Miracle-dz/UniFAR-FTUs huggingface dataset:
FMSA: FPGA-Accelerated ClustalW-Based Multiple Sequence Alignment through Pipelined Prefiltering

Multiple Sequence Alignment (MSA) is perhaps second only to sequence alignment in overall importance in Bioinformatics, being critical, e.g., in determining the structure and function of molecules from putative families of sequences. But while pair wise sequence alignment has been the subject of scores of FPGA acceleration studies, MSA only a few. The most important of these accelerate Clustal-W, the most commonly used MSA code, by either implementing the first of three phases (over 90% of the run time) with Dynamic Programming (DP) methods, or by accelerating the third phase which consumes most of the remaining time. We use a new approach: we apply prefiltering of the kind commonly used in BLAST to perform the initial all-pairs alignments. This results in a speedup of from 80× to 190× over the CPU code (8 cores) and speedup of from 2.5× to 8× over DP/FPGA- and GPU-based methods. When combined with a recently published method for phase 3, and using the original software for phase 2, the end-to-end speedup is at least 50× over an 8-core implementation of the original code. The quality is comparable to the original according to a commonly used benchmark suite evaluated with respect to multiple distance metrics.
Preliminary Study on Ductile Fracture of Imperfect Lattice Materials

The ductile fracture behavior of two-dimensional imperfect lattice material under dynamic stretching is studied by finite element analyses (FEA). Three isotopic lattice materials, including the regular hexagonal honeycomb, the Kagome lattice and the regular triangular lattice, are taken into account, which are made of an elastic/visco-plastic metal material. Two typical imperfections (vacancy defect and rigid inclusion) are introduced separately. The numerical results reveal novel deformation modes and crack growth patterns in the ductile fracture of lattice material. Various crack growth patterns as defined according to their profiles, such as “X”-type, “Butterfly”-type, “Petal”-type. Crack propagation could induce severe material softening and plastic dissipation of the lattices. Subsequently, the effects of the strain rate, relative density, microstructure topology, and defect type on the crack growth pattern, the associated macroscopic material softening and the knock-down of total plastic dissipation are investigated.
Dynamic routing for network throughput maximization in software-defined networks

Software-Defined Networking (SDN) has emerged as the paradigm of the next-generation networking through separating the data control plane from the data plane. The forwarding routing table at each of its switch nodes is usually implemented by expensive and power-hungry Ternary Content Addressable Memory (TCAM) that only has limited number of entries, and the bandwidth at each of its links is bounded too. Under this new network architecture, providing a quality service to users by admitting user requests to meet their resource demands is challenging, and very little attention has ever been paid in this regard. In this paper, we will study online unicast and multicast request admissions in SDNs with the aim to maximize the network throughput under both critical network resources and user bandwidth demand constraints, for which we first propose a novel model to characterize the usage costs of node and link resources. We then devise efficient online algorithms for unicast and multicast requests. We also analyze the competitive ratios of the proposed online algorithms, which are O(log n) and O(Kϵ log n) for unicasting and multicasting, respectively, where n is the network size, K is the maximum number of members in a multicast request, and ϵ is a constant with 0 <; e ≤ 1. We finally evaluate the proposed algorithms empirically through simulations. The simulation results demonstrate that the proposed algorithms are very promising.
Self-Assembled Masks for the Transfer of Nanometer-Scale Patterns into Surfaces: Characterization by AFM and LFM

A new methodology has been used to create an extensive array of nanometer-sized features. The Ar+ milling of Si/SiOx and gold surfaces covered with a diblock copolymer mask with an intrinsic topological nanopattern yields transfer of the nanopattern. Mask removal was tracked using XPS, and the final arrays were characterized by AFM and LFM. Friction contrast observed throughout the transferred pattern is associated with a surface water layer.
Charge moment change and lightning‐driven electric fields associated with negative sprites and halos

[1] Sprites are structured high altitude optical emissions produced by lightning-driven electric fields. Both strong positive and negative cloud to ground flashes (CGs) are capable of initiating sprites. However, reported sprites are almost exclusively produced by +CGs. The very limited number of negative polarity sprites makes it difficult to reveal their morphologies and mechanisms. Since 2008, we have operated low light cameras at 5 locations in the United States to detect lightning-driven transient luminous events (TLEs). At Duke University, two pairs of magnetic sensors simultaneously record lightning-radiated magnetic fields. During 4 years of observations, the low light cameras collectively captured 1651 sprite events. Among them, 6 were produced by −CG lightning, which was confirmed by both the National Lightning Detection Network (NLDN) and magnetic field measurements. All of these negative sprites show similar features in their morphology, lightning source current, and lightning-driven ambient electric fields. They all initiate within a few ms from their parent lightning discharges and always are accompanied by sprite halos. Compared to positive sprites, the downward streamers in negative sprites terminate at higher altitudes, about 55–60 km. The extracted source current of their parent lightning discharges is very impulsive and produces at least 450 C km charge moment change in 0.5 ms or less. Unlike most +CG strokes, essentially no continuing current follows these −CGs. Thus the uniformity of negative sprite morphology appears to reflect the uniformity of the characteristics of high charge transfer negative strokes. Numerical simulation shows these impulsive source currents produce very high (>2 Ek, where Ek is the local air breakdown field) but short-lived electric fields at halo altitudes between 70 km and 90 km. At streamer termination altitudes, the inferred background electric field is 0.2–0.3 Ek, which is close to but below the critical field (0.4 Ek) for negative streamer propagation. The simulations also show that the timescale of the lightning source current has a significant impact on the high altitude electric fields and thus the sprite initiation and morphology. With the same amount of charge transfer, a more impulsive current source produces a higher electric field of shorter duration at halo and sprite altitudes. The short timescales may explain why a larger threshold of total charge moment change is required to initiate negative sprites than short-delayed positive sprites, whose parent lightning source current is usually less impulsive.
Duplication of a Truncated Paralog of the Family B DNA Polymerase Gene Aa-polB in the Agrocybe aegerita Mitochondrial Genome

ABSTRACT The Agrocybe aegerita mitochondrial genome contains a truncated family B DNA polymerase gene (Aa-polB P1) whose nucleotide sequence is 86% identical to the previously described and potentially functional Aa-polB gene. A tRNAMetgene occurs at the 3′ end of the Aa-polB P1 gene. TheAa-polB P1 gene could result from reverse transcription of an Aa-polB mRNA primed by a tRNAMet followed by the integration of the cDNA after recombination at the mitochondrial tRNA locus. Two naturally occurring alleles of Aa-polB P1carry one or two copies of the disrupted sequence. In strains with two copies of Aa-polB P1, these copies are inverted relative to one another and separated by a short sequence carrying the tRNAMet gene. Both A. aegerita mitochondrial family B DNA polymerases were found to be related to other family B DNA polymerases (36 to 53% amino acid similarity), including the three enzymes of the archaebacterium Sulfolobus solfataricus. If mitochondria originated from a fusion between aClostridium-like eubacterium and aSulfolobus-like archaebacterium, then the A. aegerita family B DNA polymerase genes could be remnants of the archaebacterial genes.
Learning to Recognize Promoter Sequences in E. coli by Modeling Uncertainty in the Training Data

Automatic recognition of promoter sequences is an important open problem in molecular biology. Unfortunately, the usual machine learning version of this problem is critically flawed. In particular, the dataset available from the Irvine repository was drawn from a compilation of promoter sequences that were pre-processed to conform to the biologists' related notion of the consensus sequence, a first-order approximation with a number of shortcomings that are well-known in molecular biology. Although concept descriptions learned from the Irvine data may represent the consensus sequence, they do not represent promoters. More generally, imperfections in preprocessed data and statistical variations in the locations of biologically meaningful features within the raw data invalidate standard attribute-based approaches. I suggest a dataset, a concept-description language, and a model of uncertainty in the promoter data that are all biologically justified, then address the learning problem with incremental probabilistic evidence combination. This knowledge-based approach yields a more accurate and more credible solution than other more conventional machine learning systems.
TDM: Time-Driven Mesh Overlay Network for Peer-to-Peer Video-on-Demand Services

In this paper, we propose a new Time-Driven Mesh (TDM) overlay network for peer-to-peer video-on-demand systems. In our TDM, all of the peers construct a mesh network connected among them in chronological order of their playback starting times. In order to efficiently search multiple streaming suppliers, we manage the playback starting time and the network location information for all of the peers using a distributed hash table. Our TDM provides both time and space localities while locating suppliers, and the failed peers can be quickly replaced with other suitable peers. As a result, we can construct a bandwidth efficient and robust overlay network for P2P VoD systems. In simulation experiments, we show that our scheme achieves lower server stress and better playback continuity under peer random joins and leaves for providing efficient interactive VoD streaming in P2P environment.
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae. org/drap.
Global Conservative Solutions of the Camassa–Holm Equation—A Lagrangian Point of View

We show that the Camassa–Holm equation ut − uxxt + 3uux − 2uxuxx − uuxxx = 0 possesses a global continuous semigroup of weak conservative solutions for initial data u|t=0 in H1. The result is obtained by introducing a coordinate transformation into Lagrangian coordinates. To characterize conservative solutions it is necessary to include the energy density given by the positive Radon measure μ with . The total energy is preserved by the solution.
When ethnic humor goes digital

This article explores new forms of ethnic humor as emergent in a salient arena of contemporary culture: our electronic mailboxes. We argue that two processes underpin the manifestations of ethnic humor as it ‘goes online’: the global turn and the turn to genre plurality. We examine the implications of these processes through (1) content analysis of 1000 Israeli humorous ‘forwards’ and (2) a grounded analysis of 130 texts representing ethnic groups with varying degrees of proximity to Israeli culture. Regarding the global turn, we found that non-local ethnicities are ‘imported’ to the local symbolic sphere via new forms of humor. Regarding the turn to genre plurality, results indicate that while old forms of ethnic humor typically include explicit stereotyping, new forms introduce a wider variety of stances towards ethnic stereotypes, ranging from their reproduction in visual language to a polysemic stance, and finally to their neutralization.
Butyrate Enhances Disease Resistance of Chickens by Inducing Antimicrobial Host Defense Peptide Gene Expression

Host defense peptides (HDPs) constitute a large group of natural broad-spectrum antimicrobials and an important first line of immunity in virtually all forms of life. Specific augmentation of synthesis of endogenous HDPs may represent a promising antibiotic-alternative approach to disease control. In this study, we tested the hypothesis that exogenous administration of butyrate, a major type of short-chain fatty acids derived from bacterial fermentation of undigested dietary fiber, is capable of inducing HDPs and enhancing disease resistance in chickens. We have found that butyrate is a potent inducer of several, but not all, chicken HDPs in HD11 macrophages as well as in primary monocytes, bone marrow cells, and jejuna and cecal explants. In addition, butyrate treatment enhanced the antibacterial activity of chicken monocytes against Salmonella enteritidis, with a minimum impact on inflammatory cytokine production, phagocytosis, and oxidative burst capacities of the cells. Furthermore, feed supplementation with 0.1% butyrate led to a significant increase in HDP gene expression in the intestinal tract of chickens. More importantly, such a feeding strategy resulted in a nearly 10-fold reduction in the bacterial titer in the cecum following experimental infections with S. enteritidis. Collectively, the results indicated that butyrate-induced synthesis of endogenous HDPs is a phylogenetically conserved mechanism of innate host defense shared by mammals and aves, and that dietary supplementation of butyrate has potential for further development as a convenient antibiotic-alternative strategy to enhance host innate immunity and disease resistance.
Map Building in Indoor Environment for Service Robot Based on Laser Sensor

Map building is an essential problem in the field of mobile robot research. The accurate environmental map provides the important safeguard for the robot autonomous navigation and localization. In this paper, the two-dimensional environment map based on geometric features information was built by laser data when service robot worked in indoor structured environment. However, this article focused on analyzing the method of line fitting in the process of building local map and the method of global map updating. The experiment indicated that this method has the high accuracy and effectiveness, also reduces error caused by the uncertain information in the process of map building, which makes the indoor environment map update in real time.
Modality planning for preventing tunnel vision in crisis management

Crisis management is a time-critical task with high uncertainty and high risk. Stress and cognitive overload often result in a set of bias in crisis manager’s situation understanding and information confirming processes, known as “tunnel vision”. Aiming at preventing tunnel vision, we propose an information assistant system which attempts to reduce the information quantity, improve the information quality, and prevent cognitive overload of the user. The main focus of this paper is to present the design proposal of the modality planning module. It is one of the modules which play a role in the prevention of tunnel vision. The function of this module is to determine the optimum utilization of the available modalities, in order to convey information effectively and reduce the cognitive load of theperceivers. The modality planning strategies also adapt to the user’s preferences and cognitive state.
A Comparative Study of Selected Classification Accuracy in User Profiling

In recent years the used of personalization in service provisioning applications has been very popular. However, effective personalization cannot be achieved without accurate user profiles. A number of classification algorithms have been used to classify user related information to create accurate user profiles. In this study four different classification algorithms which are; naive Bayesian (NB), Bayesian Networks (BN), lazy learning of Bayesian rules (LBR) and instance-based learner (IB1) are compared using a set of user profile data. According to our simulation results NB and IB1 classifiers have the highest classification accuracy with the lowest error rate.
An efficient compiler technique for code size reduction using reduced bit-width ISAs

For many embedded applications, program code size is a critical design factor. One promising approach for reducing code size is to employ a "dual instruction set", where processor architectures support a normal (usually 32 bit) Instruction Set, and a narrow, space-efficient (usually 16 bit) Instruction Set with a limited set of opcodes and access to a limited set of registers. This future, however, requires compilers that can reduce code size by compiling for both Instruction Sets. Existing compiler techniques operate at the function-level granularity and are unable to make the trade-off between increased register pressure (resulting in more spills) and decreased code size. We present a profitability based compiler heuristic that operates at the instruction-level granularity and is able to effectively take advantage: of both Instruction Sets. We also demonstrate improved code size reduction, for the MIPS 32/16 bit ISA, using our technique. Our approach more than doubles the code size reduction achieved by existing compilers.
An Association Rule Miner with Semi-Autonomic Threshold Setting ∗

Association rule mining is well-known to depend heavily on a support threshold parameter, and on one or more thresholds for intensity of implication; among these measures, confidence is most often used and, sometimes, related alternatives such as lift, leverage, improvement, or all-confidence are employed, either separately or jointly with confidence. We describe here an association mining system which requires the user to set a single parameter, of quite clear intuitive semantics, and then uses the given value to compute autonomously the corresponding thresholds for support, confidence, blocking factor (which is a slight reformulation of improvement) and confidence width (which is a complementary, recently introduced measure of novelty for association rules). We argue that the availability of one parameter is desirable; suggest a number of desiderata for the conceptual basis of such a parameter, and explain how our implementation meets them and is able to find meaningful association rules with lesser needs of domain intuition from the user.
3D Models of Epithelial-Mesenchymal Transition in Breast Cancer Metastasis

Despite advancements in therapies developed for the treatment of cancer, patient prognosis and mortality rates have improved minimally, and metastasis remains the primary cause of cancer mortality worldwide. An underlying mechanism promoting metastasis in many types of cancer is epithelial-mesenchymal transition (EMT). Here the authors report a novel 3D model of EMT and metastatic breast cancer suitable for high-throughput screening (HTS) drug discovery. The primary assay incorporates the expression of the prognostic biomarker vimentin, as a luciferase reporter of EMT, in basil-like/triple-negative MDA-MB-231 breast carcinoma spheroids. Using this model, the authors developed a number of known antitumor agents as control modulators of EMT. U0126, PKC412, PF2341066, dasatinib, and axitinib downregulated vimentin expression by 70% to 90% as compared to untreated spheroids. Counterassays were developed to measure spheroid viability and the invasive potential of MDA-MB-231 spheroids after small-molecule treatment and used to confirm hits from primary screening. Finally, the authors conducted a pilot screen to validate this model for HTS using a purified library of marine secondary metabolites. From 230 compounds screened, they obtained a Z′ score of 0.64, indicative of an excellent assay, and confirmed 4 hits, including isonaamidine B, papuamine, mycalolide E, and jaspamide. This HTS model demonstrates the potential to identify small-molecule modulators of EMT that could be used to discover novel antimetastatic agents for the treatment of cancer.
The Internet Backplane Protocol: Storage in the Network

For distributed and network applications, efficient management of program state is critical to performance and functionality. To support domainand application-specific optimization of data movement, we have developed the Internet Backplane Protocol (IBP) for controlling storage that is implemented as part the network fabric itself. IBP allows an application to control intermediate data staging operations explicitly as data is communicated between processes. As such, the application can exploit locality and manage scarce buffer resources effectively. In this paper, we discuss the development of IBP, the implementation of a prototype system for managing network storage, and a preliminary deployment as part of the Internet-2 Distributed Storage Initiative.