Miracle-dz/UniFAR-FTUs huggingface dataset:
Apoptosis Gene Network: Description in the GeneNet and TRRD Databases

Abstract: The large volume of experimental data on apoptosis requires computer processing to systematize and provide an integrated “description of operation” of the gene network that regulates apoptosis in various cell types under varying effects. The database GeneNet contains the description of the apoptosis gene network: (http://wwwmgs.bionet.nsc.ru/systems/mgl/genenet), and the Transcription Regulatory Regions Database (TRRD) contains experimental data on transcription regulation of various genes, including apoptosis genes: (http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/).
Efficient continuous collision detection for bounding boxes under rational motion

This paper presents a simple yet precise and efficient algorithm for collision prediction of two oriented bounding boxes under univariate (piecewise) rational motion. We present an analytic solution to the problem of finding the time of collision and the feature involved, or declaring that no collision should occur. Our solution can be applied to boxes of any size, under arbitrary rational rigid motion. The algorithm is based on the efficient examination of the Minkowski sum (MS) of the two boxes, using a spherical Gauss map dual representation, and a precise extraction of the collision time, if any, as a solution to a set of rational equations that are automatically derived
The structure-function relationship of activated protein C

Summary Protein C is the central enzyme of the natural anticoagulant pathway and its activated form APC (activated protein C) is able to proteolyse non-active as well as active coagulation factors V and VIII. Proteolysis renders these cofactors inactive, resulting in an attenuation of thrombin formation and overall down-regulation of coagulation. Presences of the APC cofactor, protein S, thrombomodulin, endothelial protein C receptor and a phospholipid surface are important for the expression of anticoagulant APC activity. Notably, APC also has direct cytoprotective effects on cells: APC is able to protect the endothelial barrier function and expresses anti-inflammatory and anti-apoptotic activities. Exact molecular mechanisms have thus far not been completely described but it has been shown that both the protease activated receptor 1 and EPCR are essential for the cytoprotective activity of APC. Recently it was shown that also other receptors like sphingosine 1 phosphate receptor 1, Cd11b/CD18 and tyrosine kinase with immunoglobulin-like and EGFlike domains 2 are likewise important for APC signalling. Mutagenesis studies are being performed to map the various APC functions and interactions onto its 3D structure and to dissect anticoagulant and cytoprotective properties. The results of these studies have provided a wealth of structure-function information. With this review we describe the state-of-the-art of the intricate structure-function relationships of APC, a protein that harbours several important functions for the maintenance of both humoral and tissue homeostasis. Lessons from natural and engineered mutations
A power-aware scalable pipelined Booth multiplier

Energy-efficient power-aware design is highly desirable for DSP functions that encounter a wide diversity of operating scenarios in battery-powered wireless sensor network systems. Addressing this issue, this paper presents a low-power power-aware scalable pipelined Booth multiplier that makes use of the sharing common functional unit, ensemble of optimized Wallace-trees and a 4-bit array-based adder-tree for DSP applications. Our multiplier detects the input operands for their dynamic range and accordingly implements a 16-bit, 8-bit or 4-bit multiplication operation. "The multiplication mode is determined by the dynamic-range detection unit, which generates and dispatches the control signals for the pipeline stages. For the 8-bit and 4-bit computations, the proposed Booth multiplier leads to a 29% and 58% power consumption reduction over a non-scalable Booth multiplier, respectively. The proposed scalable pipelined Booth multiplier proves to be globally 20% more power efficient than a non-scalable pipelined Booth multiplier, and also it has fast speed due to pipelining.
Tightening non-simple paths and cycles on surfaces

We describe algorithms to compute the shortest path homotopic to a given path, or the shortest cycle freely homotopic to a given cycle, on an orientable combinatorial surface. Unlike earlier results, our algorithms do not require the input path or cycle to be simple. Given a surface with complexity n, genus g ≥ 2, and no boundary, we construct in O(n2 log n) time a tight octagonal decomposition of the surface---a set of simple cycles, each as short as possible in its free homotopy class, that decompose the surface into a complex of octagons meeting four at a vertex. After the surface is preprocessed, we can compute the shortest path homotopic to a given path of complexity k in O(gnk) time, or the shortest cycle homotopic to a given cycle of complexity k in O(gnk log(nk)) time. A similar algorithm computes shortest homotopic curves on surfaces with boundary or with genus 1. We also prove that the recent algorithms of Colin de Verdière and Lazarus for shortening embedded graphs and sets of cycles have running times polynomial in the complexity of the surface and the input curves, regardless of the surface geometry.
Soft-Decision-Driven Channel Estimation for Pipelined Turbo Receivers

We consider channel estimation specific to turbo equalization for multiple-input multiple-output (MIMO) wireless communication. We develop a soft-decision-driven sequential algorithm geared to the pipelined turbo equalizer architecture operating on orthogonal frequency division multiplexing (OFDM) symbols. One interesting feature of the pipelined turbo equalizer is that multiple soft-decisions become available at various processing stages. A tricky issue is that these multiple decisions from different pipeline stages have varying levels of reliability. This paper establishes an effective strategy for the channel estimator to track the target channel, while dealing with observation sets with different qualities. The resulting algorithm is basically a linear sequential estimation algorithm and, as such, is Kalman-based in nature. The main difference here, however, is that the proposed algorithm employs puncturing on observation samples to effectively deal with the inherent correlation among the multiple demapper/decoder module outputs that cannot easily be removed by the traditional innovations approach. The proposed algorithm continuously monitors the quality of the feedback decisions and incorporates it in the channel estimation process. The proposed channel estimation scheme shows clear performance advantages relative to existing channel estimation techniques.
Salmonella typhimurium is pathogenic for Dictyostelium cells and subverts the starvation response

In unicellular amoebae, such as Dictyostelium discoideum, bacterial phagocytosis is a food hunting device, while in higher organisms it is the first defence barrier against microbial infection. In both cases, pathogenic bacteria exploit phagocytosis to enter the cell and multiply intracellularly. Salmonella typhimurium, the agent of food‐borne gastroenteritis, is phagocytosed by both macrophages and Dictyostelium cells. By using cell biological assays and global transcriptional analysis with DNA microarrays covering the Dictyostelium genome, we show here that S. typhimurium is pathogenic for Dictyostelium cells. Depending on the degree of virulence, which in turn depended on bacterial growth conditions, Salmonella could kill Dictyostelium cells or inhibit their growth and development. In the early phase of infection in non‐nutrient buffer, the ingested bacteria escaped degradation, induced a starvation‐like transcriptional response but inhibited selectively genes required for chemotaxis and aggregation. This way differentiation of the host cells into spore and stalk cells was blocked or delayed, which in turn is likely to be favourable for the establishment of a replicative niche for Salmonella. Inhibition of the aggregation competence and chemotactic streaming of aggregation‐competent cells in the presence of Salmonella suggests interference with cAMP signalling.
A data management infrastructure for bridge monitoring

This paper discusses a data management infrastructure framework for bridge monitoring applications. As sensor technologies mature and become economically affordable, their deployment for bridge monitoring will continue to grow. Data management becomes a critical issue not only for storing the sensor data but also for integrating with the bridge model to support other functions, such as management, maintenance and inspection. The focus of this study is on the effective data management of bridge information and sensor data, which is crucial to structural health monitoring and life cycle management of bridge structures. We review the state-of-the-art of bridge information modeling and sensor data management, and propose a data management framework for bridge monitoring based on NoSQL database technologies that have been shown useful in handling high volume, time-series data and to flexibly deal with unstructured data schema. Specifically, Apache Cassandra and Mongo DB are deployed for the prototype implementation of the framework. This paper describes the database design for an XML-based Bridge Information Modeling (BrIM) schema, and the representation of sensor data using Sensor Model Language (SensorML). The proposed prototype data management framework is validated using data collected from the Yeongjong Bridge in Incheon, Korea.
Specification and management of QoS in imprecise real-time databases

Real-time applications such as e-commerce, flight control, chemical and nuclear control, and telecommunication are becoming increasingly sophisticated in their data needs, resulting in greater demands for real-time data services. Since the workload of real-time databases (RTDBs), providing real-time data services, cannot be precisely predicted, they can become overloaded and thereby cause temporal violations, resulting in a damage or even a catastrophe. Imprecise computation techniques address this problem and allow graceful degradation during overloads. In this paper, we present a framework consisting of a model for expressing QoS requirements in terms of data and transaction preciseness, an architecture based on feedback control scheduling, and a set of algorithms implementing different policies and behaviors. Our approach gives a robust and controlled behavior of RTDBs, even for transient overloads and with inaccurate run-time estimates of the transactions. Further, performance experiments show that the proposed algorithms outperform a set of baseline algorithms, including FCS-EDF that schedules the transactions using EDF and feedback control.
Structure of ice crystallized from supercooled water

The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples.
Randomized polynomial time identity testing for noncommutative circuits

In this paper we show that black-box polynomial identity testing for noncommutative polynomials f∈𝔽⟨z1,z2,…,zn⟩ of degree D and sparsity t, can be done in randomized (n,logt,logD) time. As a consequence, given a circuit C of size s computing a polynomial f∈𝔽⟨ z1,z2,…,zn⟩ with at most t non-zero monomials, then testing if f is identically zero can be done by a randomized algorithm with running time polynomial in s and n and logt. This makes significant progress on a question that has been open for over ten years. Our algorithm is based on automata-theoretic ideas that can efficiently isolate a monomial in the given polynomial. In particular, we carry out the monomial isolation using nondeterministic automata. In general, noncommutative circuits of size s can compute polynomials of degree exponential in s and number of monomials double-exponential in s. In this paper, we consider a natural class of homogeneous noncommutative circuits, that we call +-regular circuits, and give a white-box polynomial time deterministic polynomial identity test. These circuits can compute noncommutative polynomials with number of monomials double-exponential in the circuit size. Our algorithm combines some new structural results for +-regular circuits with known results for noncommutative ABP identity testing, rank bound of commutative depth three identities, and equivalence testing problem for words. Finally, we consider the black-box identity testing problem for depth three +-regular circuits and give a randomized polynomial time identity test. In particular, we show if f∈𝔽Z⟩ is a nonzero noncommutative polynomial computed by a depth three +-regular circuit of size s, then f cannot be a polynomial identity for the matrix algebra 𝕄s(𝔽) when 𝔽 is sufficiently large depending on the degree of f.
COATINGS FOR THE PROTECTION OF REFRACTORY METALS FROM OXIDATION

Abstract : Identifiers: Pack cementation, Hot dipping.A summary is presented of the current state of the art of coatings to protect refractory metals from oxidation. Coatings for Mo are the most advanced, followed by those for Nb alloys. Significant progress was made on coatings for Ta alloys. W has received some attention, but the temperature range precludes any easy solutions. No coatings are available for V alloys. Silicide-base coatings are of most importance for Mo and W. Both the aluminide and silicide-base coatings were of genuine value for the protection of Nb and Ta alloys.
Handling OS jitter on multicore multithreaded systems

Various studies have shown that OS jitter can degrade parallel program performance considerably at large processor counts. Most sources of system jitter fall broadly into 5 categories - user space processes, kernel threads, interrupts, SMT interference and hypervisor activity. Solutions to OS jitter typically consist of a combination of techniques such as synchronization of jitter across nodes (co-scheduling or gang scheduling) and use of microkernels. Both techniques present several drawbacks. Multicore and Multithreaded systems present opportunities to handle OS jitter. They have multiple cores and threads, some of which can be used for handling OS jitter, while the application threads run on remaining cores and threads. However, they are also prone to risks such as inter-thread cache interference and process migration. In this paper, we present a holistic approach that aims to reduce jitter caused by various sources of jitter by utilizing the additional threads or cores in a system. Our approach handles jitter through reduction of kernel threads, intelligent interrupt handling, and switching of hardware SMT thread priorities. This helps in reducing jitter experienced by application threads in the user space, at the kernel level, and at the hardware level. We make use of existing features available in the Linux kernel and Power Architecture as well make enhancements to the Linux kernel. We demonstrate the efficacy of our techniques by reducing jitter on two different platforms and operating system versions. In the first case our approach helps in reducing periodic jitter that improves both average and worst case performance of a simulated parallel application. In the second case our approach helps in reducing infrequent very large jitter that helps the worst case performance of a real parallel application. Our experimental results show up to 30% reduction in slowdown in the average case at 16K OS images and up to 50% reduction in slowdown in the worst case at 8 OS images using this approach as compared to a baseline configuration.
Deep learning for brain decoding

Learning low dimensional embedding spaces (manifolds) for efficient feature representation is crucial for complex and high dimensional input spaces. Functional magnetic resonance imaging (fMRI) produces high dimensional input data and with a less then ideal number of labeled samples for a classification task. In this study, we explore deep learning methods for fMRI classification tasks in order to reduce dimensions of feature space, along with improving classification performance for brain decoding. We employ sparse autoencoders for unsupervised feature learning, leveraging unlabeled fMRI data to learn efficient, non-linear representations as the building blocks of a deep learning architecture by stacking them. Proposed method is tested on a memory encoding/retrieval experiment with ten classes. The results support the efficiency compared to the baseline multi-voxel pattern analysis techniques.
Nutritional status in patients with diabetes and chronic kidney disease : a prospective study 1 – 3

Background: A poor nutritional status reduces the life expectancy of diabetes patients undergoing hemodialysis. Objective: The study objective was to specify the nutritional outcome in patients with chronic kidney disease (CKD) and wellcontrolled diabetes. Design: Forty-five diabetes patients with CKD were enrolled in a cooperative-care program designed to control glucose, blood pressure, LDL cholesterol, and the albumin excretion rate (AER). Their glomerular filtration rate (GFR), body composition, serum albumin (SA), and resting energy expenditure were assessed and compared at baseline and 2 y later. Results: Thirty-five patients did not start dialysis. Their glycated hemoglobin, blood pressure, LDL cholesterol, and AER improved; their GFR declined slowly ( 3.3 mL · min 1 · 1.73 m 2 · y ). Their body mass index (BMI), lean body mass, and SA increased. The GFR decline was correlated negatively with the initial BMI (r 0.37, P 0.05) and positively with the initial GFR (r 0.34, P 0.05). Ten patients started hemodialysis: except for higher total body water (P 0.05) and extracellular volume (P 0.01), their initial nutritional status did not differ significantly from that of 10 patients with comparable baseline severe CKD but without dialysis. At the second evaluation, patients on hemodialysis lost lean body mass, and their SA was lower than that of the patients with severe CKD (P 0.05); lean body mass was unchanged and SA was higher (P 0.01) in the patients with severe CKD. No significant difference was detected for resting energy expenditure. Conclusions: Nutritional status improved in CKD patients with well-controlled diabetes without dialysis, and it deteriorated in patients who started dialysis. A high initial BMI was associated with a slower decline in GFR. Am J Clin Nutr 2007;85:96–101.
Characterization of a Highly Evolved Vaccine-Derived Poliovirus Type 3 Isolated from Sewage in Estonia

ABSTRACT Two types of vaccine-derived polioviruses have been recently designated to emphasize the different origins of the evolved viruses: circulating vaccine-derived polioviruses (cVDPV) associated with outbreaks of paralytic disease and strains isolated from chronically infected immunodeficient individuals (iVDPV). We describe here a type 3 VDPV (PV3/EST/02/E252; later E252) isolated from sewage collected in Tallinn, Estonia, in October 2002. Due to aberrant properties in subtyping, the virus was subjected to detailed characterization. Partial genomic sequencing suggested that the closest relative was the oral vaccine strain PV3/Sabin, but the two virus strains shared only 86.7% of the 900 nucleotides (nt) coding for the capsid protein VP1. Phylogenetic analysis of the nearly complete genome [nt 19 to poly(A)] revealed multiple nucleotide substitutions throughout the genome and a possible Sabin 3/Sabin 1-recombination junction site in the 2C coding region. A calculation based on the estimated mutation frequency of the P1 region of polioviruses suggested that the E252 virus might have replicated in one or more individuals for approximately 10 years. No persons chronically excreting poliovirus are known in Estonia. Amino acid substitutions were seen in all known antigenic sites, which was consistent with the observed aberrant antigenic properties of the virus demonstrated by both monoclonal antibodies and human sera from vaccinated children. In spite of the apparent transmission potential, no evidence was obtained for circulation of the virus in the Estonian population.
The Birc 6 ( Bruce ) gene regulates p 53 and the mitochondrial pathway of apoptosis and is essential for mouse embryonic development

Baculoviral inhibitor of apoptosis repeat-containing (Birc)6 gene BIRC6 (Bruce APOLLON) encodes an inhibitor of apoptosis and a chimeric E2 E3 ubiquitin ligase in mammals. The physiological role of Bruce in antiapoptosis is unknown. Here, we show that deletion of the C-terminal half of Bruce, including the UBC domain, causes activation of caspases and apoptosis in the placenta and yolk sac, leading to embryonic lethality. This apoptosis is associated with up-regulation and nuclear localization of the tumor suppressor p53 and activation of mitochondrial apoptosis, which includes upregulation of Bax, Bak, and Pidd, translocation of Bax and caspase-2 onto mitochondria, release of cytochrome c and apoptosis-inducing factor, and activation of caspase-9 and caspase-3. Mutant mouse embryonic fibroblasts are sensitive to multiple mitochondrial death stimuli but resistant to TNF. In addition, eliminating p53 by RNA interference rescues cell viability induced by Bruce ablation in human cell line H460. This viability preservation results from reduced expression of proapoptotic factors Bax, Bak, and Pidd and from prevention of activation of caspase-2, -9, and -3. The amount of second mitochondrial-derived activator of caspase and Omi does not change. We conclude that p53 is a downstream effector of Bruce, and, in response to loss of Bruce function, p53 activates Pidd caspase-2 and Bax Bak, leading to mitochondrial apoptosis.