Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient construction of multibit tries for IP lookup

Srinivasan and Varghese (1999) have proposed the use of multibit tries to represent routing tables used for Internet (IP) address lookups. They propose dynamic programming algorithms to determine the strides of optimal multibit fixed-stride and variable-stride tries. We improve on these algorithms by providing alternative dynamic programming formulations for both fixed-and variable-stride tries. While the asymptotic complexities of our algorithms are the same as those for the corresponding algorithms of Srinivasan and Varghese, experiments using real IPv4 routing table data indicate that our algorithms run considerably faster. Our fixed-stride trie algorithm is two to four times faster on a SUN workstation and 1.5 to three times faster on a Pentium IV PC. On a SUN workstation, our variable-stride trie algorithm is between two and 17 times faster than the corresponding algorithm of Srinivasan and Varghese; on a Pentium IV PC, our algorithm is between three and 47 times faster. An added feature of our variable-stride trie algorithm is the ability to insert and delete prefixes taking a fraction of the time needed to construct an optimal variable-stride trie "from scratch. "
New Strategies in Ewing Sarcoma: Lost in Translation?

Ewing sarcoma is the second most common pediatric malignant bone tumor. Aggressive multimodality therapy has led to an improvement in outcomes, particularly in patients with localized disease. However, therapy-related toxicities are not trivial, and the prognosis for patients with relapsed and/or metastatic disease continues to be poor. In this article, we outline some of the promising therapies that have the potential to change the Ewing sarcoma therapeutic paradigm in the not-too-distant future: insulin-like growth factor receptor inhibitors, targeting of the fusion protein, epigenetic manipulation, PARP inhibitors, and immunotherapy. Clin Cancer Res; 20(12); 3050–6. ©2014 AACR.
A decentralized multiple relay selection scheme for cooperative relay networks with distributed space-time coding

In this paper, we develop a novel relay selection scheme for amplify-and-forward relay network with distributed space time coding. Using the criterion of maximizing the received signal-to-noise ratio (SNR), the multiple relay selection problem is presented. The optimal solution of this problem can be obtained by exhaustive search, which has computational complexity growing with the number of relays and leads to a centralized implementation. To circumvent this problem, an opportunistic relaying scheme is introduced and the associated selection function is derived, which is based on the approximate of the received SNR. This selection function can be computed based on the local channel information and, hence can be implemented in decentralized strategy. Simulation results show that the proposed scheme outperforms the existing opportunistic schemes. Moreover, the BER performance of the proposed scheme approaches to that of the optimal scheme with a considerably lower complexity.
Integrative Analysis for Lung Adenocarcinoma Predicts Morphological Features Associated with Genetic Variations

Lung cancer is one of the most deadly cancers and lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. However, LUAD is highly heterogeneous due to genetic difference as well as phenotypic differences such as cellular and tissue morphology. In this paper, we systematically examine the relationships between histological features and gene transcription. Specifically, we calculated 283 morphological features from histology images for 201 LUAD patients from TCGA project and identified the morphological feature with strong correlation with patient outcome. We then modeled the morphology feature using multiple co-expressed gene clusters using Lasso-regression. Many of the gene clusters are highly associated with genetic variations, specifically DNA copy number variations, implying that genetic variations play important roles in the development cancer morphology. As far as we know, our finding is the first to directly link the genetic variations and functional genomics to LUAD histology. These observations will lead to new insight on lung cancer development and potential new integrative biomarkers for prediction patient prognosis and response to treatments.
Salvianolic acid B protects human endothelial cells from oxidative stress damage: a possible protective role of glucose-regulated protein 78 induction.

AIMS The purposes of the present study were to both evaluate the protective effects of Salvianolic acid B (Sal B) and to determine the possible molecular mechanisms by which Sal B protects endothelial cells from damage caused by oxidative stress. METHODS AND RESULTS Pretreatment with Sal B markedly attenuated H(2)O(2)-induced viability loss, lactate dehydrogenase leakage and apoptosis in human umbilical vein endothelial cells (HUVECs). The mechanism of Sal B protection was studied using two-dimensional gel electrophoresis coupled with hybrid quadrupole time-of-flight mass spectrometry. Database searching implicated that glucose-regulated protein 78 (GRP78), a central regulator for endoplasmic reticulum (ER) stress, was up-regulated in Sal B-exposed HUVECs. GRP78 expression regulation was confirmed by western blot and RT-PCR (reverse transcription-polymerase chain reaction) analyses. Additionally, GRP94, which shares significant sequence homology with GRP78, was also up-regulated in Sal B-treated cells. Sal B caused pancreatic ER kinase (PKR)-like ER kinase (PERK) activation followed by the phosphorylation of eukaryotic translation initiation factor 2 alpha (eIF2 alpha) and the expression of activating transcription factor 4 (ATF4). Knockdown of endogenous ATF4 expression partially repressed Sal B-induced GRP78 induction. Further investigation showed that ATF6 was also activated by Sal B. Knockdown of GRP78 by siRNA significantly reduced the protective effects of Sal B. CONCLUSION The results suggest that Sal B induces the expression of GRP78 by activating ATF6 and the PERK-eIF2 alpha-ATF4 pathway. Furthermore, up-regulation of GRP78 by Sal B may play an important role in protecting human endothelial cells from oxidative stress-induced cellular damage.
Human Papilloma Virus (HPV) and Genital Cancer

Epidemiological relationships were established more than 100 years ago between precursory lesions of cervical cancer and risky sexual behaviour. For various decades medicine has, unsuccessfully, tried to find the relationships between the agents responsible for sexually transmitted infections with this neoplasia. Thus, epidemiological studies supported by liquid cytological and molecular techniques have confirmed the role of certain strains of human papilloma virus (HPV) in the development of cervical, vulvar and vaginal cancer. It has been shown that, in an international series using high PCR, 90.7% of cervical-uterine carcinomas have DNA from HPV, and, 100% of the cases have been confirmed with exhaustive histological examinations, and in the majority of the intraepithelial lesions of the lower genital tract. Persistent infection with high-risk HPV-types is associated with genital cancers. Smoking and HIV infection have consistently been associated with longer duration of HPV infection and risk for genital cancer. We present the most important clinical manifestations of HPV infection within the spectrum of epithelial anomalies, considered as precursors or pre-colonizers of genital cancer and an update of their possible treatments.
Progress in Neonatal Neurology with a Focus on Neuroimaging in the Preterm Infant

Abstract There have been tremendous changes in the methods used to evaluate brain injury in the preterm infant in the past 30 years. In particular, major improvements have been made in how we use neuroimaging techniques and now magnetic resonance imaging (MRI) is used more often and considered complimentary to routine and sequential cranial ultrasound. The focus has shifted from severe lesions such as large intraventricular and parenchymal hemorrhages and cystic periventricular leukomalacia to assessing and understanding the etiology of more subtle noncystic white matter injury, punctate hemorrhage, and cerebellar lesions. The more severe lesions that dominated the early period of preterm neonatal brain imaging occur less frequently but are still associated with major disabilities, such as, cerebral palsy, while subtle white matter injury and cerebellar lesions are more often associated with cognitive and behavioral problems, which have become the most prevalent issues among the survivors of extremely preterm birth.
Notes on Ramapithecus, the earliest known hominid, and Dryopithecus.

Recent paleontological analysis of the Higher Primate subfamily Dryopithecinae shows that fossils in this group can be referred to two genera, Ramapithecus and Dryopithecus. Ramapithecus is known from India and East Africa in Late Miocene or Early Pliocene time (about 14 m. years ago). The remains of Ramapithecus resemble closely the equivalent parts of the later Hominidae and contrast with those of the Pongidae. It is concluded that Ramapithecus is the earliest known hominid, some 5 or 6 times older than the oldest Pleistocene hominids. Dryopithecus is a pongid and contains as subgenera (Dryopithecus), (Proconsul), and (Sivapithecus). Probably part of (Proconsul) is ancestral to the chimpanzee and part to the gorilla, while part of (Sivapithecus) is ancestral to the orang-utan.
Mobile IP: enabling user mobility

This review paper gives a brief insight about Mobile IP, its features and entities constituting Mobile IP environment. The paper explores the working and routing mechanism of Mobile IP with a deep insight about triangle routing in Mobile IP Version 4(MIPv4) and route optimization in Mobile IP Version 6(MIPv6). This paper discusses several security issues regarding Mobile IP implementation. This paper also highlights route optimization problems and focuses on the solution of those problems.
A novel endothelial-specific membrane protein is a marker of cell-cell contacts

mAbs were raised in mice against cultured human endothelial cells (EC) and screened by indirect immunofluorescence for their ability to stain intercellular contacts. One mAb denoted 7B4 was identified which, out of many cultured cell types, specifically decorated cultured human EC. The antigen recognized by mAb 7B4 is bound at the appositional surfaces of cultured EC only as they become confluent and is stably expressed at intercellular boundaries of confluent monolayers. EC recognition specificity was maintained when the antibody was assayed by immuno- histochemistry in tissue sections of many normal and malignant tissues and in blood vessels of different size and type. The antigen recognized by 7B4 was enriched at EC intercellular boundaries similarly in vitro and in situ. In vitro, addition of mAb 7B4 to confluent EC increased permeation of macromolecules across monolayers even without any obvious changes of cell morphology. In addition, when EC permeability was increased by agents such as thrombin, elastase, and TNF/gamma IFN, its distribution pattern at intercellular contact rims was severely altered. mAb 7B4 immunoprecipitated a major protein of 140 kD from metabolically and surface-labeled cultured EC extracts which appeared to be an integral membrane glycoprotein. On the basis of its distribution in cultured cells and in tissues in situ, 7B4 antigen is distinct from other described EC proteins enriched at intercellular contacts. NH2-terminal sequencing of the antigen, immunopurified from human placenta, and sequencing of peptides from tryptic peptide maps revealed identity to the cDNA deduced sequence of a recently identified new member of the cadherin family (Suzuki, S., K. Sano, and H. Tanihara. 1991. Cell Regul. 2:261-270.) These data indicate that 7B4 antigen is an endothelial-specific cadherin that plays a role in the organization of lateral endothelial junctions and in the control of permeability properties of vascular endothelium.
Contributions of host and symbiont pigments to the coloration of reef corals

For a variety of coral species, we have studied the molecular origin of their coloration to assess the contributions of host and symbiont pigments. For the corals Catalaphyllia jardinei and an orange‐emitting color morph of Lobophyllia hemprichii, the pigments belong to a particular class of green fluorescent protein‐like proteins that change their color from green to red upon irradiation with ∼400 nm light. The optical absorption and emission properties of these proteins were characterized in detail. Their spectra were found to be similar to those of phycoerythrin from cyanobacterial symbionts. To unambiguously determine the molecular origin of the coloration, we performed immunochemical studies using double diffusion in gel analysis on tissue extracts, including also a third coral species, Montastrea cavernosa, which allowed us to attribute the red fluorescent coloration to green‐to‐red photoconvertible fluorescent proteins. The red fluorescent proteins are localized mainly in the ectodermal tissue and contribute up to 7.0% of the total soluble cellular proteins in these species. Distinct spatial distributions of green and cyan fluorescent proteins were observed for the tissues of M. cavernosa. This observation may suggest that differently colored green fluorescent protein‐like proteins have different, specific functions. In addition to green fluorescent protein‐like proteins, the pigments of zooxanthellae have a strong effect on the visual appearance of the latter species.
Genome-Wide Association Data Reveal a Global Map of Genetic Interactions among Protein Complexes

This work demonstrates how gene association studies can be analyzed to map a global landscape of genetic interactions among protein complexes and pathways. Despite the immense potential of gene association studies, they have been challenging to analyze because most traits are complex, involving the combined effect of mutations at many different genes. Due to lack of statistical power, only the strongest single markers are typically identified. Here, we present an integrative approach that greatly increases power through marker clustering and projection of marker interactions within and across protein complexes. Applied to a recent gene association study in yeast, this approach identifies 2,023 genetic interactions which map to 208 functional interactions among protein complexes. We show that such interactions are analogous to interactions derived through reverse genetic screens and that they provide coverage in areas not yet tested by reverse genetic analysis. This work has the potential to transform gene association studies, by elevating the analysis from the level of individual markers to global maps of genetic interactions. As proof of principle, we use synthetic genetic screens to confirm numerous novel genetic interactions for the INO80 chromatin remodeling complex.
Compression-based Similarity Measures in Symbolic, Polyphonic Music

We present a novel compression-based method for measuring similarity between sequences of symbolic, polyphonic music. The method is based on mapping the values of binary chromagrams extracted from MIDI files to tonal centroids, then quantizing the tonal centroid representation values to sequences, and finally measuring the similarity between the quantized sequences using Normalized Compression Distance (NCD). The method is comprehensively evaluated with a test set of classical music variations, and the highest achieved precision and recall values suggest that the proposed method can be applied for similarity measuring. Also, we analyze the performance of the method and discuss what should be taken into consideration when applying the method for measurement tasks.
Receptor‐Mediated Self‐Assembly of Multi‐Component Magnetic Nanowires

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Efficient content-based retrieval of humans from video databases

An efficient algorithm for humans' retrieval from large video databases is presented in this paper. Such an extraction is very useful for a variety of applications, including video surveillance for security purposes and systems of speaker identification. A human face and body detector is first proposed, based on a simple probabilistic model, to approximately estimate human face and body regions. The adopted approach significantly reduces the required computational cost and simultaneously exploits information existing in MPEG-coded video data. A segmentation fusion scheme is then applied to improve segmentation accuracy. Based on the created segmentation map, a graph is then constructed, which represents the spatial relationship of the extracted segments. Color, texture, motion and shape characteristics are included as additional features to the nodes of the graph. To enhance the flexibility of the proposed system, each node is further decomposed into other graphs (sub-graphs) resulting in a pyramidal graph representation of the visual content.
Evaluation of observers' sensitivity to lens distortion discrepancies in stereoscopic moving pictures

One potential factor of distorted stereoscopic perception of a 3D movie may be slightly different lens aberrations between the two lenses of the stereoscopic camera. We considered typical lens distortions discrepancies of several stereoscopic camera types ranging from cine to small action cameras. The determination of a detection threshold of different groups of observers with respect to gender, stereoscopic ability, media affinity, etc. was a main research topic. In one of our subjective assessments we used a gaze tracking system by which the eye movement of the observers could be roughly determined. We found out that image texture and content-driven gaze sequence had a strong impact on observer's detection of stereoscopic aberrations. Minimal lens distortion discrepancy was already detected by at least 15.4% of the participants. The number of irritation statements increased with the magnitude of discrepancy. Observers showed highest sensitivity in still images or smooth camera travelling presenting many simple geometric objects. Still, up to 29% of the participants seemed to be quite immune against lens distortion discrepancies in spite of good stereo acuity as proven in Randot Stereo Vision test.
Modeling and automated containment of worms

Self-propagating codes, called worms, such as Code Red, Nimda, and Slammer, have drawn significant attention due to their enormous adverse impact on the Internet. There is a great interest in the research community in modeling the spread of worms and in providing adequate defense mechanisms against them. In this paper, we present a (stochastic) branching process model for characterizing the propagation of Internet worms. This model leads to the development of an automatic worm containment strategy that prevents the spread of worms beyond its early stages. Specifically, using the branching process model, we are able to (1) provide a precise condition that determines whether the worm will eventually die out and (2) provide the probability that the total number of hosts that the worm infects will be below a certain level. We use these insights to develop a simple automatic worm containment scheme, which is demonstrated, through simulations and real trace data, to be both effective and non-intrusive.
Envelope tracking power supply for volume-sensitive low-power applications based on a resonant switched-capacitor converter

This paper introduces a new envelope tracking power supply to enhance the performance and reduce the overall volume of transmitter modules. The realization is based on a gyrator resonant switched-capacitor converter (GRSCC) that acts as a controlled bi-directional current source with a virtually instantaneous response to create the desired envelope. A quasi-non-casual control method is further applied to closely track high-rate signals without further increasing the switching frequency. The resultant dynamic performance for a given envelope reference signal is significantly improved, providing envelope supply voltage without clipping distortion. Design example and simulations are detailed, and the operation of envelope tracker is verified on a 150mW prototype switched at 2.3MHz, able to track a 1MHz envelope with less than half the losses of a linear regulator.
Hamiltonian Formulation of Quantum Error Correction and Correlated Noise

We analyze the long time behavior of a quantum computer running a quantum error correction (QEC) code in the presence of a correlated environment. Starting from a Hamiltonian formulation of realistic noise models, and assuming that QEC is indeed possible, we find formal expre ssions for the probability of a given syndrome history and the associated residual decoherence encoded in the reduced density matrix. Systems with non-zero gate times (“long gates”) are included in our analysis by using an upper bound on the noise. In order to introduce the local error probability for a qubit, we assume that propagation of signals through the environment is slower than the QEC period (hypercube assumption). This allows an explicit calculation in the case of a generalized spin-boson model and a quantum frustration model. The key result is a dimensional criterion: If the correlations decay sufficiently fast, the system evolves toward a stochas tic error model for which the threshold theorem of fault-tolerant quantum computation has been proven. On the other hand, if the correlations decay slowly, the traditional proof of this threshold theorem does not hold. T his dimensional criterion bears many similarities to criteria that occur in the theory of quantum phase transitio ns.