Miracle-dz/UniFAR-FTUs huggingface dataset:
The Thoughtful Researcher: Teaching the Research Process to Middle School Students

How are students to become question generators, note takers, efficient planners, critical users of information, and creators of quality products? This book takes an instructional approach with a broad range of activities that can be used to develop these qualities in students. Moving beyond the usual theoretical discussions of the research process, Rankin provides learning activities to help middle and junior high students develop the skills necessary to carry out the steps of the research process. She also explores the roles of time management and the visual display of information and she outlines techniques that can help practitioners reach their own insights and conclusions about teaching the research process. Rankin's straightforward text is illustrated with numerous anecdotes and examples which make for a practical and fascinating read.
Do Lenders Favor Politically Connected Firms? Rent Provision in an Emerging Financial Market

Corruption by the politically connected is often blamed for economic ills, particularly in less developed economies. Using a loan-level data set of more than 90,000 firms that represents the universe of corporate lending in Pakistan between 1996 and 2002, we investigate rents to politically connected firms in banking. Classifying a firm as "political" if its director participates in an election, we examine the extent, nature, and economic costs of political rent provision. We find that political firms borrow 45 percent more and have 50 percent higher default rates. Such preferential treatment occurs exclusively in government banks—private banks provide no political favors. Using firm fixed effects and exploiting variation for the same firm across lenders or over time allows for cleaner identification of the political preference result. We also find that political rents increase with the strength of the firm's politician and whether he or his party is in power, and fall with the degree of electoral participation in his constituency. We provide direct evidence against alternative explanations such as socially motivated lending by government banks to politicians. The economy-wide costs of the rents identified are estimated to be 0.3 to 1.9 percent of GDP every year.
Numerical simulation of acoustic streaming within the cochlea

This paper is concerned with the numerical examination of acoustically driven flows within the inner ear on the basis of a computational model. For this purpose, a comprehensive system of differential equations and boundary conditions is deduced, which takes, to a satisfactory extent, the complexity of the main biophysical mechanisms of the cochlea into account. Beside an appropriate representation of the fluid dynamics, also the biomechanical properties of the basilar membrane as well as the internal amplification mechanism caused by the outer hair cell motility are considered in order to get realistic estimates of the structure and magnitude of the mean flow field. The present paper introduces a two-stage approach for the numerical evaluation of the solutions on the basis of the finite element method. The first step deals with the calculation of the linear acoustic reaction whereas the second step is associated with the determination of a first-order approximation of the acoustic streaming field. It is shown that the results are essentially consistent with measurements as well as analytical and experimental considerations. In addition, the numerical estimates of the acoustically driven flows provide an instrument for a more profound discussion on their physiological impact.
Precision measurements of large scale structure with future type Ia supernova surveys

Type Ia supernovae are currently the best known standard candles at cosmological distances. In addition to providing a powerful probe of dark energy they are an ideal source of information about the peculiar velocity field of the local universe. Even with the very small number of supernovae presently available it has been possible to measure the dipole and quadrupole of the local velocity field out to z∼0.025. With future continuous all-sky surveys like the Large Synoptic Survey Telescope (LSST) project the luminosity distances of tens of thousands of nearby supernovae will be measured accurately. This will allow for a determination of the local velocity structure of the universe as a function of redshift with unprecedented accuracy, provided the redshifts of the host galaxies are known. Using catalogues of mock surveys we estimate that future low redshift supernova surveys will be able to probe σ8 to a precision of roughly 5% at 95% C.L. This is comparable to the precision in future galaxy and weak lensing surveys, and with a relatively modest observational effort it will provide a crucial cross-check on future measurements of the matter power spectrum.
Mural Crohn disease: correlation of dynamic contrast-enhanced MR imaging findings with angiogenesis and inflammation at histologic examination--pilot study.

PURPOSE To determine mural perfusion dynamics in Crohn disease by using dynamic contrast material-enhanced magnetic resonance (MR) imaging and to correlate these with histopathologic markers of inflammation and angiogenesis. MATERIALS AND METHODS Ethical permission was given by the University College London Hospital ethics committee, and informed consent was obtained from all participants. Eleven consecutive patients with Crohn disease (eight female patients, three men; mean age, 39.5 years; range, 16.4-66.6 years) undergoing elective small-bowel resection were recruited between July 2006 and December 2007. Harvey-Bradshaw index, C-reactive protein (CRP) level, and disease chronicity were recorded. Preoperatively, dynamic contrast-enhanced MR imaging was performed through the section of bowel destined for resection, and slope of enhancement, time to maximum enhancement, enhancement ratio, the volume transfer coefficient K(trans), and the extracellular volume fraction v(e) were calculated for the affected segment. Ex vivo surgical specimens were imaged to facilitate imaging-pathologic correlation. Histopathologic sampling of the specimen was performed through the imaged tissue, and microvascular density (MVD) was determined, together with acute and chronic inflammation scores. Correlations between clinical, MR imaging, and histopathologic data were made by using the Kendall rank correlation and linear regression. RESULTS Disease chronicity was positively correlated with enhancement ratio (correlation coefficient, 0.82; P = .002). Slope of enhancement demonstrated a significant negative correlation with MVD (correlation coefficient, -0.86; P < .001). There was a negative correlation between CRP level and slope of enhancement (correlation coefficient, -0.77; P = .006). Neither acute nor chronic inflammation score correlated with any other parameter. CONCLUSION Certain MR imaging-derived mural hemodynamic parameters correlate with disease chronicity and angiogenesis in Crohn disease, but not with histologic and clinical markers of inflammation. Data support the working hypothesis that microvessel permeability increases with disease chronicity and that tissue MVD is actually inversely related to mural blood flow.
Inspiring Change: Exercise Self-Efficacy, Dispositional Optimism, and Perceived Stress in College Seniors

Inspiring Change: Exercise Self-Efficacy, Dispositional Optimism, and Perceived Stress in College Seniors by Joshua M. Garrin MS, Pace University, 1998 BS, State University of New York at New Paltz, 1993 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy
Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity

Short-chain alkanes play a substantial role in carbon and sulfur cycling at hydrocarbon-rich environments globally, yet few studies have examined the metabolism of ethane (C2), propane (C3), and butane (C4) in anoxic sediments in contrast to methane (C1). In hydrothermal vent systems, short-chain alkanes are formed over relatively short geological time scales via thermogenic processes and often exist at high concentrations. The sediment-covered hydrothermal vent systems at Middle Valley (MV, Juan de Fuca Ridge) are an ideal site for investigating the anaerobic oxidation of C1–C4 alkanes, given the elevated temperatures and dissolved hydrocarbon species characteristic of these metalliferous sediments. We examined whether MV microbial communities oxidized C1–C4 alkanes under mesophilic to thermophilic sulfate-reducing conditions. Here we present data from discrete temperature (25, 55, and 75°C) anaerobic batch reactor incubations of MV sediments supplemented with individual alkanes. Co-registered alkane consumption and sulfate reduction (SR) measurements provide clear evidence for C1–C4 alkane oxidation linked to SR over time and across temperatures. In these anaerobic batch reactor sediments, 16S ribosomal RNA pyrosequencing revealed that Deltaproteobacteria, particularly a novel sulfate-reducing lineage, were the likely phylotypes mediating the oxidation of C2–C4 alkanes. Maximum C1–C4 alkane oxidation rates occurred at 55°C, which reflects the mid-core sediment temperature profile and corroborates previous studies of rate maxima for the anaerobic oxidation of methane (AOM). Of the alkanes investigated, C3 was oxidized at the highest rate over time, then C4, C2, and C1, respectively. The implications of these results are discussed with respect to the potential competition between the anaerobic oxidation of C2–C4alkanes with AOM for available oxidants and the influence on the fate of C1 derived from these hydrothermal systems.
Atmosphere, ecology and evolution: what drove the Miocene expansion of C4 grasslands?

1 Grasses using the C4 photosynthetic pathway dominate today's savanna ecosystems and account for ~20% of terrestrial carbon fixation. However, this dominant status was reached only recently, during a period of C4 grassland expansion in the Late Miocene and Early Pliocene (4–8 Myr ago). Declining atmospheric CO2 has long been considered the key driver of this event, but new geological evidence casts doubt on the idea, forcing a reconsideration of the environmental cues for C4 plant success. 2 Here, I evaluate the current hypotheses and debate in this field, beginning with a discussion of the role of CO2 in the evolutionary origins, rather than expansion, of C4 grasses. Atmospheric CO2 starvation is a plausible selection agent for the C4 pathway, but a time gap of around 10 Myr remains between major decreases in CO2 during the Oligocene, and the earliest current evidence of C4 plants. 3 An emerging ecological perspective explains the Miocene expansion of C4 grasslands via changes in climatic seasonality and the occurrence of fire. However, the climatic drivers of this event are debated and may vary among geographical regions. 4 Uncertainty in these areas could be reduced significantly by new directions in ecological research, especially the discovery that grass species richness along rainfall gradients shows contrasting patterns in different C4 clades. By re‐evaluating a published data set, I show that increasing seasonality of rainfall is linked to changes in the relative abundance of the major C4 grass clades Paniceae and Andropogoneae. I propose that the explicit inclusion of these ecological patterns would significantly strengthen climate change hypotheses of Miocene C4 grassland expansion. Critically, they allow a new series of testable predictions to be made about the fossil record. 5 Synthesis. This paper offers a novel framework for integrating modern ecological patterns into theories about the geological history of C4 plants.
Presence of hpv 16 sequences in laryngeal carcinomas

Human papillomavirus types HPV 16 and HPV II DNA sequences were analyzed in normal and neoplastic tissues of the larynx, using the technique of polymerase chain reaction (PCR). An amplified region of E6 ORF was hybridized with 3′ end‐labelled oligonucleotide probe. Twenty six out of 48 (54%) squamous‐cell carcinomas, and 3 out of 3 verrucous‐cell carcinomas hybridized with HPV 16 DNA sequences, whereas we did not detect HPV II sequences. HPV 16 DNA sequences were also found in normal, autologous mucosa and lymphnode metastases, although these were absent in other tissues analyzed. HPV‐16‐positive tumors were most frequently poorly differentiated squamous‐cell carcinomas.
Molecular mechanisms of activation of endothelial nitric oxide synthase mediated by transient receptor potential vanilloid type 1.

AIMS We investigated the molecular mechanism underlying the role of transient receptor potential vanilloid type 1 (TRPV1), a Ca(2+)-permeable non-selective cation channel, in the activation of endothelial nitric oxide (NO) synthase (eNOS) in endothelial cells (ECs) and mice. METHODS AND RESULTS In ECs, TRPV1 ligands (evodiamine or capsaicin) promoted NO production, eNOS phosphorylation, and the formation of a TRPV1-eNOS complex, which were all abrogated by the TRPV1 antagonist capsazepine. TRPV1 ligands promoted the phosphorylation of Akt, calmodulin-dependent protein kinase II (CaMKII) and TRPV1, and increased the formation of a TRPV1-Akt-CaMKII complex. Removal of extracellular Ca(2+) abolished the ligand-induced increase in the phosphorylation of Akt and CaMKII, formation of a TRPV1-eNOS complex, and eNOS activation. Inhibition of PI3K and CaMKII suppressed the ligand-induced increase in TRPV1 phosphorylation, formation of a TRPV1-eNOS complex, and eNOS activation. TRPV1 activation increased the phosphorylation of Akt, CaMKII, and eNOS in the aortas of wild-type mice but failed to activate eNOS in TRPV1-deficient aortas. Additionally, TRPV1 ligand-induced angiogenesis was diminished in eNOS- or TRPV1-deficient mice. When compared with apolipoprotein E (ApoE)-deficient mice, ApoE/TRPV1-double-knockout mice displayed reduced phosphorylation of eNOS, Akt, and CaMKII in aortas but worsened atherosclerotic lesions. CONCLUSION TRPV1 activation in ECs may trigger Ca(2+)-dependent PI3K/Akt/CaMKII signalling, which leads to enhanced phosphorylation of TRPV1, increased TRPV1-eNOS complex formation, eNOS activation and, ultimately, NO production.
Heritable variation in bleaching responses and its functional genomic basis in reef‐building corals (Orbicella faveolata)

Reef‐building corals are highly sensitive to rising ocean temperatures, and substantial adaptation will be required for corals and the ecosystems they support to persist in changing ocean conditions. Genetic variation that might support adaptive responses has been measured in larval stages of some corals, but these estimates remain unavailable for adult corals and the functional basis of this variation remains unclear. In this study, we focused on the potential for adaptation in Orbicella faveolata, a dominant reef‐builder in the Caribbean. We conducted thermal stress experiments using corals collected from natural populations in Bocas del Toro, Panama, and used multilocus SNP genotypes to estimate genetic relatedness among samples. This allowed us to estimate narrow‐sense heritability of variation in bleaching responses, revealing that variation in these responses was highly heritable (h2 = 0.58). This suggests substantial potential for adaptive responses to warming by natural populations of O. faveolata in this region. We further investigated the functional basis for this variation using genomic and transcriptomic approaches. We used a publicly available genetic linkage map and genome assembly to map markers associated with bleaching responses, identifying twelve markers associated with variation in bleaching responses. We also profiled gene expression in corals with contrasting bleaching phenotypes, uncovering substantial differences in transcriptional stress responses between heat‐tolerant and heat‐susceptible corals. Together, our findings contribute to the growing body of evidence that natural populations of corals possess genetic variation in thermal stress responses that may potentially support adaptive responses to rising ocean temperatures.
Starting simple: adding value to static visualisation through simple interaction

Interactive visualisation has been one of the most exciting areas in HCI over recent years. The key term here is 'interactive', and in this paper we assert that virtually any static representation can become more powerful by the addition of simple interactive elements. This is demonstrated by adding interactivity to standard representations including stacked histograms, pie charts and scatter plots. We show how adding interactivity can help resolve many of the trade-offs inherent in static visualisations by allowing multiple options to be available and most importantly for them to be interactively related. Many years of creativity and effort have been invested in traditional generic and bespoke visualisations. Adding interactivity leverages this accumulated experience, but also adds an extra dimension.
Kernel Belief Propagation

We propose a nonparametric generalization of belief propagation, Kernel Belief Propagation (KBP), for pairwise Markov random fields. Messages are represented as functions in a reproducing kernel Hilbert space (RKHS), and message updates are simple linear operations in the RKHS. KBP makes none of the assumptions commonly required in classical BP algorithms: the variables need not arise from a finite domain or a Gaussian distribution, nor must their relations take any particular parametric form. Rather, the relations between variables are represented implicitly, and are learned nonparametrically from training data. KBP has the advantage that it may be used on any domain where kernels are defined (R d , strings, groups), even where explicit parametric models are not known, or closed form expressions for the BP updates do not exist. The computational cost of message updates in KBP is polynomial in the training data size. We also propose a constant time approximate message update procedure by representing messages using a small number of basis functions. In experiments, we apply KBP to image denoising, depth prediction from still images, and protein configuration prediction: KBP is faster than competing classical and nonparametric approaches (by orders of magnitude, in some cases), while providing significantly more accurate results.
Deficient responses from the lateral geniculate nucleus in humans with amblyopia

Amblyopia or lazy eye is the most common cause of uniocular blindness in adults. It is caused by a disruption to normal visual development as a consequence of unmatched inputs from the two eyes in early life, arising from a turned eye (strabismus), unequal refractive error (anisometropia) or form deprivation (e.g. cataract). Animal models based on extracellular recordings in anesthetized animals suggest that the earliest site of the anomaly in the primate visual pathway is the primary visual cortex (corresponding to the striate cortex, cytoarchitectonic area 17 and area V1), which is where inputs from the two eyes are first combined in an excitatory fashion, whereas more distal and monocular processing structures such as the retina and lateral geniculate nucleus (LGN) are normal. Using high‐field functional magnetic resonance imaging in a group of human adults with amblyopia, we demonstrate that functional deficits are first observable at a thalamic level, that of the LGN. Our results suggest the need to re‐evaluate the current models of amblyopia that are based on the assumption of a purely cortical dysfunction, as well as the role for the LGN in visual development.
Optically Levitating Dielectrics in the Quantum Regime: Theory and Protocols

We provide a general quantum theory to describe the coupling of light with the motion of a dielectric object inside a high-finesse optical cavity. In particular, we derive the total Hamiltonian of the system as well as a master equation describing the state of the center-of-mass mode of the dielectric and the cavity-field mode. In addition, a quantum theory of elasticity is used to study the coupling of the center-of-mass motion with internal vibrational excitations of the dielectric. This general theory is applied to the recent proposal of using an optically levitating nanodielectric as a cavity optomechanical system [see Romero-Isart et al., New J. Phys. 12, 033015 (2010); Chang et al., Proc. Natl. Acad. Sci. USA 107, 1005 (2010)]. On this basis, we also design a light-mechanics interface to prepare non-Gaussian states of the mechanical motion, such as quantum superpositions of Fock states. Finally, we introduce a direct mechanical tomography scheme to probe these genuine quantum states by time-of- flight experiments.
Developing severity adjusted quality measures for intensive care units.

PURPOSE Intensive care unit performance evaluation is usually affected by variations in the severity of inpatients' health status. This paper aims, therefore, to standardize two performance measures: intensive care unit survival and length of stay using the Acute Physiology and Chronic Health Evaluation II (APACHE II) severity of illness score. DESIGN/METHODOLOGY/APPROACH A records study in three Ain Shams University Hospital intensive care units, from January 1-December 31, 2003 was carried out to examine illness severity effect using APACHE II, length of stay and survival. Retrospective data were used to model length of stay in days and the survival using the APACHE II score as a predictor. This was followed by a prospective study to monitor the standardized measures in two intensive care units for one year. FINDINGS APACHE II scores predicted length of stay of those who were discharged and control charts for severity-adjusted length of stay were drawn up. The APACHE II score predicted survival for those with APACHE II score >16. The model is significant with a specificity of 89.9 percent while sensitivity was 25 percent. Control charts for severity-adjusted mortality were drawn up to monitor mortality. RESEARCH LIMITATIONS/IMPLICATIONS Only 60 percent of the files examined in the retrospective part of the study had enough data to calculate APACHE II scores. PRACTICAL IMPLICATIONS Standardized APACHE II severity of illness score can monitor intensive care unit length of stay and mortality. ORIGINALITY/VALUE The paper underlines the need to implement a standardized measurement system to evaluate intensive care patient outcomes.