydromethanopterin is a coenzyme playing a key role in the energy metabolism of methanogenic archaea. In Methanobacterium thermoautotrophicum, the reduction of N5, N10-methenyl-5,6,7,8-tetrahydromethanopterin at C(14a) with H2 to N5, N10-methylene-5,6,7,8-tetrahydromethanopterin can be catalyzed by H2-forming methylenetetrahydromethanopterin dehydrogenase, a new hydrogenase present in most methanogenic archaea, which is unique because it does not contain nickel or iron/sulfur clusters. In this work, the stereochemistry of this enzymatic hydride-transfer reaction is elucidated by means of a series of heteronuclear two-dimensional NMR experiments. It is found that the hydride from H2 is transferred by the enzyme into the rel-(pro-R) position of the C(14a) methylene group of the reaction product N5, N10-methylene-5,6,7,8-tetrahydromethanopterin. NMR experiments are described that show that the hydrogen nucleus of the hydride transferred to the oxidized coenzyme partially originates from water. The stereochemical course of this reaction is the same as that for direct hydride transfer. It is demonstrated that the diastereotopic atoms at C(14a) of the reaction product epimerize in an uncatalyzed reaction under the conditions of operation of the enzyme (k = 0.01 s-1 at 58 degree C and pH 6.5). (ABSTRACT TRUNCATED AT 250 WORDS)