Miracle-dz/UniFAR-FTUs huggingface dataset:
Survey of Fusarium species associated with crown rot of wheat and barley in eastern Australia

Fusarium species associated with crown rot were isolated and identified from 409 wheat, barley or durum wheat crops from the eastern Australian grain belt between 1996 and 1999. Fusarium pseudograminearum was almost the only species isolated from crops in Queensland and New South Wales. F pseudograminearum was also the most common species in Victoria and South Australia, but F. culmorum was frequently isolated in these states. F. culmorum accounted for more than 70% of isolates from the Victorian high-rainfall (> 500 mm) region and the South-East region of South Australia. F culmorum comprised 18% of isolates from the Victorian medium-rainfall (350–500 mm) region, and 7% of isolates from each of the Victorian low-rainfall region and the Mid-North region of South Australia. F avenaceum, F crookwellense and F. graminearum were isolated very infrequently. The proportion of F. culmorum among isolates of Fusarium from districts in Victoria and South Australia was strongly correlated with climatic conditions around the end of the growing season, especially with rainfall in November.
Partial-Match Retrieval Algorithms

We examine the efficiency of hash-coding and tree-search algorithms for retrieving from a file of k-letter words all words which match a partially-specified input queryword (for example, retrieving all six-letter English words of the form S**R*H where "*" is a "don't care" character). We precisely characterize those balanced hash-coding algorithms withminimum average number of lists examined. Use of the first few letters of each word as a list index is shown to be one such optimal algorithm.A new class of combinatorial designs (called associative block designs) provides better hash functions with a greatly reduced worst-case number of lists examined, yet with optimal average behavior maintained. Another efficient variant involves storing each word in several lists. Tree-search algorithms are shown to be approximately as efficient as hash-coding algorithms, on the average. In general, these algorithms require time about O(n <k-s)/k) to respond to a query word with s letters specified, given a file of n k-letter words. Previous algorithms either required time O(s n/k) or else used exorbitant amounts of storage.
Association of Wild Bird Density and Farm Management Factors with the Prevalence of E. coli O157 in Dairy Herds in Ohio (2007–2009)

Our objective was to determine the role that European starlings (Sturnus vulgaris) play in the epidemiology of Escherichia coli O157:H7 in dairy cattle. We visited 150 dairy farms in Ohio twice during summer and fall months from 2007 to 2009. Fresh faecal pats from 30 lactating cows were collected during each visit. Information on farm management and environmental variables was gathered through a questionnaire administered to the farm owner. The number of starlings observed on the farm was also recorded. Approximately 1% of dairy cattle and 24% of farms were positive for E. coli O157. Risk factors associated with the presence of E. coli O157 in faecal pats included contact between adult cattle and calves, types or number of ventilation and manure management systems and number of birds per milking cow.
Design of exposure questionnaires for epidemiological studies

Questionnaires are frequently used in the exposure assessment of occupational and environmental epidemiological studies. Questionnaires may be the method of choice for assessing exposure because no other sources of information are available, or because they provide the most efficient data collection method, allowing a larger study size and greater statistical power than would be possible with other more accurate measurement techniques. They may be used in combination with other methods. Information on presence of exposure (yes/no), duration, frequency, and pattern of exposure is often obtained by questionnaire. Very few, if any, standardised questionnaires that have been validated are available in this area. This is one of the major limitations of questionnaires and researchers should be extremely careful how they use self-reported exposure since it may bias the exposure-disease association. The design of new questionnaires often depends on the experience acquired with previous questionnaires. Questionnaires require careful consideration of design and administration issues, including, for example, the length, detail of the required information, logistics, participation and completion rate, and costs involved.1,2 Exposures of interest may often be past exposures; subjects may not be able to recall these which may lead to underreporting.3 Furthermore, lack of understanding of the questions or knowledge of the exposure may bias the reporting. Recall bias, where those with disease are more likely to report their exposures compared to those without disease, even though there is no true difference, needs to be avoided; this requires careful consideration of the questions that are asked.4 Questionnaires can be self-administered or administered by an interviewer and either be handed or sent out, or administered over the phone or in person (face to face) respectively. This may affect the design of the questionnaire. A self-administered questionnaire is general the easiest, cheapest, and requires least involvement from both …
Bite force measurement based on fiber Bragg grating sensor

Abstract. The maximum level of voluntary bite force, which results from the combined action of muscle of mastication, joints, and teeth, i.e., craniomandibular structure, is considered as one of the major indicators for the functional state of the masticatory system. Measurement of voluntary bite force provides useful data for the jaw muscle function and activity along with assessment of prosthetics. This study proposes an in vivo methodology for the dynamic measurement of bite force employing a fiber Bragg grating (FBG) sensor known as bite force measurement device (BFMD). The BFMD developed is a noninvasive intraoral device, which transduces the bite force exerted at the occlusal surface into strain variations on a metal plate. These strain variations are acquired by the FBG sensor bonded over it. The BFMD developed facilitates adjustment of the distance between the biting platform, which is essential to capture the maximum voluntary bite force at three different positions of teeth, namely incisor, premolar, and molar sites. The clinically relevant bite forces are measured at incisor, molar, and premolar position and have been compared against each other. Furthermore, the bite forces measured with all subjects are segregated according to gender and also compared against each other.
Explaining the Birth Order Effect: The Role of Prenatal and Early Childhood Investments

The critical role of prenatal and early childhood conditions on adult outcomes has been the focus of a rich body of research. In this paper, we examine various pre- and postnatal investments as possible sources behind the "birth order effect" – significant differences in the educational and labor market outcomes across children of varying birth orders. Taking advantage of a rich set of information on in utero and early childhood conditions in the Children of the NLSY79, we find that, within the same household, siblings of higher birth order experience a lower reduction in cigarette usage during pregnancy, are breastfed less often, and experience less cognitive stimulation and emotional support at ages 0 to 1. Next, we test for the presence of birth order effects in early cognitive and non-cognitive test scores and examine whether these differences can be explained by variations in prenatal and early childhood investments. Although there exists a significant negative relationship between birth order and early cognitive/non-cognitive test scores, the size and the significance of the negative birth order effects in test scores and educational attainment are robust to controlling for variations in early childhood factors.
BRAFV600E: Implications for Carcinogenesis and Molecular Therapy

The mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathway is frequently mutated in human cancer. This pathway consists of a small GTP protein of the RAS family that is activated in response to extracellular signaling to recruit a member of the RAF kinase family to the cell membrane. Active RAF signals through MAP/ERK kinase to activate ERK and its downstream effectors to regulate a wide range of biological activities including cell differentiation, proliferation, senescence, and survival. Mutations in the v-raf murine sarcoma viral oncogenes homolog B1 (BRAF) isoform of the RAF kinase or KRAS isoform of the RAS protein are found as activating mutations in approximately 30% of all human cancers. The BRAF pathway has become a target of interest for molecular therapy, with promising results emerging from clinical trials. Here, the role of the most common BRAF mutation BRAFV600E in human carcinogenesis is investigated through a review of the literature, with specific focus on its role in melanoma, colorectal, and thyroid cancers and its potential as a therapeutic target. Mol Cancer Ther; 10(3); 385–94. ©2011 AACR.
The Prevalence and Cost of Unapproved Uses of Top-Selling Orphan Drugs

Introduction The Orphan Drug Act encourages drug development for rare conditions. However, some orphan drugs become top sellers for unclear reasons. We sought to evaluate the extent and cost of approved and unapproved uses of orphan drugs with the highest unit sales. Methods We assessed prescription patterns for four top-selling orphan drugs: lidocaine patch (Lidoderm) approved for post-herpetic neuralgia, modafinil (Provigil) approved for narcolepsy, cinacalcet (Sensipar) approved for hypercalcemia of parathyroid carcinoma, and imatinib (Gleevec) approved for chronic myelogenous leukemia and gastrointestinal stromal tumor. We pooled patient-specific diagnosis and prescription data from two large US state pharmaceutical benefit programs for the elderly. We analyzed the number of new and total patients using each drug and patterns of reimbursement for approved and unapproved uses. For lidocaine patch, we subcategorized approved prescriptions into two subtypes of unapproved uses: neuropathic pain, for which some evidence of efficacy exists, and non-neuropathic pain. Results We found that prescriptions for lidocaine patch, modafinil, and cinacalcet associated with non-orphan diagnoses rose at substantially higher rates (average monthly increases in number of patients of 14.6, 1.45, and 1.58) than prescriptions associated with their orphan diagnoses (3.12, 0.24, and 0.03, respectively (p<0.001 for all)). By contrast, for imatinib, approved uses increased significantly over off-label (0.97 vs. 0.47 patients, p<0.001). Spending on off-label uses was highest for lidocaine patch and modafinil (>75%). Increases in lidocaine patch use for non-neuropathic pain far exceeded neuropathic pain (10.2 vs. 3.6 patients, p<0.001). Discussion In our sample, three of four top-selling orphan drugs were used more commonly for non-orphan indications. These orphan drugs treated common clinical symptoms (pain and fatigue) or laboratory abnormalities. We should continue to monitor orphan drug use after approval to identify products that come to be widely used for non-FDA approved indications, particularly those without adequate evidence of efficacy.
Scholarometer: A Social Framework for Analyzing Impact across Disciplines

The use of quantitative metrics to gauge the impact of scholarly publications, authors, and disciplines is predicated on the availability of reliable usage and annotation data. Citation and download counts are widely available from digital libraries. However, current annotation systems rely on proprietary labels, refer to journals but not articles or authors, and are manually curated. To address these limitations, we propose a social framework based on crowdsourced annotations of scholars, designed to keep up with the rapidly evolving disciplinary and interdisciplinary landscape. We describe a system called Scholarometer, which provides a service to scholars by computing citation-based impact measures. This creates an incentive for users to provide disciplinary annotations of authors, which in turn can be used to compute disciplinary metrics. We first present the system architecture and several heuristics to deal with noisy bibliographic and annotation data. We report on data sharing and interactive visualization services enabled by Scholarometer. Usage statistics, illustrating the data collected and shared through the framework, suggest that the proposed crowdsourcing approach can be successful. Secondly, we illustrate how the disciplinary bibliometric indicators elicited by Scholarometer allow us to implement for the first time a universal impact measure proposed in the literature. Our evaluation suggests that this metric provides an effective means for comparing scholarly impact across disciplinary boundaries.
Process optimization and consumable development for Chemical Mechanical Planarization (CMP) processes

xiii CHAPTER 1: INTRODUCTION. 1 1.1 Semiconductor manufacturing trends . 1 1.2 Need for planarization. 4 1.3 Damascene architecture for MLM using metal CMP. 5 1.4 Other CMP applications. 7 1.5 Outline of the thesis . 8 CHAPTER 2: BACKGROUND OF CMP PROCESS. 11 2.1 CMP process . 11 2.1.1 Material removal mechanism. 12 2.1.1.1 Mechanical aspects of CMP. 13 2.1.1.2 Chemical aspects of CMP process. 14 2.1.2 Governing factors of CMP process. 15 2.1.2.1 Process parameters. 17 2.1.2.2 Consumable characteristics. 17 2.2 Tribology of CMP process. 19 2.2.1 Tribology during CMP process. 19
Expression of StMYB1R-1, a Novel Potato Single MYB-Like Domain Transcription Factor, Increases Drought Tolerance1[C][W]

Potato (Solanum tuberosum) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms for such stresses in potato are largely unknown. To identify stress-related factors in potato, we previously carried out a genetic screen of potato plants exposed to abiotic environmental stress conditions using reverse northern-blot analysis. A cDNA encoding a putative R1-type MYB-like transcription factor (StMYB1R-1) was identified as a putative stress-response gene. Here, the transcript levels of StMYB1R-1 were enhanced in response to several environmental stresses in addition to drought but were unaffected by biotic stresses. The results of intracellular targeting and quadruple 9-mer protein-binding microarray analysis indicated that StMYB1R-1 localizes to the nucleus and binds to the DNA sequence G/AGATAA. Overexpression of a StMYB1R-1 transgene in potato plants improved plant tolerance to drought stress while having no significant effects on other agricultural traits. Transgenic plants exhibited reduced rates of water loss and more rapid stomatal closing than wild-type plants under drought stress conditions. In addition, overexpression of StMYB1R-1 enhanced the expression of drought-regulated genes such as AtHB-7, RD28, ALDH22a1, and ERD1-like. Thus, the expression of StMYB1R-1 in potato enhanced drought tolerance via regulation of water loss. These results indicated that StMYB1R-1 functions as a transcription factor involved in the activation of drought-related genes.
Automatic indexing

In information retrieval and text processing systems the search requests and stored information items are normally represented by sets of content identifiers, known as keywords or index terms. The choice of effective indexing products designed accurately to reflect document content is by far the most crucial task in retrieval. A wide variety of automatic indexing theories and systems have been developed over the years based in part on the occurrence frequencies of individual terms in the documents of a collection, on the ability of specific terms to distinguish the documents from each other, and on the distribution of terms in the relevant as opposed to the nonrelevant items in a collection. These theories lead to the automatic generation of content identifiers consisting of individual terms, term phrases, and classes of terms, and to the assignment of term weights reflecting the relative importance of the terms for content representation. The various indexing theories are covered and analytical as well as experimental results are given to demonstrate their effectiveness.
Transparent Synchronization Protocols for Compositional Real-Time Systems

Hierarchical scheduling frameworks (HSFs) provide means for composing complex real-time systems from well-defined, independently analyzed components. To support resource sharing in two-level HSFs, three synchronization protocols based on the stack resource policy (SRP) have recently been presented for single-processor execution platforms, i.e., HSRP, SIRAP, and BROE. This paper presents a transparent implementation of these three protocols side-by-side in an HSF-enabled real-time operating system. Transparent synchronization interfaces make it possible to select a protocol during integration time based on its relative strengths. A timing interface describes the required budget to execute a component on a shared platform and an accessor's maximum critical-section execution time to global shared resources. These resources are arbitrated based on the available budget of the accessing task. We enable this explicit synchronization of virtual time with global time by means of a novel virtual-timer mechanism. Moreover, we investigate system overheads caused by each synchronization protocol, so that these can be included in the system analysis. Based on the analytical and implementation overheads of each protocol, we present guidelines for the selection of a synchronization protocol during system integration. Finally, we show that unknown task-arrival times considerably complicate an efficient implementation of SIRAP's self-suspension mechanism. We briefly discuss the implementation complexity caused by these arrivals for bandwidth-preserving servers, e.g., deferrable servers and BROE.
IL-1β Causes an Increase in Intestinal Epithelial Tight Junction Permeability1

IL-1β is a prototypical proinflammatory cytokine that plays a central role in the intestinal inflammation amplification cascade. Recent studies have indicated that a TNF-α- and IFN-γ-induced increase in intestinal epithelial paracellular permeability may be an important mechanism contributing to intestinal inflammation. Despite its central role in promoting intestinal inflammation, the role of IL-1β on intestinal epithelial tight junction (TJ) barrier function remains unclear. The major aims of this study were to determine the effect of IL-1β on intestinal epithelial TJ permeability and to elucidate the mechanisms involved in this process, using a well-established in vitro intestinal epithelial model system consisting of filter-grown Caco-2 intestinal epithelial monolayers. IL-1β (0–100 ng/ml) produced a concentration- and time-dependent decrease in Caco-2 transepithelial resistance. Conversely, IL-1β caused a progressive time-dependent increase in transepithelial permeability to paracellular marker inulin. IL-1β-induced increase in Caco-2 TJ permeability was accompanied by a rapid activation of NF-κB. NF-κB inhibitors, pyrrolidine dithiocarbamate and curcumin, prevented the IL-1β-induced increase in Caco-2 TJ permeability. To further confirm the role of NF-κB in the IL-1β-induced increase in Caco-2 TJ permeability, NF-κB p65 expression was silenced by small interfering RNA transfection. NF-κB p65 depletion completely inhibited the IL-1β-induced increase in Caco-2 TJ permeability. IL-1β did not induce apoptosis in the Caco-2 cell. In conclusion, our findings show for the first time that IL-1β at physiologically relevant concentrations causes an increase in intestinal epithelial TJ permeability. The IL-1β-induced increase in Caco-2 TJ permeability was mediated in part by the activation of NF-κB pathways but not apoptosis.
On Wallis-type Products and Pólya's Urn Schemes

Abstract A famous “curious identity” of Wallis gives a representation of the constant π in terms of a simply structured infinite product of fractions. Sondow and Yi [Amer. Math. Monthly 117 (2010) 912–917] identified a general scheme for evaluating Wallis-type infinite products. The main purpose of this paper is to discuss an interpretation of the scheme by means of Pólya urn models.
Permissive-nominal logic: First-order logic over nominal terms and sets

Permissive-Nominal Logic (PNL) is an extension of first-order predicate logic in which term-formers can bind names in their arguments. This allows for direct axiomatizations with binders, such as of the λ-binder of the lambda-calculus or the ∀-binder of first-order logic. It also allows us to finitely axiomatize arithmetic, and similarly to axiomatize “nominal” datatypes-with-binding. Just like first- and higher-order logic, equality reasoning is not necessary to α-rename. This gives PNL much of the expressive power of higher-order logic, but models and derivations of PNL are first-order in character, and the logic seems to strike a good balance between expressivity and simplicity.
A low-cost interface to high-value resistive sensors varying over a wide range

This paper presents a low-cost interface for high-value resistive sensors varying over a wide range, from k/spl Omega/ to G/spl Omega/. The proposed circuit that acts as a "resistance to period converter" is suitable to be interfaced to a microcontroller or a counting device. The behavior of real electronic components that produce estimation errors, is taken into account. Experimental results obtained by the realized prototype show a good resolution and repeatability.
Research Opportunities

"Research Opportunities" is a regular feature of this journal that transmits information regarding sources of support for basic and applied research in spine and musculoskeletal rehabilitation. In the previous issue, this feature provided a historical and legislative overview of the National Center for Medical Rehabilitation Research (NCMRR), a newly created unit of the National Institutes of Health. In this issue, we provide additional information on the NCMRR, including the types of grants available through the center, possible research topics, and filing deadlines.
Exploiting Linguistic Knowledge to Infer Properties of Neologisms

Exploiting linguistic knowledge to infer properties of neologisms C. Paul Cook Doctor of Philosophy Graduate Department of Computer Science University of Toronto 2010 Neologisms, or newly-coined words, pose problems for natural language processing (NLP) systems. Due to the recency of their coinage, neologisms are typically not listed in computational lexicons—dictionary-like resources that many NLP applications depend on. Therefore when a neologism is encountered in a text being processed, the performance of an NLP system will likely suffer due to the missing word-level information. Identifying and documenting the usage of neologisms is also a challenge in lexicography, the making of dictionaries. The traditional approach to these tasks has been to manually read a lot of text. However, due to the vast quantities of text being produced nowadays, particularly in electronic media such as blogs, it is no longer possible to manually analyze it all in search of neologisms. Methods for automatically identifying and inferring syntactic and semantic properties of neologisms would therefore address problems encountered in both natural language processing and lexicography. Because neologisms are typically infrequent due to their recent addition to the language, approaches to automatically learning word-level information relying on statistical distributional information are in many cases inappropriate. Moreover, neologisms occur in many domains and genres, and therefore approaches relying on domain-specific resources are also inappropriate. The hypothesis of this thesis is that knowledge about etymology—including word formation processes and types of semantic change—can be exploited for the acquisition of aspects of the syntax and semantics of neologisms. Evidence supporting this hypothesis is found