Miracle-dz/UniFAR-FTUs huggingface dataset:
LabVIEW and digital signal processor implementation of a channel vocoder based model of a cochlear implant

A cochlear implant is a prosthetic device used to mimic the function of a cochlea in a person with profound and bilateral hearing loss caused by a damaged inner ear. The current work revolves around the design of real time channel vocoder based model of a cochlear implant in LabVIEW and the TMS320C6713 DSK. First, a uniform band 16-channel vocoder is designed for the analysis and synthesis of English vowels, where filters of 400 Hz bandwidth, with cut off frequencies up to 6200Hz are used, based on MATLAB analysis performed previously. To extend the analysis to words and sentences, short time features, namely, short time energy, short time zero crossing rate and main lobe width of the short time autocorrelation function, are extracted and Gaussian Mixture Modelling (GMM) is used to classify the speech segments as voiced or unvoiced. In an attempt to make the synthetic speech sound natural, the synthesis in the channel vocoder is done using a train of glottal pulses instead of a train of impulses. The intelligibility of the synthetic speech is measured by the Mean Opinion Score (MOS). For a channel vocoder where the synthesis section uses a train of glottal pulses, an MOS of 3.6 is obtained as against 3.5 when a train of impulses is used. The lab model of the cochlear implant, that is, the analysis section of the 16-channel vocoder is then realised in the TMS320C6713 DSK. Individual channel outputs are obtained by programming the DIP switches of the DSK and a DSK_AUDIO16_BASE, a 16-channel audio daughter card, is interfaced with the DSK to obtain the outputs from multiple channels simultaneously.
Efficient repair of A/C mismatches in mouse cells deficient in long‐patch mismatch repair

A previously unrecognized mismatch repair activity is described. Extracts of immortalized MSH2‐deficient mouse fibroblasts did not correct most single base mispairs. The same extracts carried out efficient repair of A/C mismatches. A/G mispairs were less efficiently corrected and there was no significant repair of A/A. MLH1‐defective mouse extracts also repaired an A/C mispair. A/C correction by Msh2−/− mouse cell extracts was not affected by antibodies against the PMS2 protein, which inhibited long‐patch mismatch repair. A/C repair activity is thus independent of MutSα, MutSβ and MutLα. A/C mismatches were corrected 5‐fold more efficiently by extracts of Msh2 knockout mouse cells than by comparable extracts prepared from hMSH2‐ or hMLH1‐deficient human cells. MSH2‐independent A/C correction by mouse cell extracts did not require a nick in the circular duplex DNA substrate. Repair involved replacement of the A and was associated with the resynthesis of a limited stretch of ≤25 bases of DNA.
Identifying patterns in spatial information: A survey of methods

Explosive growth in geospatial data and the emergence of new spatial technologies emphasize the need for automated discovery of spatial knowledge. Spatial data mining is the process of discovering interesting and previously unknown, but potentially useful patterns from large spatial databases. The complexity of spatial data and implicit spatial relationships limits the usefulness of conventional data mining techniques for extracting spatial patterns. In this paper, we explore the emerging field of spatial data mining, focusing on different methods to extract patterns from spatial information. We conclude with a look at future research needs. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 193–214 DOI: 10.1002/widm.25
Dominant-Negative Inhibition of Prion Formation Diminished by Deletion Mutagenesis of the Prion Protein

ABSTRACT Polymorphic basic residues near the C terminus of the prion protein (PrP) in humans and sheep appear to protect against prion disease. In heterozygotes, inhibition of prion formation appears to be dominant negative and has been simulated in cultured cells persistently infected with scrapie prions. The results of nuclear magnetic resonance and mutagenesis studies indicate that specific substitutions at the C-terminal residues 167, 171, 214, and 218 of PrPC act as dominant-negative, inhibitors of PrPSc formation (K. Kaneko et al., Proc. Natl. Acad. Sci. USA 94:10069–10074, 1997). Trafficking of substituted PrPC to caveaola-like domains or rafts by the glycolipid anchor was required for the dominant-negative phenotype; interestingly, amino acid replacements at multiple sites were less effective than single-residue substitutions. To elucidate which domains of PrPC are responsible for dominant-negative inhibition of PrPSc formation, we analyzed whether N-terminally truncated PrP(Q218K) molecules exhibited dominant-negative effects in the conversion of full-length PrPC to PrPSc. We found that the C-terminal domain of PrP is not sufficient to impede the conversion of the full-length PrPC molecule and that N-terminally truncated molecules (with residues 23 to 88 and 23 to 120 deleted) have reduced dominant-negative activity. Whether the N-terminal region of PrP acts by stabilizing the C-terminal domain of the molecule or by modulating the binding of PrPC to an auxiliary molecule that participates in PrPSc formation remains to be established.
Design and analysis of a novel temporal dissimilarity measure using Gaussian membership function

Earlier research works addressing the problem of mining time profiled temporal association patterns did not address the possibility of using new similarity measures in the context of time stamped temporal databases except some of our previous works. This research throws focus on designing a new similarity measure for mining similarity profiled temporal association patterns. The objective is to design a fuzzy similarity measure which can be used to discover all valid similarity profiled temporal association patterns.
College and the Learning Disabled Student

Section 504 of the Rehabilitation Act of 1973 was the federal legislation having the most direct impact on college opportunities for LD students. The provisions of Section 504 were reinforced with the passage of the Americans with Disabilities Act of 1990. Although Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990 require that all colleges and universities receiving federal funds take action to meet the needs of students with disabilities, many institutions comply with these laws but lack the resources and/or philosophical commitment to go beyond only compliance. However, there are approximately 1,000 of 3,500+ colleges and universities in the United States which go far beyond compliance and offer LD students a broad range of services to help them succeed. Therefore, all two-year and four-year post secondary institutions across the country can be divided into the following three categories:
An Efficient Resilience Mechanism for Data Centric Storage in Mobile Ad Hoc Networks

Data Centric Storage (DCS) is a powerful storage paradigm for wireless ad hoc networks. In mobile ad hoc networks (MANETs), however, the mobility and varying density of nodes may significantly impact the efficiency of data access and the level of data consistency for existing DCS mechanisms. In this paper, we propose an efficient resilience mechanism for data centric storage that supports DCS in mobile environments. We introduce a novel indirection strategy that enables us to distinguish the storage of data at dedicated server nodes from the storage of additional information to locate these servers. Our approach places server location information dynamically in strategic parts of the network based on its current topology. Combining our server location advertisement with any geographic routing protocol, we provide a robust data update and query processing technique for data centric storage in MANETs. We show analytically and by means of experimental evaluations that, despite the additional indirection during packet forwarding, our approach provides superior storage and retrieval performance than the original DCS algorithm even for large amounts of dynamic data.
Expression of basic fibroblast growth factor and its receptors FGFR1 and FGFR2 in human benign prostatic hyperplasia treated with finasteride

The development of benign prostatic hyperplasia (BPH) is an androgen‐dependent process which may be mediated by a number of locally produced growth factors. One of these, the basic fibroblast growth factor (bFGF or FGF2), has a mitogenic effect on prostatic stroma. High expression levels of bFGF have been reported in BPH. FGFR1 and FGFR2 receptors, that exhibit affinity for bFGF, have been identified in normal and hyperplastic prostate. Finasteride, a 5α‐reductase inhibitor, is an effective drug in the treatment of BPH, inducing regressive changes in the prostate of treated patients, even though its mechanisms of action are not yet completely elucidated. This study was designed to assess the effects of finasteride on the expression levels of bFGF, FGFR1, and FGFR2 in patients with BPH.
Male-specific lethal complex of Drosophila targets activated regions of the X chromosome for chromatin remodeling

The male-specific lethal (MSL) complex of Drosophila is responsible for the presence of a monoacetylated isoform of histone H4 (H4Ac16), found exclusively on the X chromosome of males. This particular covalent modification of histone H4 is correlated with a 2-fold enhancement of the transcription of most X-linked genes in Drosophila males, which is the basis of dosage compensation in this organism. Although widespread along the X chromosome, the MSL complex is not distributed uniformly, as can be seen by the indirect cytoimmunofluorescence staining of larval salivary-gland polytene chromosomes. This distribution pattern has been interpreted as a reflection of the tissue-specific transcriptional activity of the larval salivary gland and as an indication that the MSL complex associates with active chromatin. We have tested this hypothesis by comparing the chromosomal distribution of the complex in two different tissues. We performed this comparison by following the pattern of association of the complex at a specific site on salivary-gland chromosomes during larval development and determining whether an ectopic promoter located in a complex-devoid region of the X chromosome is able to attract the complex upon activation. Our results indicate that, in contrast to other chromatin-remodeling complexes that enhance transcription, the MSL complex targets active chromatin.
Sex Differences and Similarities in Urban Home Ranges and in the Accuracy of Cognitive Maps

Former research has examined potential human sex differences in spatial abilities or home range size. Both are assumed to have an adaptive function. In this study we combined the investigation of home range size in an urban environment and spatial abilities by accuracy analysis of cognitive maps. Participants (n = 87) drew a sketch of their home range in Vienna depicting all places regularly visited in every-day life. We used the sketches' geographical locations to calculate the size of the home range. With the Geometric Morphometric Methodology, we quantified the accuracy of cognitive maps by measuring Euclidean distances between corresponding landmarks in the sketches and the geographical maps of home ranges. Our results showed a non-significant trend for men to have a larger home range. Overall, participants' cognitive maps were fairly accurate. However, men sketched their home range more precisely than women. Female map accuracy increased as a function of residency duration. In addition, accuracy of cognitive maps was influenced by home range size and number of frequently visited places. In summary, findings indicate that sex differences in home range size and spatial abilities may still persist in humans living in urbanized Western societies, but are also influenced by environmental experience.
Antioxidant Potential of Bark Extracts from Boreal Forest Conifers

The bark of boreal forest conifers has been traditionally used by Native Americans to treat various ailments and diseases. Some of these diseases involve reactive oxygen species (ROS) that can be prevented by the consumption of antioxidants such as phenolic compounds that can be found in medicinal plants. In this study, ultrasonic assisted extraction has been performed under various solvent conditions (water:ethanol mixtures) on the bark of seven boreal forest conifers used by Native Americans including: Pinus strobus, Pinus resinosa, Pinus banksiana, Picea mariana, Picea glauca, Larix laricina, and Abies balsamea. The total phenolic content, as well as ORACFL potency and cellular antioxidant activity (IC50), were evaluated for all bark extracts, and compared with the standardized water extract of Pinus maritima bark (Pycnogenol), which showed clinical efficiency to prevent ROS deleterious effects. The best overall phenolic extraction yield and antioxidant potential was obtained with Picea glauca and Picea mariana. Interestingly, total phenolic content of these bark extracts was similar to Pycnogenol but their antioxidant activity were higher. Moreover, most of the extracts did not inhibit the growth of human skin fibroblasts, WS1. A significant correlation was found between the total phenolic content and the antioxidant activity for water extracts suggesting that these compounds are involved in the activity.
Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

The recent resurgence of wheat stem rust caused by new virulent races of Puccinia graminis f. sp. tritici (Pgt) poses a threat to food security. These concerns have catalyzed an extensive global effort toward controlling this disease. Substantial research and breeding programs target the identification and introduction of new stem rust resistance (Sr) genes in cultivars for genetic protection against the disease. Such resistance genes typically encode immune receptor proteins that recognize specific components of the pathogen, known as avirulence (Avr) proteins. A significant drawback to deploying cultivars with single Sr genes is that they are often overcome by evolution of the pathogen to escape recognition through alterations in Avr genes. Thus, a key element in achieving durable rust control is the deployment of multiple effective Sr genes in combination, either through conventional breeding or transgenic approaches, to minimize the risk of resistance breakdown. In this situation, evolution of pathogen virulence would require changes in multiple Avr genes in order to bypass recognition. However, choosing the optimal Sr gene combinations to deploy is a challenge that requires detailed knowledge of the pathogen Avr genes with which they interact and the virulence phenotypes of Pgt existing in nature. Identifying specific Avr genes from Pgt will provide screening tools to enhance pathogen virulence monitoring, assess heterozygosity and propensity for mutation in pathogen populations, and confirm individual Sr gene functions in crop varieties carrying multiple effective resistance genes. Toward this goal, much progress has been made in assembling a high quality reference genome sequence for Pgt, as well as a Pan-genome encompassing variation between multiple field isolates with diverse virulence spectra. In turn this has allowed prediction of Pgt effector gene candidates based on known features of Avr genes in other plant pathogens, including the related flax rust fungus. Upregulation of gene expression in haustoria and evidence for diversifying selection are two useful parameters to identify candidate Avr genes. Recently, we have also applied machine learning approaches to agnostically predict candidate effectors. Here, we review progress in stem rust pathogenomics and approaches currently underway to identify Avr genes recognized by wheat Sr genes.
Chianti: a change impact analysis tool for Java programs

Chianti is a change impact analysis tool for Java that is implemented in the context of the eclipse environment. Chianti analyzes two versions of a Java program, decomposes their difference into a set of atomic changes, and a partial order inter-dependences of these changes is calculated. Change impact is then reported in terms of affected (regression or unit) tests whose execution behavior may have been modified by the applied changes. For each affected test, Chianti also determines a set of affecting changes that were responsible for the test's modified behavior. This latter step of isolating failure inducing changes for one specific test from irrelevant changes can be used as a debugging technique in situations where a test fails unexpectedly after a long editing session.
Optimal common-mode Voltage reduction PWM technique for inverter control with consideration of the dead-time effects-part I: basic development

The objective of this paper is to investigate the optimal common-mode voltage reduction pulsewidth modulation (PWM) technique when dead-time effect is taken into account. The effect of dead time on common-mode voltage for inverter control and the associated solution are discussed. Based upon these results, an optimal common-mode voltage reduction PWM technique, which requires no extra voltage/current sensors and compensation mechanism while not being affected by the dead time, is recommended. The common-mode voltage can be reduced to one-third for the inverter with diode front end, which is widely used in industry. Intensive measured results are presented to fully support the claims.
A new algorithm for graph mining

Mining frequent substructures has gained importance in the recent past. Number of algorithms has been presented for mining undirected graphs. Focus of this paper is on mining frequent substructures in directed labeled graphs since it has variety of applications in the area of biology, web mining etc. A novel approach of using equivalence class principle has been proposed for reducing the size of the graph database to be processed for finding frequent substructures. For generating candidate substructures a combination of L-R join operation, serial and mixed extensions have been carried out. This avoids missing of any candidate substructures and at the same time candidate substructures that have high probability of becoming frequent are generated.
Drosophila BEND 6 is a nuclear antagonist of Notch signaling during self-renewal of neural stem cells

INTRODUCTION The Notch pathway is an ancient cell communication system that is broadly utilized to determine cell fates and pattern tissues throughout the Metazoa (Lai, 2004). At its core are the transmembrane ligand and receptor pair, Delta and Notch, respectively. Their productive interaction induces Notch cleavage and nuclear translocation of the Notch intracellular domain (NICD). There, it functions as a transcriptional co-activator for a member of the CSL transcription factor family, so-named for human CBF1 (now known as RBPJ), Drosophila Suppressor of Hairless [Su(H)] and nematode LAG-1. A tripartite complex of NICD, CSL and Mastermind activates various target genes, often in a setting-specific manner. However, multiple genes encoding basic helix-loop-helix (bHLH) repressors figure prominently as conserved effectors of, and are activated in response to Notch signaling in diverse developmental settings. Historically, studies of gene regulation by transcription factors in signaling pathways focused on targets that are 'turned on'. However, growing attention has been paid to the fact that many signal-regulated transcription factors function as active repressors in the absence of pathway activity, referred to as 'default repression'. Indeed, such dual transcriptional activity has been argued to be a fundamental attribute of signal-regulated transcription factors (Barolo and Posakony, 2002). This might serve to heighten the differential between 'on' and 'off' states of signaling, prevent spurious target gene activity, and/or help impose temporal precision on signaling.
Quantifying the benefits of infrastructure sharing

We analyze the benefits of network sharing between telecommunications operators. Sharing is seen as one way to speed the roll out of expensive technologies such as 5G since it allows the service providers to divide the cost of providing ubiquitous coverage. Our theoretical analysis focuses on scenarios with two service providers and compares the system dynamics when they are competing with the dynamics when they are cooperating. We show that sharing can be beneficial to a service provider even when it has the power to drive the other service provider out of the market, a byproduct of a non-convex cost function. A key element of this study is an analysis of the competitive equilibria for both cooperative and non-cooperative 2-person games in the presence of (non-convex) cost functions that involve a fixed cost component.
Applying Formal Methods to a Protocol Standard and its Implementations

We explore the use of formal methods in the analysis of the SONET Automatic Protection Switching (APS) protocol. Unlike most protocol studies, we look at both conformance and interoperability aspect of APS. We use the Concurrency Workbench of North Carolina [9] to show proper interoperation of network elements running the protocol, and use the VeriSoft tool [12] to show conformance of Lucent Technologies APS implementation to the APS standard. We define a new notion of conformance, identify problems with APS, suggest general improvements to the structure of protocol standards, and suggest how protocol implementations can be written to allow conformance checks to be automated.
Identi W cation of a candidate gene for the wheat endopeptidase EpD 1 locus and two other STS markers linked to the eyespot resistance gene Pch

Wheat is prone to strawbreaker foot rot (eyespot), a fungal disease caused by Oculimacula yallundae and O. acuformis. The most eVective source of genetic resistance is Pch1, a gene derived from Aegilops ventricosa. The endopeptidase isozyme marker allele Ep-D1b, linked to Pch1, has been shown to be more eVective for tracking resistance than DNA-based markers developed to date. Therefore, we sought to identify a candidate gene for Ep-D1 as a basis for a DNA-based marker. Comparative mapping suggested that the endopeptidase loci Ep-D1 (wheat), enp1 (maize), and Enp (rice) were orthologous. Since the product of the maize endopeptidase locus enp1 has been shown to exhibit biochemical properties similar to oligopeptidase B puriWed from E. coli, we reasoned that Ep-D1 may also encode an oligopeptidase B. Consistent with this hypothesis, a sequence-tagged-site (STS) marker, Xorw1, derived from an oligopeptidase B-encoding wheat expressed-sequence-tag (EST) showed complete linkage with Ep-D1 and Pch1 in a population of 254 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Coda and Brundage. Two other STS markers, Xorw5 and Xorw6, and three microsatellite markers (Xwmc14, Xbarc97, and Xcfd175) were also completely linked to Pch1. On the other hand, Xwmc14, Xbarc97, and Xcfd175 showed recombination in the W7984 £ Opata85 RIL population suggesting that recombination near Pch1 is reduced in the Coda/Brundage population. In a panel of 44 wheat varieties with known eyespot reactions, Xorw1, Xorw5, and Xorw6 were 100% accurate in predicting the presence or absence of Pch1 whereas Xwmc14, Xbarc97, and Xcfd175 were less eVective. Thus, linkage mapping and a germplasm survey suggest that the STS markers identiWed here should be useful for indirect selection of Pch1.