Miracle-dz/UniFAR-FTUs huggingface dataset:
Infection rates after tympanostomy tube insertion, comparing Aboriginal and non-Aboriginal children in the Northern Territory, Australia: a retrospective, comparative study.

OBJECTIVE To determine if there is a difference in infection rates between Aboriginal and non-Aboriginal children, following tympanostomy and ventilation tube placement, in the Northern Territory, Australia. MATERIALS AND METHODS A cohort of 213 patients aged zero to 10 years who had undergone tympanostomy and ventilation tube placement at the Royal Darwin Hospital between 1996 and 2004 were identified. Patients were divided into Aboriginal or non-Aboriginal groups, from their medical record. Factors such as age, sex, dwelling (remote or urban) and season were compared for each group, in order to ascertain if they contributed to infection rates. A retrospective analysis of cases was conducted for the two-year post-operative period. RESULTS There was no statistically significant difference in infection rates between the two groups (37 vs 35 per cent). There was no statistically significant difference when comparing the two groups for age, sex, season, or remote vs urban dwelling. CONCLUSION Aboriginal children were not prone to more infections following tympanostomy tube placement when compared with non-Aboriginal children.
Analysis of a tractable model for combustion instability: the effect of delay and low pass filtering

In this paper a new analytically tractable model for combustion instability is proposed. The model is based on two coupled resonators in a feedforward path, and a feedback path composed of a delay, generalized Van der Pol term and a low pass filter. The model is analyzed and approximated using a refined Krylov-Bogoliubov (K-B) method. The analysis shows that the model captures the phenomenon of two coexisting oscillating modes which has been noted in combustion instability by Dunstan (2003). Conditions for the occurrence of various operation regimes have been established. The importance of delay and low pass filtering is discussed in this article. A frequency domain comparison between K-B approximations and the true outputs of the model has been provided in the end of the paper
An explicit example with non‐Gaussian probability distribution for nontrivial scalar mean and fluctuation

Recently, one of the authors, studying a model for turbulent diffusion involving a large‐scale velocity field rapidly fluctuating in time, rigorously demonstrated intermittency in a diffusing scalar field by exhibiting broader than Gaussian tails in the scalar PDF. Here, we explore this model further with exact formulas within the context of general initial data possessing both a mean and a fluctuating component. Several new phenomena due to the presence of a nonzero scalar mean are documented here. We will establish that the limiting long time scalar PDF has long tails, as well as persisting skewness. Further, we show that the limiting PDF depends on the large‐scale energy of initial temperature fluctuations and exhibits long time memory of the initial data. Additionally, we will exhibit an explicit phase transition occurring in the scalar PDF as this large scale energy is varied, whereby the limiting PDF switches between states arising from deterministic initial data and states dominated by fluctuation.
Analisis Kesulitan Mahasiswa Dalam Penyelesaian Skripsi Di Prodi Pendidikan Matematika STKIP PGRI

Skripsi merupakan tugas akhir yang harus diselesaikan mahasiswa pada program sarjana di STKIP PGRI Sumbar. Namun banyak mahasiswa yang mengalami kesulitan dalam penyelesaian skirpsi, ini ditandai dengan lamanya masa bimbingan yang mereka tempuh. Penelitian bertujuan untuk mendeskripsikan jenis kesulitan/ bentuk kesulitan yang dialami mahasiswa dalam penyelesaian skripsi dan melihat efektivitas bimbingan oleh dosen pembimbing. Jenis penelitian ini adalah penelitian deskriptif. Subjek penelitian ini adalah dosen pembimbing dan mahasiswa S1 Program studi pendidikan matematika yang sedang bimbingan skripsi tahun 2014.Teknik pengumpulan data dalam penelitian ini menggunakan angket. Angket kesulitan diberikan kepada mahasiswa yang sedang menulis skripsi. Teknik analisis data menggunakan teknik persentase danselanjutnya di deskripsikan. Hasil penelitian secara umum diperoleh informasi mahasiswa mengalami kesulitan dalam penuangan ide ke dalam tulisan ilmiah yakni sekitar 66,67 %. , penggunaan ilmu statistik dalam pengolahan data yakni dengan persentase 61,54%,serta menarasikan hasil penelitian yani dengan persentase 64,10 %. Hasil penelitian diharapkan dapat menjadi masukan, informasi dan referensi kepada Prodi Pendidikan Matematika STKIP PGRI Sumbar sehingga faktor-faktor kesulitan mahasiswa dalam penyelesaian skripsi akan bisa diatasi
Mitochondrial Ferredoxin Is Required for Heme A Synthesis inSaccharomyces cerevisiae *

Heme A is a prosthetic group of all eukaryotic and some prokaryotic cytochrome oxidases. This heme differs from heme B (protoheme) at two carbon positions of the porphyrin ring. The synthesis of heme A begins with farnesylation of the vinyl group at carbon C-2 of heme B. The heme O product of this reaction is then converted to heme A by a further oxidation of a methyl to a formyl group on C-8. In a previous study (Barros, M. H., Carlson, C. G., Glerum, D. M., and Tzagoloff, A. (2001) FEBS Lett.492, 133–138) we proposed that the formyl group is formed by an initial hydroxylation of the C-8 methyl by a three-component monooxygenase consisting of Cox15p, ferredoxin, and ferredoxin reductase. In the present study three lines of evidence confirm a requirement of ferredoxin in heme A synthesis. 1) Temperature-conditional yah1 mutants grown under restrictive conditions display a decrease in heme A relative to heme B. 2) The incorporation of radioactive δ-aminolevulinic acid into heme A is reduced in yah1 ts but not in the wild type after the shift to the restrictive temperature; and 3) the overexpression of Cox15p in cytochrome oxidase mutants that accumulate heme O leads to an increased mitochondrial concentration of heme A. The increase in heme A is greater in mutants that overexpress Cox15p and ferredoxin. These results are consistent with a requirement of ferredoxin and indirectly of ferredoxin reductase in hydroxylation of heme O.
Efficient reachability testing of asynchronous message-passing programs

An asynchronous message-passing program P is nondeterministic. Given the same input, multiple executions of P may exercise different send/receive event sequences (or SR-sequences) and may even produce different results. Such nondeterminacy makes it difficult to determine the correctness of P. Let X be an input of P. Assume that any execution of P with X terminates. Reachability testing of P with X is to execute, in a systematic manner, all possible SR-sequences of P with X such that the correctness of P with X can be determined. The basic idea of reachability testing is described as follows. We first execute P with X nondeterministically to collect one or more SR-sequences. For each collected SR-sequence, we analyze its race conditions and generate race variants, which are prefixes of other SR-sequences. We replay race variants to generate new SR-sequences. For each new SR-sequence, we repeat the same process until we eventually execute all possible SR-sequences of P with X. We describe an efficient implementation of reachability testing of asynchronous message-passing programs. Our technique deals with partially-ordered SR-sequences and reduces the complexity and redundancy caused by totally-ordered SR-sequences.
You Should Be the Specialist! Weak Mental Rotation Performance in Aviation Security Screeners – Reduced Performance Level in Aviation Security with No Gender Effect

Aviation security screeners analyze a large number of X-ray images per day and seem to be experts in mentally rotating diverse kinds of visual objects. A robust gender-effect that men outperform women in the Vandenberg & Kuse mental rotation task has been well documented over the last years. In addition it has been shown that training can positively influence the overall task-performance. Considering this, the aim of the present study was to investigate whether security screeners show better performance in the Mental Rotation Test (MRT) independently of gender. Forty-seven security screeners of both sexes from two German airports were examined with a computer based MRT. Their performance was compared to a large sample of control subjects. The well-known gender-effect favoring men on mental rotation was significant within the control group. However, the security screeners did not show any sex differences suggesting an effect of training and professional performance. Surprisingly this specialized group showed a lower level of overall MRT performance than the control participants. Possible aviation related influences such as secondary effects of work-shift or expertise which can cumulatively cause this result are discussed.
Examining the Validity of Cross-Lingual Word Sense Disambiguation

This paper describes a set of experiments in which the viability of a classification-based Word Sense Disambiguation system that uses evidence from multiple languages is investigated. Instead of using a predefined monolingual sense-inventory such as WordNet, we use a language-independent framework and start from a manually constructed gold standard in which the word senses are made up by the translations that result from word alignments on a parallel corpus. To train and test the classifier, we used English as an input language and we incorporated the translations of our target words in five languages (viz. Spanish, Italian, French, Dutch and German) as features in the feature vectors. Our results show that the multilingual approach outperforms the classification experiments where no additional evidence from other languages is used. These results confirm our initial hypothesis that each language adds evidence to further refine the senses of a given word. This allows us to develop a proof of concept for a multilingual approach to Word Sense Disambiguation. Index Terms—Word Sense Disambiguation, multilingual, cross-lingual.
Causes of ecological success: the case of the ants. The sixth tansley lecture

The key remaining questions of evolutionary biology are more ecological than genetic in nature. In spite of the continuing great vitality of genetics in general, the known mechanisms of heredity appear to be sufficient to explain the observed phenomena of evolution. This is not to say that all processes of genetic change have been discovered. It may even prove true that extragenetic constraints on embryonic development, such as fundamental physical limits on cell size and configuration, play a role in evolution. What I am suggesting instead is that nothing empirically known at the present time about the nature and rate of evolution even hints at the existence of undiscovered hereditary processes. Consequently, what we know for sure that we do not know is largely ecological in nature. And ecologically-based problems of basic importance abound. One of the more obvious is why there are a certain number of species on Earth and not some other, in particular why 10 million (if that, say, proves to be the number) and not a thousand or a hundred million. Another unanswered question is why certain groups of organisms speciate profusely and spread over the world while otherwise similar ones remain undiversified and static. And that leads ineluctably to a third, related question, the meaning of ecological success. The subject has received remarkably little attention, perhaps because it is difficult to express with any precision and may appear to be more semantic than scientific. To take an example on which all can hopefully agree, we intuitively think of the ants as a successful group. Can success be usefully defined in such organisms? And if so, which if any evolutionary strategies consistently confer it?
The Chymotrypsin-Like Protease Complex of Treponema denticola ATCC 35405 Mediates Fibrinogen Adherence and Degradation

ABSTRACT Treponema denticola is an anaerobic spirochete strongly associated with human periodontal disease. T. denticola bacteria interact with a range of host tissue proteins, including fibronectin, laminin, and fibrinogen. The latter localizes in the extracellular matrix where tissue damage has occurred, and interactions with fibrinogen may play a key role in T. denticola colonization of the damaged sites. T. denticola ATCC 35405 showed saturable binding of fluid-phase fibrinogen to the cell surface and saturable adherence to immobilized fibrinogen. Levels of fibrinogen binding were enhanced in the presence of the serine protease inhibitor phenylmethylsulfonyl fluoride. The Aα and Bβ chains of fibrinogen, but not the γ chains, were specifically recognized by T. denticola. Following fibrinogen affinity chromatography analysis of cell surface extracts, a major fibrinogen-binding component (polypeptide molecular mass, ∼100 kDa), which also degraded fibrinogen, was purified. Upon heating at 100°C, the polypeptide was dissociated into three components (apparent molecular masses, 80, 48, and 45 kDa) that did not individually bind or degrade fibrinogen. The native 100-kDa polypeptide complex was identified as chymotrypsin-like protease (CTLP), or dentilisin. In an isogenic CTLP− mutant strain, CKE, chymotrypsin-like activity was reduced >90% compared to that in the wild type and fibrinogen binding and hydrolysis were ablated. Isogenic mutant strain MHE, deficient in the production of Msp (major surface protein), showed levels of CTLP reduced 40% relative to those in the wild type and exhibited correspondingly reduced levels of fibrinogen binding and proteolysis. Thrombin clotting times in the presence of wild-type T. denticola cells, but not strain CKE (CTLP−) cells, were extended. These results suggest that interactions of T. denticola with fibrinogen, which may promote colonization and modulate hemostasis, are mediated principally by CTLP.
Effect of CNV of Production Related Genes on Expression of Production Traits in Dairy Cattle

ACKNOWLEDGEMENT This project would not have been possible without the help and support of many people. I would first like to thank my parents, who raised me to have a love for the dairy industry and have supported me throughout my education here at Cal Poly and previously in high school and elementary school. Their continued desire for my success has been a driving force behind my accomplishments. Second, I would like to thank my project supervisor, Dr. Bruce Golden, for his help during this learning experience. His enthusiasm for the topic of interest encouraged me to dig deeper and deeper in order to see this project to completion. I would also like to extend my gratitude to Steve Maddox of Maddox Dairy for providing me with the necessary production information for particular animals. Without this information I would not have been able to make the conclusions that I did. iii ABSTRACT The objective of this project was to determine if copy number variation (CNV) at specific genes related to BST had an effect on milk production. Hair samples from 1000 fresh heifers from Maddox Dairy in Riverdale, CA were sent to Geneseek, a Neogen Company for DNA extraction and processing. The DNA was processed using the BovineSNP50 BeadChip and the data were loaded into the GenomeStudio software. The data were manipulated in GenomeStudio to estimate the CNV at each single nucleotide polymorphism (SNP) of which a vast majority was two. The SNPs with a copy number of two were excluded and all remaining copy number values were converted into a comma separated value file and loaded into an Excel spreadsheet for final processing. This resulted in 283,558 SNPs from 578 individuals. The genes studied were growth hormone (GH1), growth hormone receptor (GHR), growth hormone releasing hormone (GHRH), growth hormone releasing hormone receptor (GHRHR), insulin-like growth factor (IGF-1), and insulin (INS). SNPs located near the start and end of the gene sequences for those genes were found that had a copy number of three. PTAs of animals with SNPs located near these gene sequences were analyzed to determine if copy number had an effect on production. There were 138,411 total SNPs with a copy number of three. Of these 138,411 SNPs, 28 were intronic with the exception of IGF-1 which had no SNPs with CNV in the intron. For IGF-1, the closest exonic SNPs were used. Copy number variation did …
Detection of cracking in mild steel fatigue specimens using acoustic emission and digital image correlation

The aim of this investigation was to identify sources of AE in mild steel fatigue specimens and rel1ate them to damage mechanisms. Digital Image Correlation (DIC), a full-field strain measurement technique, was used to validate the findings. This paper describes in detail the results of a ‘dog bone’ style specimen undergoing uni-axial fatigue loading. This test forms part of a much larger programme designed to develop an AE monitoring system to identify damage initiation and growth from background noise in fatigue testing of automotive steels subjected to corrosion. Crack growth was monitored in the test using two AE sensors and, to allow a comparison with the detected and located signals, DIC images were captured periodically at peak loads. As part of the initial analysis located signals were compared with areas of high deformation and crack growth as identified by the DIC system. Results demonstrated that it is possible to distinguish the different AE signals originating from various possible failure mechanisms such as Plastic deformation, delamination of DIC paint and crack initiation and propagation. This might be utilized for an effective and powerful approach to monitor multiple failure mechanisms; this has significant applications in automotive chassis testing.
Molecular Motor Proteins and Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder affecting motor neurons in the brain, brainstem and spinal cord, which is characterized by motor dysfunction, muscle dystrophy and progressive paralysis. Both inherited and sporadic forms of ALS share common pathological features, however, the initial trigger of neurodegeneration remains unknown. Motor neurons are uniquely targeted by ubiquitously expressed proteins in ALS but the reason for this selectively vulnerability is unclear. However motor neurons have unique characteristics such as very long axons, large cell bodies and high energetic metabolism, therefore placing high demands on cellular transport processes. Defects in cellular trafficking are now widely reported in ALS, including dysfunction to the molecular motors dynein and kinesin. Abnormalities to dynein in particular are linked to ALS, and defects in dynein-mediated axonal transport processes have been reported as one of the earliest pathologies in transgenic SOD1 mice. Furthermore, dynein is very highly expressed in neurons and neurons are particularly sensitive to dynein dysfunction. Hence, unravelling cellular transport processes mediated by molecular motor proteins may help shed light on motor neuron loss in ALS.
Chemical and physical characteristics of lakes in the northeastern United States.

A survey of the chemical status of 252 lakes, representing an estimated 2424 lakes, was conducted in the Southern Blue Ridge province and in Florida during Fall 1984. This survey was part of the Eastern Lake Survey designed to quantify the number of acidic lakes and lakes with low acid neutralizing capacity (ANC) with surface area greater than 4 ha. Of the 102 lakes sampled in the Southern Blue Ridge, none were acidic (ANC {le} 0) and only 1.4% of the population of 258 lakes were estimated to have low (ANC {<=}50 {mu}equiv/L). In contrast, an estimated 22% of the lakes in the Florida subregion were acidic, and 35.3% were estimated to have low ANC. Almost 90% of the lakes in the Southern Blue Ridge were reservoirs. These lakes generally had moderate ANC values (median = 250 {mu}equiv/L) and had low concentrations of aluminum, dissolved organic carbon (DOC), and sulfate compared to those of Florida, the upper Midwest, and the Northeast. The lakes in the Southern Blue Ridge showed a high degree of chemical homogeneity relative to those of other regions in the East. In contrast, the chemistry of lakes in Florida exhibited a high degree of heterogeneity, indicating themore » presence of several distinct subpopulations. Florida had the highest proportion of acidic lakes in the East, some of which had moderately high concentrations of aluminum, DOC, and sulfate. Some of the Florida lakes are naturally acidic from organic acids. However, the many clear water, acidic lakes exhibit chemical characteristics that are not inconsistent with a hypothesis of acidification from deposition. The geographic separation of the Southern Blue Ridge from Florida and the strong contrasts in physical and chemical characteristics of the respective subregions require that they be treated as distinct regions. « less
Using hidden Markov models and observed evolution to annotate viral genomes

MOTIVATION ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. RESULTS The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.