Miracle-dz/UniFAR-FTUs huggingface dataset:
Journal of Graph Algorithms and Applications on a Tree and a Path with No Geometric Simultaneous Embedding

Two graphs G1 = (V, E1) and G2 = (V, E2) admit a geometric simultaneous embedding if there exist a set of points P and a bijection M : V → P that induce planar straight-line embeddings both for G1 and for G2. The most prominent problem in this area is the question of whether a tree and a path can always be simultaneously embedded. We answer this question in the negative by providing a counterexample. Additionally, since the counterexample uses disjoint edge sets for the two graphs, we also negatively answer another open question, that is, whether it is possible to simultaneously embed two edge-disjoint trees. Finally, we study the same problem when some constraints on the tree are imposed. Namely, we show that a tree of height 2 and a path always admit a geometric simultaneous embedding. In fact, such a strong constraint is not so far from closing the gap with the instances not admitting any solution, as the tree used in our counterexample has height 4.
Inter-Paradigm Translation of Process Models using Simulation and Mining

Process modeling is usually done using imperative modeling languages like BPMN or EPCs. In order to cope with the complexity of human-centric and flexible business processes several declarative process modeling languages (DPMLs) have been developed during the last years. DPMLs allow for the specification of constraints that restrict execution flows. They differ widely in terms of their level of expressiveness and tool support. Furthermore, research has shown that the understandability of declarative process models is rather low. Since there are applications for both classes of process modeling languages, there arises a need for an automatic translation of process models from one language into another. Our approach is based upon well-established methodologies in process management for process model simulation and process mining without requiring the specification of model transformation rules. In this paper, we present the technique in principle and evaluate it by transforming process models between two exemplary process modeling languages.
Architecture of Wireless Sensor Nodes for Water Monitoring Applications: From Microcontroller-based System to SoC Solutions

A significant amount of research and development work has been initiated by several research groups in the recent years to tackle the issue of water monitoring. Wireless sensor network (WSN) is predominantly used for water monitoring application. Depending on the application constraints and performance required, different implementations are considered for the development of wireless sensor nodes for water monitoring applications. Some are based on microcontroller, digital signal processor (DSP), application-specific integrated circuit (ASIC), field programmable gate array (FPGA), system-on-chip (SoC), programmable system-on-chip (PSoC) or a combination of these technologies. This paper presents a survey of state-of-the-art research on sensor node technologies used for water monitoring which includes pipeline monitoring, fresh water monitoring for quality and composition. The relative strengths and weaknesses of microcontroller, DSP, ASIC and FPGA-based wireless sensor nodes for water monitoring applications are presented. Finally, a fully-integrated energy aware SoC solution using reconfigurable hardware is proposed to achieve optimal results.
Structure of the Human 3α-Hydroxysteroid Dehydrogenase Type 3 in Complex with Testosterone and NADP at 1.25-Å Resolution*

The first crystallographic structure of human type 3 3α-hydroxysteroid dehydrogenase (3α-HSD3, AKR1C2), an enzyme playing a critical role in steroid hormone metabolism, has been determined in complex with testosterone and NADP at 1.25-Å resolution. The enzyme's 17β-HSD activity was studied in comparison with its 3α-HSD activity. The enzyme catalyzes the inactivation of dihydrotestosterone into 5α-androstane-3α,17β-diol (3α-diol) as well as the transformation of androstenedione into testosterone. Using our homogeneous and highly active enzyme preparation, we have obtained 150-fold higher 3α-HSD specificity as compared with the former reports in the literature. Although the rat and the human 3α-HSDs share 81% sequence homology, our structure reveals significantly different geometries of the active sites. Substitution of the Ser222 by a histidine in the human enzyme may compel the steroid to adopt a different binding to that previously described for the rat (Bennett, M. J., Albert, R. H., Jez, J. M., Ma, H., Penning, T. M., and Lewis, M. (1997) Structure5, 799–T812). Furthermore, we showed that the affinity for the cofactor is higher in the human 3α-HSD3 than the rat enzyme due to the presence of additional hydrogen bonds on the adenine moiety and that the cofactor is present under its reduced form in the active site in our preparation.
Cellobiose Prevents the Development of Dextran Sulfate Sodium (DSS)-Induced Experimental Colitis

Cellobiose is produced from cellulose using specific bacterial enzymes, and is hydrolyzed into glucose by the enzymes cellobiosidase and cellulase. In this study, we examined the effects of cellobiose on colonic mucosal damage in a dextran sulfate sodium (DSS) colitis model. BALB/c mice were divided into two groups. In the first group, the mice were fed 3.5% DSS mixed with normal chow. In the second group, the mice were fed 3.5% DSS plus 6.0 or 9.0% (weight/weight) cellobiose mixed with normal chow. The development of colitis was assessed on day 21. Mucosal cytokine expression was analyzed by RT-PCR. Body weight loss was significantly attenuated in the 9.0% cellobiose-fed DSS mice as compared to the DSS mice. Colonic weight/length ratio, a maker of tissue edema, was significantly higher in the DSS mice than in the 9.0% cellobiose-fed DSS mice. The disease activity index and histological colitis score were also significantly higher in the DSS mice than in the 9.0% cellobiose-fed DSS mice. Mucosal mRNA expression for IL-1β, TNF-α, IL-17 and IP-10 were markedly reduced in the 9.0% cellobiose-fed DSS mice. In conclusion, a preventive effect of cellobiose against DSS colitis suggests its clinical use for inflammatory bowel diseases patients.
Mitral repair best practice: proposed standards

Objectives: To define best practice standards for mitral valve repair surgery. Design: Development of standards for process and outcome by consensus. Setting: Multidisciplinary panel of surgeons, anaesthetists, and cardiologists with interests and expertise in caring for patients with severe mitral regurgitation. Main outcome measures: Standards for best practice were defined including the full spectrum of multidisciplinary aspects of care. Results: 19 criteria for best practice were defined including recommendations on surgical training, intraoperative transoesophageal echocardiography, surgery for atrial fibrillation, audit, and cardiology and imaging issues. Conclusions: Standards for best practice in mitral valve repair were defined by multidisciplinary consensus. This study gives centres undertaking mitral valve repair an opportunity to benchmark their care against agreed standards that are challenging but achievable. Working towards these standards should act as a stimulus towards improvements in care.
Visualizing the phage T4 activated transcription complex of DNA and E. coli RNA polymerase

The ability of RNA polymerase (RNAP) to select the right promoter sequence at the right time is fundamental to the control of gene expression in all organisms. However, there is only one crystallized structure of a complete activator/RNAP/DNA complex. In a process called σ appropriation, bacteriophage T4 activates a class of phage promoters using an activator (MotA) and a co-activator (AsiA), which function through interactions with the σ70 subunit of RNAP. We have developed a holistic, structure-based model for σ appropriation using multiple experimentally determined 3D structures (Escherichia coli RNAP, the Thermus aquaticus RNAP/DNA complex, AsiA /σ70 Region 4, the N-terminal domain of MotA [MotANTD], and the C-terminal domain of MotA [MotACTD]), molecular modeling, and extensive biochemical observations indicating the position of the proteins relative to each other and to the DNA. Our results visualize how AsiA/MotA redirects σ, and therefore RNAP activity, to T4 promoter DNA, and demonstrate at a molecular level how the tactful interaction of transcriptional factors with even small segments of RNAP can alter promoter specificity. Furthermore, our model provides a rational basis for understanding how a mutation within the β subunit of RNAP (G1249D), which is far removed from AsiA or MotA, impairs σ appropriation.
Crank it up or dial it down: Coordinated multiprocessor frequency and folding control

Dynamic power management features are now an integral part of processor chip and system design. Dynamic voltage and frequency scaling (DVFS), core folding and per-core power gating (PCPG) are power control actuators (or "knobs") that are available in modern multi-core systems. However, figuring out the actuation protocol for such knobs in order to achieve maximum efficiency has so far remained an open research problem. In the context of specific system utilization dynamics, the desirable order of applying these knobs is not easy to determine. For complexity-effective algorithm development, DVFS, core folding and PCPG control methods have evolved in a somewhat decoupled manner. However, as we show in this paper, independent actuation of these techniques can lead to conflicting decisions that jeopardize the system in terms of power-performance efficiency. Therefore, a more robust coordination protocol is necessary in orchestrating the power management functions. Heuristics for achieving such coordinated control are already becoming available in server systems. It remains an open research problem to optimally adjust power and performance management options at runtime for a wide range of time-varying workload applications, environmental conditions, and power constraints. This research paper contributes a novel approach for a systematically architected, robust, multi-knob power management protocol, which we empirically analyze on live server systems. We use a latest generation POWER7+ multi-core system to demonstrate the benefits of our proposed new coordinated power management algorithm (called PAMPA). We report measurement-based analysis to show that PAMPA achieves comparable power-performance efficiencies (relative to a baseline decoupled control system) while achieving conflict-free actuation and robust operation.
Rice-Barnyard Grass Allelopathic Interaction: A Role of Jasmonic Acid and Salicylic Acid

Exogenous jasmonic acid (JA) and salicylic acid (SA) can have an important effect on rice allelopathy. Currently, the role of endogenous JA and SA on rice-barnyard grass interaction is largely unknown. In this study, the levels of JA and SA in tissues and their correlation to rice allelochemicals inducing with barnyard grass are analyzed. Rice allelochemicals production was enhanced by coexistence with barnyard grass and allelochemicals of the allelopathic variety, PI312777 were generally higher than those of non-allelopathic variety, Liaojing9. Furthermore, JA contents of two rice varieties were generally greater in roots than in shoots, and differed clearly with tested times. The SA levels of PI312777 were generally higher than those of Liaojing9 in shoots but opposite trend in roots. The contents of total allelochemicals correlated positively with SA (Pearson correlation, r = 0.91, P < 0.001). These results indicate that as the phytohormones, JA and SA play a provable role in chemical communication between rice and barnyard grass and participate in rice-barnyard grass allelopathic interaction. Future studies should determine the signal molecules in root exudates of barnyard grass and their functions.
Heterogeneity of chromogranin A-derived peptides in bovine gut, pancreas and adrenal medulla.

Chromogranin A is produced in many endocrine cell types, and is widely used as a marker in endocrine-cell pathology and secretory-cell biology. There is some evidence that it may be proteolytically processed to yield the putative pancreatic regulatory peptide, pancreastatin, and, in order to characterize the relevant pathways in gastrointestinal and pancreatic endocrine cells, we have used, in radioimmunoassay, site-directed antibodies to pancreastatin itself (L331) and to a sequence of chromogranin A immediately C-terminal to pancreastatin (L300). The latter antibody revealed three major forms of immunoreactivity of 8 kDa and five peptides of approx. 3 kDa in bovine pancreas and gut extracts. The 8 kDa peptides were characterized as chromogranin A-(248-313)-peptides, i.e. C-terminally extended forms of pancreastatin; two of the 8 kDa variants differed in two positions, confirming a polymorphism predicted from cDNA sequencing. One of the 3 kDa peptides was characterized as chromogranin A-(297-313)-peptide, i.e. the C-terminal heptadecapeptide of the 8 kDa peptide that would be liberated after cleavage to yield pancreastatin. On the basis of chromatographic studies, immunohistochemistry and the stoichiometry of different immunoreactive peptides, three different pathways of chromogranin A processing were identified: in adrenal chromaffin cells chromogranin A existed mainly as the unmodified intact protein, in pancreatic islet and gastric antral endocrine cells pancreastatin and the 3 kDa peptides were major products, but in small intestine and gastric corpus endocrine cells there was little nor no pancreastatin and the 8 kDa cleavage product predominated. There are therefore important differences in the distribution of chromogranin A-derived peptides between quite closely related populations of endocrine cells that are attributable not only to variable post-translational cleavage but also to the expression of different primary sequences. It seems possible that in different cell types chromogranin A-derived peptides might subserve a variety of different functions.
A better constant approximation for minimum 3-connected m-dominating set problem in unit disk graph using Tutte decomposition

Over years, virtual backbone has attracted lots of attentions as a promising approach to deal with the broadcasting storm problem in wireless networks. One popular way to construct a quality virtual backbone is to solve the minimum connected dominating set problem. However, a virtual backbone computed in this way is not resilient against topology change since the induced graph by the connected dominating set is one-vertex-connected. As a result, the minimum k-connected m-dominating set problem is introduced to construct a fault-tolerant virtual backbone. Currently, the best known approximation algorithm for the problem in unit disk graph assumes k ≤ 3 and m ≥ 1 and its performance ratio is 280 when k = m = 3. In this paper, we use a classical result from graph theory, Tutte decomposition, to design a new approximation algorithm for the problem in unit disk graph for k ≤ 3 and m ≥ 3. In particular, the algorithm features with much simpler structure and much smaller performance ratio, e.g. nearly 66 when k = m = 3. We also conduct simulation to evaluate the performance of our algorithm.
Development of fine grained structures using severe plastic deformation

Abstract Severe plastic deformation provides a processing tool for introducing fine grain sizes into polycrystalline materials. This paper describes the principles of equal channel angular pressing (ECAP) in which a material is pressed through a die where two channels form an L shaped configuration. The process of ECAP imposes a severe strain on the sample but there is no concomitant change in the cross-sectional dimensions so that repetitive pressings may be undertaken to achieve very high total strains. Several factors influence the nature of the microstructures attained in ECAP including the processing route by which the sample is rotated between consecutive pressings, the angle subtended by the two channels within the die, and the speed and temperature associated with the pressing. These various factors are described for a series of experiments conducted on samples of pure aluminium.
Comparison of fuzzy connectedness and graph cut segmentation algorithms

The goal of this paper is a theoretical and experimental comparison of two popular image segmentation algorithms: fuzzy connectedness (FC) and graph cut (GC). On the theoretical side, our emphasis will be on describing a common framework in which both of these methods can be expressed. We will give a full analysis of the framework and describe precisely a place which each of the two methods occupies in it. Within the same framework, other region based segmentation methods, like watershed, can also be expressed. We will also discuss in detail the relationship between FC segmentations obtained via image forest transform (IFT) algorithms, as opposed to FC segmentations obtained by other standard versions of FC algorithms. We also present an experimental comparison of the performance of FC and GC algorithms. This concentrates on comparing the actual (as opposed to provable worst scenario) algorithms' running time, as well as influence of the choice of the seeds on the output.
Antitumor effect and potentiation of cytotoxic drugs activity in human cancer cells by ZD-1839 (Iressa), an epidermal growth factor receptor-selective tyrosine kinase inhibitor.

Transforming growth factor alpha (TGF-alpha) is an autocrine growth factor for human cancer. Overexpression of TGF-alpha and its specific receptor, the epidermal growth factor receptor (EGFR), is associated with aggressive disease and poor prognosis. The EGFR has been proposed as a target for anticancer therapy. Compounds that block ligand-induced EGFR activation have been developed. ZD-1839 (Iressa) is a p.o. -active, quinazoline derivative that selectively inhibits the EGFR tyrosine kinase and is under clinical development in cancer patients. The antiproliferative activity of ZD-1839 alone or in combination with cytotoxic drugs differing in mechanism(s) of action, such as cisplatin, carboplatin, oxaliplatin, paclitaxel, docetaxel, doxorubicin, etoposide, topotecan, and raltitrexed, was evaluated in human ovarian (OVCAR-3), breast (ZR-75-1, MCF-10A ras), and colon cancer (GEO) cells that coexpress EGFR and TGF-alpha. ZD-1839 inhibited colony formation in soft agar in a dose-dependent manner in all cancer cell lines. The antiproliferative effect was mainly cytostatic. However, treatment with higher doses resulted in a 2-4-fold increase in apoptosis. A dose-dependent supra-additive increase in growth inhibition was observed when cancer cells were treated with each cytotoxic drug and ZD-1839. The combined treatment markedly enhanced apoptotic cell death induced by single-agent treatment. ZD-1839 treatment of nude mice bearing established human GEO colon cancer xenografts revealed a reversible dose-dependent inhibition of tumor growth because GEO tumors resumed the growth rate of controls at the end of the treatment. In contrast, the combined treatment with a cytotoxic agent, such as topotecan, raltitrexed, or paclitaxel, and ZD-1839 produced tumor growth arrest in all mice. Tumors grew slowly for approximately 4-8 weeks after the end of treatment, when they finally resumed a growth rate similar to controls. GEO tumors reached a size not compatible with normal life in all control mice within 4-6 weeks and in all single agent-treated mice within 6-8 weeks after GEO cell injection. In contrast, 50% of mice treated with ZD-1839 plus topotecan, raltitrexed, or paclitaxel were still alive 10, 12, and 15 weeks after cancer cell injection, respectively. These results demonstrate the antitumor effect of this EGFR-selective tyrosine kinase inhibitor and provide a rationale for its clinical evaluation in combination with cytotoxic drugs.
Spantide I decreases type I cytokines, enhances IL-10, and reduces corneal perforation in susceptible mice after Pseudomonas aeruginosa infection.

PURPOSE To determine the effects of blocking substance P (SP) interactions with its major receptor (NK1-R) using the antagonist spantide I in susceptible mice infected with Pseudomonas aeruginosa. METHODS Immunohistochemistry and enzyme immunosorbent assay (EIA) tested levels of SP in the cornea of B6 and BALB/c mice. B6 mice were treated with spantide, and after infection, slit lamp examination; clinical score; bacterial counts; and myeloperoxidase (MPO), RT-PCR, ELISA, and polymorphonuclear (PMN) cell chemotaxis assays were performed. RESULTS SP corneal levels were significantly elevated constitutively and after infection in the B6 more than in BALB/c mice. Spantide treatment of B6 mice significantly decreased the number of perforated corneas, bacterial counts, and PMNs. mRNA levels for type I cytokines (e.g., IFN-gamma) as well as MIP-2, IL-6, TNF-alpha, and IL-1beta (mRNA and protein) also were significantly reduced after spantide treatment. The type II cytokine IL-10 (mRNA and protein) was elevated, whereas TGF-beta mRNA levels were unchanged after spantide treatment. PMN chemotaxis was induced by SP and other neuropeptides in vitro, but was not affected by spantide I. mRNA for neurokinin-1-receptor-1 (NK-1R) was detected in the normal and infected corneas and on macrophages (Mphis), but not on PMNs (unstimulated or stimulated with endotoxin [LPS]). Spantide treatment of Mphis reduced IL-1beta after LPS+SP treatment but not after either alone. CONCLUSIONS The SP antagonist Spantide provides a novel approach to reduce type 1 and enhance the type 2 cytokine IL-10 in the infected cornea of B6 mice, leading to a significant reduction in corneal perforation and improved disease outcome.
Ensuring the data integrity in cloud data storage

Along with variant advantages, the cloud storage gained great attention from both industry and academics since 2007. However, it also brings new challenges in creating a secure and reliable data storage and access facility over insecure or unreliable service providers. The integrity of data stored in the cloud is one of the challenges to be addressed before the novel storage model is applied widely. In this paper, we propose a remote data integrity checking protocol based on HLAs and RSA signature with the support public verifiability. The support of public verifiability makes the protocol very flexible, since the user can commission the data possession to check the TPA.