Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multicopper Oxidase (Cj1516) and a CopA Homologue (Cj1161) Are Major Components of the Copper Homeostasis System of Campylobacter jejuni

ABSTRACT Metal ion homeostasis mechanisms in the food-borne human pathogen Campylobacter jejuni are poorly understood. The Cj1516 gene product is homologous to the multicopper oxidase CueO, which is known to contribute to copper tolerance in Escherichia coli. Here we show, by optical absorbance and electron paramagnetic resonance spectroscopy, that purified recombinant Cj1516 contains both T1 and trinuclear copper centers, which are characteristic of multicopper oxidases. Inductively coupled plasma mass spectrometry revealed that the protein contained approximately six copper atoms per polypeptide. The presence of an N-terminal “twin arginine” signal sequence suggested a periplasmic location for Cj1516, which was confirmed by the presence of p-phenylenediamine (p-PD) oxidase activity in periplasmic fractions of wild-type but not Cj1516 mutant cells. Kinetic studies showed that the pure protein exhibited p-PD, ferroxidase, and cuprous oxidase activities and was able to oxidize an analogue of the bacterial siderophore anthrachelin (3,4-dihydroxybenzoate), although no iron uptake impairment was observed in a Cj1516 mutant. However, this mutant was very sensitive to increased copper levels in minimal media, suggesting a role in copper tolerance. This was supported by increased expression of the Cj1516 gene in copper-rich media. A mutation in a second gene, the Cj1161c gene, encoding a putative CopA homologue, was also found to result in copper hypersensitivity, and a Cj1516 Cj1161c double mutant was found to be more copper sensitive than either single mutant. These observations and the apparent lack of alternative copper tolerance systems suggest that Cj1516 (CueO) and Cj1161 (CopA) are major proteins involved in copper homeostasis in C. jejuni.
The neuropsychology of language development

Book synopsis: Based on the most up-to-date research, Child Neuropsychology is a thorough and accessible guide to the key concepts and basic processes central to neuropsychological assessment and child evaluation. Essays by leading experts in the field cover basic neuropsychological functions and related disorders in the context of brain development. Divided into three parts, the text begins with clear definitions of the concepts and methodology of brain development in child neuropsychology. Part two examines normal and abnormal functional development. The final part considers professional practice and provides valuable insights into the special problems of neuropsychological assessment of infants and children in clinical and educational settings.
The ontogeny of ultraviolet photosensitivity in rainbow trout (Salmo gairdneri)

Abstract The present study examines the changes in ultraviolet (UV) photosensitivity that occur during the growth of rainbow trout (Salmo gairdneri). A comparison of the ocular media transmission of small (n = 3) and large (n = 3) trout eyes did not reveal large changes in the transmission of UV radiation through the eye. We used the heart-rate conditioning technique to measure spectral sensitivity in immobilized trout. Four trout, each weighing less than 30 g, exhibited a UV-sensitivity peak at 360 nm while four additional trout weighing more than 60 g each exhibited no evidence of UV sensitivity. Spectral-sensitivity measurements of two trout weighing 44 g and 60 g revealed UV sensitivity, but when measured one month later (after a 25% increase in body weight) both fish exhibited no UV-sensitivity peak. At this time their sensitivity appeared to conform to the known blue-sensitive cone mechanism.
Hypoxia‐inducible factor‐1 and oncogenic signalling

An understanding of underlying mechanisms involved in the activation of HIF‐1 in response to both hypoxic stress and oncogenic signals has important implications for how these processes may become deregulated in human cancer. Changes in microenvironmental stimuli such as hypoxia and growth factors in combination with genetic lesions, such as loss or inactivation of p53, PTEN or pVHL or oncogenic activation, can all lead to increased HIF‐1 activity. This provides cancer cells with a distinct advantage for survival and proliferation, resulting in their ability to form vascular tumours, which are aggressive and metastatic. Accordingly, upregulation of HIF‐1α, a key component of HIF‐1, correlates with a poor treatment outcome using conventional therapies. A variety of mechanisms exist that regulate expression of HIF‐1α. In recent years, it has become clear that an extensive network of signalling cascades converge on HIF‐1α to regulate the transcriptional response. A better understanding of this regulation may provide a basis for the development of new cancer therapies. BioEssays 26:262–269, 2004. © 2004 Wiley Periodicals, Inc.
Dimensional reduction study of piezoelectric ceramics constitutive equations from 3-D to 2-D and 1-D

Accurate performance evaluation is crucial to the design and development of macro/micro-sized piezoelectric devices, and key to this is the proper use of the stiffness/ compliance and piezoelectric coefficients of the piezoelectric ceramics involved. Although the literature points out effective piezoelectric coefficients e31,f and d33,f for thin film materials and reduced dimensionality of equations for bulk material, the elastic and piezoelectric coefficients remain unchanged from the 3-D equations in most reported 1-D and 2-D analyses of the macro/micro-sized devices involving the e form of the constitutive equations. The use of unchanged coefficients leads to variations between numerically predicted and experimental results in most devices. To understand effects of the dimensional reduction from 3-D to 2-D and 1-D on stiffness/compliance and piezoelectric coefficients, this paper derives the 2-D and 1-D constitutive equations from the 3-D equations, focusing on the discussion of often-required device configurations for sensor and actuator design and analysis. Two modified coefficients are proposed, termed reduced and enhanced, which enable better understanding of effects of the dimensional reduction and also effects on the design and analysis of sensors and actuators.
PROGRESSION OF AGE-RELATED MACULAR DEGENERATION OVERLYING A LARGE CHOROIDAL VESSEL.

PURPOSE To describe a patient who showed progression of age-related macular degeneration along the course of an underlying large choroidal vessel. METHODS Retrospective case report. RESULTS An 84-year-old woman was diagnosed with age-related macular degeneration and followed for more than 6 years. Retinal pigment epithelial changes were more advanced in her right eye which had a thinner choroid than the fellow left eye. Multimodal imaging with swept-source optical coherence tomography showed that the progression of outer retinal and retinal pigment epithelial changes appeared to follow the course of a large choroidal vessel. CONCLUSION The authors hypothesize that large choroidal vessels can compress the overlying choriocapillaris, possibly leading to outer retinal ischemia, which subsequently could focally accelerate the course of age-related macular degeneration.
Operative Management of Primary Retroperitoneal Sarcomas: A Reappraisal of an Institutional Experience

Objective:To review our recent experience with primary retroperitoneal sarcomas, determine prognostic factors for disease recurrence and patient survival, and compare them to our previous results. Background:Medical therapies have shown little efficacy in the management of retroperitoneal sarcomas, making total surgical extirpation the best chance for patient cure. Methods:The case histories of all patients operated upon for retroperitoneal sarcomas between January 1983 and December 1995 were retrospectively reviewed. Results:Ninety-seven patients underwent attempted surgical resection of a primary retroperitoneal sarcoma. There were 54 (56%) men and 43 (44%) women, with a mean age of 59 years. Seventy-six (78%) patients underwent gross total resection, 13 (14%) had residual disease, and 8 (8%) underwent biopsy only with an actuarial 1-year survival of 88%, 51%, and 47%, respectively (P = 0.001). The actuarial 5- and 10-year survivals for patients who underwent gross total resection were 51% and 36%, respectively. Thirty-three patients (43%) developed locoregional recurrence, and 20 patients (26%) developed distant metastases at a median time of 12 months. The cumulative probability at 5 years was 44% for locoregional recurrence and 29% for distant metastases. On univariate analysis, factors associated with improved survival were complete resection of the tumor (P = 0.001), nonmetastatic disease at presentation (P = 0.01), low-grade tumors (P = 0.02), liposarcomas (P = 0.003), and no disease recurrence (P = 0.0001). Contrary to previous reports, the histologic subtype (P = 0.04) was the only significant factor predicting survival on multivariate analysis. Conclusions:Compared with our earlier experience, the rates of complete resection and overall survival have improved. Local control continues to be a significant problem in the management of retroperitoneal sarcomas. Because new surgical options for this problem are limited, further outcome improvement requires novel adjuvant therapies.
Cetra: A trace and analysis framework for the evaluation of Cell BE systems

The Cell Broadband Engine Architecture (CBEA) is an heterogeneous multiprocessor architecture developed by Sony, Toshiba and IBM. The major implementation of this architecture is the Cell Broadband Engine (Cell for short), a processor that contains one generic PowerPC core and eight accelerators. The Cell is targeted at high-performance computing systems and consumer-level devices that have high computational requirements. The workloads for the former are generally run in a queue-based environment while those for the latter are multiprogrammed.
GENERALIZED COHERENT RISK MEASURES IN DECISION-MAKING UNDER RISK

Coherent risk measures have lately become a hot topic in both theoretical research and practical applications. Since they possess a number of disadvantages, some generalizations and modifications have been proposed recently. In the present paper we propose one more generalization which holds a number of attractive properties. A representation theorem for the risk measures class has been obtained, properties of functionals have been established, partial cases and examples are also presented.
Living at high altitude and risk of hospitalisation for atopic asthma in children: results from a large prospective birth-cohort study

Background: Asthma is among the most common chronic diseases in childhood and is steadily increasing in prevalence. Better characterisation of factors that determine the risk of hospitalisation for atopic asthma in childhood may help design prevention programmes and improve our understanding of disease pathobiology. This study will focus on the altitude of residence. Methods: This is an ongoing prospective birth-cohort study that enrolled all live-born infants in the Tyrol. Between 1994 and 1999, baseline data were collected for 33 808 infants. From 2000 to 2005, all children hospitalised for atopic asthma at the age of ⩾6 years (n = 305) were identified by a careful search of hospital databases. Disease status was ascertained from the typical medical history, a thorough examination and proof of atopy. Results: Living at higher altitude was associated with an enhanced risk of hospitalisation for atopic asthma (multivariate RRs (95% confidence interval 2.08 (1.45 to 2.98) and 1.49 (1.05 to 2.11) for a comparison between altitude categories ⩾1200 m and 900–1199 m versus <900 m; p<0.001). This finding applied equally to hospital admissions in spring, summer, autumn and winter. When altitude of residence was analysed as a continuous variable, the risk for asthma hospitalisation increased by 7% for each 100-m increase in altitude (p = 0.013). Conclusions: This large prospective study shows a significant association between the risk of hospitalisation for atopic asthma and altitude of residence between 450 and 1800 m. The underlying mechanisms remain to be elucidated, but it is tempting to speculate about a role for altitude characteristics such as the decline in outdoor temperature and air humidity and increase in ozone levels, which may trigger airway hyper-responsiveness and attenuate lung function.
Photothermal killing of Staphylococcus aureus using antibody-targeted gold nanoparticles

Purpose The continued emergence of multidrug resistant bacterial infections and the decline in discovery of new antibiotics are major challenges for health care throughout the world. This situation has heightened the need for novel antimicrobial therapies as alternatives to traditional antibiotics. The combination of metallic nanoparticles and laser exposure has been proposed as a strategy to induce physical damage to bacteria, regardless of antibiotic sensitivity. The purpose of this study was to test the antibacterial effect of antibody-targeted gold nanoparticles combined with pulsed laser irradiation. Methods Gold nanoparticles conjugated to antibodies specific to Staphylococcus aureus peptidoglycan were incubated with suspensions of methicillin-resistant and methicillin-sensitive S. aureus (MRSA and MSSA). Bacterial suspensions were then exposed to 8 ns pulsed laser irradiation at a wavelength of 532 nm and fluences ranging from 1 to 5 J/cm2. Viability of the bacteria following laser exposure was determined using colony forming unit assays. Scanning electron microscopy was used to confirm the binding of nanoparticles to bacteria and the presence of cellular damage. Results The laser-activated nanoparticle treatment reduced the surviving population to 31% of control in the MSSA population, while the survival in the MRSA population was reduced to 58% of control. Significant decreases in bacterial viability occurred when the laser fluence exceeded 1 J/cm2, and this effect was linear from 0 to 5 J/cm2 (r2=0.97). Significantly less bactericidal effect was observed for nonfunctionalized nanoparticles or functionalized nanoparticles without laser activation. Conclusion Laser-activated nanoparticles targeted to S. aureus surface antigens significantly reduced the percentage of viable organisms and represents a promising new treatment modality that could be used either alone or as an adjunct to existing, conventional antibiotic therapy.
How does increased fire frequency affect carbon loss from fire? A case study in the northern boreal forest

Fire frequency is expected to increase due to climate warming in many areas, particularly the boreal forests. Anincreaseinfirefrequencymayhaveimportanteffectsontheglobalcarboncyclebydecreasingthesizeofborealcarbon stores. Our objective was to quantify and compare the amount of carbon consumed during and the amount of carbon remaining following fire in black spruce (Picea mariana (Mill.) BSP) forests burned after long v. short intervals. We hypothesised that stands with a shortened fire return interval would have a higher carbon consumption than those experiencing a historically typical fire return interval. Using field measurements of forest canopy, soil organic horizons andadventitiousroots,wereconstructedpre-firestandconditionstoestimatethebiomasslostineachfireandtheeffectson post-fireresidualcarbonstores.Wefoundevidenceofahigherlossofcarbonfollowingtwofireeventsthatrecurredaftera short interval, resulting in a much greater total reduction in carbon relative to pre-fire or mature stand conditions. Consequently, carbon storage across disturbance intervals was dramatically reduced following short-interval burns. Recovery of these stores would require a subsequent lengthening of the fire cycle, which appears unlikely under future climate scenarios. Additional keywords: adventitious root method, biomass, fire return interval, soil organic layer, Yukon.
Distinguishing Opinion from News

Newspapers have separate sections for opinion articles and news articles. The goal of this project is to classify articles as opinion versus news and also to do analysis of the results to figure out the factors that distinguish the two. Preliminary results show that classification is possible with unigram features in an SVM with F1 of . 94. Introduction This project focuses on subjectivity classification for news articles. Much prior work on subjectivity has focused on distinguishing positive and negative sentiment (for instance, in product reviews) or classifying phrases or clauses as subjective (Liu, 2008). Here we attempt to distinguish entire articles as reporting news or expressing opinion. The task is related but has some key differences. For instance, review-type sentiment analysis often relies on pre-made lexicons or focuses on classifying words as positive or negative (Toprak and Gurevych, 2009; Turney and Littman, 2010; Potts). Words associated with positivity and negativity are not necessarily those associated with editorials and opinion pieces in which authors pose sophisticated arguments about current events, policies, etc. One goal of the project was to gain a lexical understanding of words that can distinguish the two categories, and thus be able to generate a lexicon similar those already existing for sentiment analysis of reviews that would work for articles. Prior Work There has been thorough research into document classification. "Machine Learning in Automated Text Categorization" (Sebastiani, 2003) provides an overview of work up to 2002. Within the area of subjectivity/sentiment analysis there is also a wide variety of work. Pang and Lee give an overview of the field of subjectivity (Pang and Lee, 2008). Liu defines many different problems within the field including sentiment and subjectivity classification: (1) classifying an opinionated document as expressing a positive or negative opinion, and (2) classifying a sentence or a clause of the sentence as subjective or objective (Liu, 2010) Liu also gives an overview of the field thus far from a teaching perspective. Turney and Littman provide a method for sentiment for particular words based on their context (Turney and Littman, 2003). Yu and Hatzivassiloglou specifically address distinguishing opinion from news using a Naive Bayes classifier and are able to achieve very high results (Yu and Hatzivassiloglou, 2003). However, their method did not generalize to my dataset. Data I use two datasets, both consisting of articles from the New York Times. The primary dataset consists of 140 articles over the course of the 7 years up to and including 2012. For comparison, I also test on a dataset of articles from October and November 2012 in which news events are covered repeatedly. The data was collected by scraping the New York Times website. The first
Evolution of signal form

We trained chickens to react to an average human female face but not to an average male face (or vice versa). In a subsequent test, the animals showed preferences for faces consistent with human sexual preferences (obtained from university students). This suggests that human preferences arise from general properties of nervous systems, rather than from face-specific adaptations. We discuss this result in the light of current debate on the meaning of sexual signals and suggest further tests of existing hypotheses about the origin of sexual preferences.
Pose Estimation and Segmentation of People in 3D Movies

We seek to obtain a pixel-wise segmentation and pose estimation of multiple people in a stereoscopic video. This involves challenges such as dealing with unconstrained stereoscopic video, non-stationary cameras, and complex indoor and outdoor dynamic scenes. The contributions of our work are two-fold: First, we develop a segmentation model incorporating person detection, pose estimation, as well as colour, motion, and disparity cues. Our new model explicitly represents depth ordering and occlusion. Second, we introduce a stereoscopic dataset with frames extracted from feature-length movies "Street Dance 3D" and "Pina". The dataset contains 2727 realistic stereo pairs and includes annotation of human poses, person bounding boxes, and pixel-wise segmentations for hundreds of people. The dataset is composed of indoor and outdoor scenes depicting multiple people with frequent occlusions. We demonstrate results on our new challenging dataset, as well as on the H2view dataset from (Sheasby et al. ACCV 2012).
Efficient Automatic Resolution of Encoding Conflicts Using STG Unfoldings

Synthesis of asynchronous circuits from signal transition graphs (STGs) involves resolution of state encoding conflicts by means of refining the STG specification. In this paper, a fully automatic technique for resolving such conflicts by means of insertion of new signals is proposed. It is based on conflict cores, i.e., sets of transitions causing encoding conflicts, which are represented at the level of finite and complete unfolding prefixes, and a SAT solver is used to find where in the STG the transitions of new signals should be inserted. The experimental results show significant improvements over the state space based approach in terms of runtime and memory consumption, as well as some improvements in the quality of the resulting circuits.
The automatic assessment of Z specifications

The need to automate the process of assessing a specification in a learning environment is identified to be one of the fundamental ways to improve the use of formal notation in specifying a real system. General issues involved in building an automatic marking system for computer-based courses are explored. Techniques that have been proposed for assessing a specification are also discussed. By considering the issues and the techniques, we describe how they can be used to build a system that is able to give a quality grade to a specification that is written in the Z language. In the system, four quality factors are taken into consideration; maintainability of a specification (which considers the typographic arrangement of a specification and the specification complexity), and correctness of a specification (which reflects the static correctness and the dynamic correctness of a specification). By using suitable quality metrics for specification maintainability, the results that are produced are compared to some values which can either be absolute values or relative to the model answer. The marks awarded for this factor are based on this comparison. Static correctness is carried out by applying a syntax and type checker. The marks granted for this factor depend on the outcome of the checker. Dynamic correctness is determined by employing a testing technique. In the context of a specification, the behaviour of a system-state, which is represented by so-called state variables, is analysed. The specification is 'executed' by using animation. The marks are given according to the correctness of the output and the final state. The system is implemented within the well-known courseware management system, Ceilidh. There are fundamental differences between Z specifications, and the subject matter of other courses taught using the Ceilidh system (which are mostly computer programming courses). For this reason we take some time in this thesis to explain (in some detail) the incorporation of the system within Ceilidh. The need for the fundamental components (i.e the editor, the syntax and type checker, the animator and the automatic marker) are discussed and described. The system has been used by a group of 13 students who attended a Z course within the School of Computer Science and Information Technology at the University of Nottingham during the 1997-1998 academic year. The students were given a questionnaire about the system. An analysis of these questionnaires shows that the currently implemented tools are beneficial and helpful to the students. We also test the results of the system and compare them with a small selected group of human markers. The testing reveals very encouraging results and shows that the system can mark student scripts with a good degree of accuracy. We conclude that this system can provide a very useful aid for teachers of the Z Specification language.