Miracle-dz/UniFAR-FTUs huggingface dataset:
Computing selected eigenvalues of sparse unsymmetric matrices using subspace iteration

This paper discusses the design and development of a code to calculate the eigenvalues of a large sparse real unsymmetric matrix that are the rightmost, leftmost, or are of the largest modulus. A subspace iteration algorithm is used to compute a sequence of sets of vectors that converge to an orthonormal basis for the invariant subspace corresponding to the required eigenvalues. This algorithm is combined with Chebychev acceleration if the rightmost or leftmost eigenvalues are sought, or if the eigenvalues of largest modulus are known to be the rightmost or leftmost eigenvalues. An option exists for computing the corresponding eigenvectors. The code does not need the matrix explicitly since it only requires the user to multiply sets of vectors by the matrix. Sophisticated and novel iteration controls, stopping criteria, and restart facilities are provided. The code is shown to be efficient and competitive on a range of test problems.
Truthful approximation mechanisms for restricted combinatorial auctions: extended abstract

When attempting to design a truthful mechanism for a computationally hard problem such as combinatorial auctions, one is faced with the problem that most efficiently computable heuristics can not be embedded in any truthful mechanism (e.g. VCG-like payment rules will not ensure truthfulness). We develop a set of techniques that allow constructing efficiently computable truthful mechanisms for combinatorial auctions in the special case where only the valuation is unknown by the mechanism (the single parameter case). For this case we extend the work of Lehmann O'Callaghan, and Shoham, who presented greedy heuristics, and show how to use IF-THEN-ELSE constructs, perform a partial search, and use the LP relaxation. We apply these techniques for several types of combinatorial auctions, obtaining truthful mechanisms with provable approximation ratios.
Curriculum of Mathematics in Pakistan and International Standards: A Comparative Study

Curriculum which is considered as the main tool education cannot remain the same endlessly. With the expansion of spectrum of knowledge, upgrading of the curriculum is needed with the passage of time. It is nevertheless, the timely updates and restructuring of curriculum can enhance the standard of education. It is therefore, change in curriculum and comparative analysis of the curriculum has been a hot debated topic not only in Pakistan but also all around the world. Current design of the study can be used to analyze the curriculum of mathematics for secondary level of education prescribed by the Punjab Text Book Board. The sole purpose of this comparative study of mathematics is to better analyze the policy objectives of the subject of mathematics curriculum for education at secondary level in Pakistan. Secondly, the study was aiming to analyze curriculum processes while referring to certain objectives, content, methodology and assessment techniques. Thirdly, this research study was aiming to critically review the subject matter of mathematics while highlighting the strengths and weaknesses of the subject of mathematics taught at secondary level of education in Pakistan. Fourth, the aim of this research study is to explore the suggestions of curriculum specialists about the salability of the value of mathematics curriculum in education of secondary level in Pakistan. Fifthly, the study used to recommend measures to upgrade the curriculum of mathematics implemented for secondary school education in the country. The population under study comprised of teachers, students, opinion of national curriculum professionals and materials provided about the mathematics curriculum from the Curriculum Bureau in Provinces of Pakistan. Suggestions and recommendations are provided in the end of the research study while better concluding the results and findings in the end of the paper.
Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion

It was recently shown that haloarchaeal strains of different genera are able to adhere to surfaces and form surface-attached biofilms. However, the surface structures mediating the adhesion were still unknown. We have identified a novel surface structure with Halobacterium salinarum strain R1, crucial for surface adhesion. Electron microscopic studies of surface-attached cells frequently showed pili-like surface structures of two different diameters that were irregularly distributed on the surface. The thinner filaments, 7–8 nm in diameter, represented a so far unobserved novel pili-like structure. Examination of the Hbt. salinarum R1 genome identified two putative gene loci (pil-1 and pil-2) encoding type IV pilus biogenesis complexes besides the archaellum encoding fla gene locus. Both pil-1 and pil-2 were expressed as transcriptional units, and the transcriptional start of pil-1 was identified. In silico analyses revealed that the pil-1 locus is present with other euryarchaeal genomes whereas the pil-2 is restricted to haloarchaea. Comparative real time qRT-PCR studies indicated that the general transcriptional activity was reduced in adherent vs. planktonic cells. In contrast, the transcription of pilB1 and pilB2, encoding putative type IV pilus assembly ATPases, was induced in comparison to the archaella assembly/motor ATPase (flaI) and the ferredoxin gene. Mutant strains were constructed that incurred a flaI deletion or flaI/pilB1 gene deletions. The absence of flaI caused the loss of the archaella while the additional absence of pilB1 led to loss of the novel pili-like surface structures. The ΔflaI/ΔpilB1 double mutants showed a 10-fold reduction in surface adhesion compared to the parental strain. Since surface adhesion was not reduced with the non-archaellated ΔflaI mutants, the pil-1 filaments have a distinct function in the adhesion process.
Leader-Containing Uncapped Viral Transcript Activates RIG-I in Antiviral Stress Granules

RIG-I triggers antiviral responses by recognizing viral RNA (vRNA) in the cytoplasm. However, the spatio-temporal dynamics of vRNA sensing and signal transduction remain elusive. We investigated the time course of events in cells infected with Newcastle disease virus (NDV), a non-segmented negative-strand RNA virus. RIG-I was recruited to viral replication complexes (vRC) and triggered minimal primary type I interferon (IFN) production. RIG-I subsequently localized to antiviral stress granules (avSG) induced after vRC formation. The inhibition of avSG attenuated secondary IFN production, suggesting avSG as a platform for efficient vRNA detection. avSG selectively captured positive-strand vRNA, and poly(A)+ RNA induced IFN production. Further investigations suggested that uncapped vRNA derived from read-through transcription was sensed by RIG-I in avSG. These results highlight how viral infections stimulate host stress responses, thereby selectively recruiting uncapped vRNA to avSG, in which RIG-I and other components cooperate in an efficient antiviral program.
Searching for Tissue-Specific Expression Pattern-Linked Nucleotides of UGT1A Isoforms

UDP-glucuronosyltransferases 1A isoforms belong to a superfamily of microsomal enzymes responsible for glucuronidation of numerous endogenous and exogenous compounds. The nine functional UGT1A isoforms are encoded by a single UGT1A gene locus with multiple first exons. The expression of the UGT1A transcripts was measured by quantitative RT-PCR in 23 normal human tissues. The tissue-specific expression patterns were observed in 13 tissues. To understand the regulation mechanism that is responsible for the tissue-specific expression patterns, we scanned the DNA sequence alignments of the putative promoter regions, exon 1 sequences and intron 1 sequences for those expression-pattern-linked nucleotides. Using one of the expression-pattern-linked nucleotides for livers as an example, we showed that a database comprised of these expression-pattern-linked nucleotides could be used to generate focused hypotheses on the problem of tissue-specific expression, which is critical for tissue-specific pharmacodynamics of anticancer drugs.
CaJOINTLESS is a MADS-box gene involved in suppression of vegetative growth in all shoot meristems in pepper

In aiming to decipher the genetic control of shoot architecture in pepper (Capsicum spp.), the allelic late-flowering mutants E-252 and E-2537 were identified. These mutants exhibit multiple pleiotropic effects on the organization of the sympodial shoot. Genetic mapping and sequence analysis indicated that the mutants are disrupted at CaJOINTLESS, the orthologue of the MADS-box genes JOINTLESS and SVP in tomato and Arabidopsis, respectively. Late flowering of the primary and sympodial shoots of Cajointless indicates that the gene functions as a suppressor of vegetative growth in all shoot meristems. While CaJOINTLESS and JOINTLESS have partially conserved functions, the effect on flowering time and on sympodial development in pepper, as well as the epistasis over FASCICULATE, the homologue of the major determinant of sympodial development SELF-PRUNING, is stronger than in tomato. Furthermore, the solitary terminal flower of pepper is converted into a structure composed of flowers and leaves in the mutant lines. This conversion supports the hypothesis that the solitary flowers of pepper have a cryptic inflorescence identity that is suppressed by CaJOINTLESS. Formation of solitary flowers in wild-type pepper is suggested to result from precocious maturation of the inflorescence meristem.
Data extraction from Web data sources

An explanation is given of the basic data structures used in a new page analysis technique to create wrappers (data extractors) for the result pages produced by Web sites in response to user qeries via Web page forms. The key structure called a tpGrid is a representation of the web page, which is easier to analyse than the raw HTML code. The analysis looks for repetition patterns of sets of tagSets, which are defined in the paper.
Efficient Retrieval of DNA Sequences Using Multi-way Clustering

A retrieval on large DNA sequence data is very important in bioinformatics. However, it takes much time to search and comparison on large DNA sequence data. In this paper, we propose multi-way clustering for improving both the speed of retrieval and implement them. The result shows that multi-way clustering is a more efficient approach for retrieval of DNA sequence.
Changes in microRNA expression in the brachial plexus avulsion model of neuropathic pain

The present study aimed to perform microRNA (miRNA/miR) expression profiling of the thalamus (T), the anterior cingulate (AC), the dorsal horn of the spinal cord (DHSC) and the blood (B) in post-complete brachial plexus avulsion (CBPA) pain model, and analyze biological functions. Neuropathic pain was induced in Sprague-Dawley rats by CBPA. Animal behavioral tests were performed to differentiate the pain and control groups. DHSC, T, AC and B tissues were collected from the two groups for miRNA array analysis. The predicted mRNA targets were investigated by Gene Ontology analysis and pathway analysis. The results revealed that in the post-CBPA pain model, there were 10 differentially expressed miRNAs revealed among 4 different tissues. A total of 4 microRNAs in the AC and 3 microRNAs in the T were shown to be significantly upregulated. The functions of the differentially expressed miRNAs in the AC and T were synergetic in the aspect of positive regulation of neuron apoptotic process, inhibition of long-term potentiation and formation of synapse plasticity. miR-30c-1-3p and its predicted genes [calcium/calmodulin dependent protein kinase IIβ (Camk2b) and protein kinase Cγ (Prkcg)] existed in the AC and T groups with significant changes in expression. There were 2 miRNAs in the DHSC and B groups, respectively, with significant downregulation. The function of the change in miRNAs in the DHSC group was opposite to that in the AC and T groups. The differentially expressed microRNAs in the B group were revealed to be negative for the regulation of cell apoptosis. In conclusion, the central nerve groups (AC and T) and the peripheral nerve group (DHSC) exhibited contrasting effects on synapse plasticity and neuron apoptosis. miR-30c-1-3p and its predicted genes (Camk2b and Prkcg) existed in the AC and T groups with significant changes in expression.
QuickCheck: a lightweight tool for random testing of Haskell programs

QuickCheck is a tool which aids the Haskell programmer in formulating and testing properties of programs. Properties are discribed as Haskell functions, and can be automatically tested on random input, but it is also possible to define custom test data generators. We present a number of case studies, in which the tool was successfully used, and also point out some pitfalls to avoid. Random testing is especially suitable for functional programs because properties can be stated at a fine grain. When a function is built from separately tested components, then random testing suffuces to obtain good coverage of the definition under test.
Constructive algebraic topology

Abstract The classical “computation” methods in Algebraic Topology most often work by means of highly infinite objects and in fact are not constructive. Typical examples are shown to describe the nature of the problem. The Rubio–Sergeraert solution for Constructive Algebraic Topology is recalled. This is not only a theoretical solution: the concrete computer program Kenzo has been written down which precisely follows this method. This program has been used in various cases, opening new research subjects and producing in several cases significant results unreachable by hand. In particular the Kenzo program can compute the first homotopy groups of a simply connected arbitrary simplicial set.
The role-set of the truck driver: Issues of worker autonomy, ideology, and identity

In this dissertation, I explore occupational socialization and identity formation within the context of work, the workplace, and work practices. The workers presented in this study are long-haul, freight carrying truck drivers. The components of this study include: (a) a socio-historical analysis of the trucking industry, and (b) how characteristics of the truck drivers' work influence his identity, and how this influence is different for various types of drivers. I have reviewed changes in the trucking industry from its beginnings at the start of this century to its current status in 1996. This includes looking at organizations developed in response to the growth of the trucking industry such as the Interstate Commerce Commission, large hauling companies, and the union. The second component of this study is concerned with how the truck driver maintains his professional identity when faced with influences from contradictory groups that make up his role-set. For this purpose, I conducted 76 in-depth interviews: 70 interviews were conducted with long haul truck drivers; 6, with other individuals in the industry. I asked them open-ended questions about aspects of their work as truck drivers as well as questions about their family life. An overall finding of this study is that workers who experience more autonomy in their day-to-day work activities are more likely to resist understanding their identity through lay interpretations they receive from their role-set members. These differences in autonomy are experienced through two elements that might be present for any driver: (a) the Industry Status of the driver as independent or self-employed, or as working for a trucking company, or (b) the Length of Service of the driver in his occupation. These different elements that drivers experience at different levels allow the truck driver's socialization process to be mediated, resulting in a variety of attitudes towards work that seem to vary according to the independence of the driver (Industry Status) and how long the worker has been driving (Length of Service).
A New Hybrid Particle Swarm Optimization Algorithm for Adaptive Polarization Mode Dispersion Compensation

In this paper, we presented a new hybrid particle swarm optimization algorithm which is used to design the control unit of an adaptive polarization mode dispersion compensation. Comparing with the conventional particle swarm optimization algorithm, the new algorithm converges to the global optima much faster than the conventional particle swarm optimization algorithm. Experiments show that the new algorithm is easy to implementation, has lower probability to lock into sub-optima and need less time to obtain a result with sufficient accuracy.
Convex Programming Upper Bounds on the Capacity of 2-D Constraints

The capacity of 1-D constraints is given by the entropy of a corresponding stationary maxentropic Markov chain. Namely, the entropy is maximized over a set of probability distributions, which is defined by some linear equalities and inequalities. In this paper, certain aspects of this characterization are extended to 2-D constraints. The result is a method for calculating an upper bound on the capacity of 2-D constraints. The key steps are as follows: The maxentropic stationary probability distribution on square configurations is considered; set of linear equalities and inequalities is derived from this stationarity; the result is then a convex program, which can be easily solved numerically. Our method improves upon previous upper bounds for the capacity of the 2-D “no isolated bits” constraint, as well as certain 2-D RLL constraints.
Increased exposure to chilling advances the time to budburst in North American tree species

The phenology of trees is highly susceptible to changing global temperatures. Leaf budburst advances with increasing spring temperatures, but can also be delayed when warmer winters reduce chilling exposure. Results from long-term observations show that increasing temperatures have triggered advanced budburst in the past decades, but some studies also show that budburst advance has slowed recently. Here, we conducted an experiment with five temperate deciduous tree species (Acer rubrum L., Larix laricina (Du Rois) K. Koch, Populus tremuloides Michx. , Quercus ellipsoidalis E. j. Hill, Betula papyrifera Marsh. ) and one invasive species (Rhamnus cathartica L.) in Minnesota, USA, to assess the impact of chilling on the timing of leaf budburst. We collected twigs over two winter seasons (2011/2012 and 2012/2013) on a biweekly basis and exposed them to spring-like temperatures of 21 °C/16 °C day and night, long day photoperiod (16 h). We found a significant relationship of advanced budbreak with increased chilling for all species tested (P < 0.001) and significant differences in the timing to budburst among all species (P < 0.001). Acer rubrum responded strongly to chilling, showing a very steep linear decline in days to budburst with increased exposure to chilling. On the other end of the spectrum, L. laricina responded least to increases in chilling. These results suggest that rising global temperatures will likely have diverse impacts on tree species with potential implications for species interactions such as competition.
Robust design for linear non-regenerative MIMO relays

Optimal source precoding matrix and relay amplifying matrices have been developed in recent works for linear non-regenerative multiple-input multiple-output (MIMO) relay communication systems. All these works require the channel state information (CSI) knowledge in order to perform the optimization. However, in practical relay systems, the CSI is unknown and has to be estimated. There is always mismatch between the true and the estimated CSI. In this paper, the true CSI is modelled as a Gaussian random matrix with the estimated CSI as the mean value. First, by using the averaged mean-squared error (MSE) matrix of the signal waveform estimation, we develop the source and relay matrices which optimize most commonly used objective functions subjecting to the averaged transmission power constraints. Second, we consider the quality-of-service (QoS) issue by minimizing the averaged total transmission power subjecting to the averaged MSE constraints at each data stream. Simulation results demonstrate the improved robustness of the proposed algorithms against CSI errors.
Analysis of simple anti-windup compensation in approximate pole-placement control of a second order oscillatory system with time-delay

The main aim of this paper is to present analysis of anti-windup compensation impact on tracking performance for a second-order plant with time delay and continuous-time PID controller tuned by pole-placement. The paper uses a first-order non-Pade approximation of the delay in order to streamline the solution of the Diophantine equation. In the case of using Pade approximation, the solution could only be obtained approximately, because of greater number of variables than equations. The paper also studies influence of time delay approximation with first-order model to make approximate pole-placement possible. The performance of the system is compared on the basis of computing differences between integral of absolute and squared tracking errors for the system with and without compensation, as well as observing the excess of windup phenomenon taking place. The control system quality is described on the basis of two quality indices in the case of stable oscillatory second-order plant and square-wave reference signal.
Projecting the Hydrologic Impacts of Climate Change on Montane Wetlands

Wetlands are globally important ecosystems that provide critical services for natural communities and human society. Montane wetland ecosystems are expected to be among the most sensitive to changing climate, as their persistence depends on factors directly influenced by climate (e.g. precipitation, snowpack, evaporation). Despite their importance and climate sensitivity, wetlands tend to be understudied due to a lack of tools and data relative to what is available for other ecosystem types. Here, we develop and demonstrate a new method for projecting climate-induced hydrologic changes in montane wetlands. Using observed wetland water levels and soil moisture simulated by the physically based Variable Infiltration Capacity (VIC) hydrologic model, we developed site-specific regression models relating soil moisture to observed wetland water levels to simulate the hydrologic behavior of four types of montane wetlands (ephemeral, intermediate, perennial, permanent wetlands) in the U. S. Pacific Northwest. The hybrid models captured observed wetland dynamics in many cases, though were less robust in others. We then used these models to a) hindcast historical wetland behavior in response to observed climate variability (1916–2010 or later) and classify wetland types, and b) project the impacts of climate change on montane wetlands using global climate model scenarios for the 2040s and 2080s (A1B emissions scenario). These future projections show that climate-induced changes to key driving variables (reduced snowpack, higher evapotranspiration, extended summer drought) will result in earlier and faster drawdown in Pacific Northwest montane wetlands, leading to systematic reductions in water levels, shortened wetland hydroperiods, and increased probability of drying. Intermediate hydroperiod wetlands are projected to experience the greatest changes. For the 2080s scenario, widespread conversion of intermediate wetlands to fast-drying ephemeral wetlands will likely reduce wetland habitat availability for many species.