Miracle-dz/UniFAR-FTUs huggingface dataset:
Joint intensity-and-point based registration of free-hand B-mode ultrasound and MRI of the carotid artery.

PURPOSE To introduce a semiautomatic algorithm to perform the registration of free-hand B-Mode ultrasound (US) and magnetic resonance imaging (MRI) of the carotid artery. METHODS The authors' approach combines geometrical features and intensity information. The only user interaction consists of placing three seed points in US and MRI. First, the lumen centerlines are used as landmarks for point based registration. Subsequently, in a joint optimization the distance between centerlines and the dissimilarity of the image intensities is minimized. Evaluation is performed in left and right carotids from six healthy volunteers and five patients with atherosclerosis. For the validation, the authors measure the Dice similarity coefficient (DSC) and the mean surface distance (MSD) between carotid lumen segmentations in US and MRI after registration. The effect of several design parameters on the registration accuracy is investigated by an exhaustive search on a training set of five volunteers and three patients. The optimum configuration is validated on the remaining images of one volunteer and two patients. RESULTS On the training set, the authors achieve an average DSC of 0.74 and a MSD of 0.66 mm on volunteer data. For the patient data, the authors obtain a DSC of 0.77 and a MSD of 0.69 mm. In the independent set composed of patient and volunteer data, the DSC is 0.69 and the MSD is 0.87 mm. The experiments with different design parameters show that nonrigid registration outperforms rigid registration, and that the combination of intensity and point information is superior to approaches that use intensity or points only. CONCLUSIONS The proposed method achieves an accurate registration of US and MRI, and may thus enable multimodal analysis of the carotid plaque.
IL-18-based combinatorial adjuvants promote the intranodal production of CCL19 by NK cells and dendritic cells of cancer patients

The effective accumulation and interaction of mature dendritic cells (DCs) and naïve T cells within lymph nodes (LNs), which are driven by the CCR7-CCL19/CCL21 chemokine axis, are critical for the induction of adaptive T-cell immunity. Human natural killer (NK) cells activated by interleukin (IL)-18 exhibit a unique ‘helper’ activity in promoting productive DC-T cell interactions, inducing DC maturation and shifting DC-primed T-cell responses toward a TH1 polarization. Here, we demonstrate that such IL-18-activated ‘helper’ NK cells uniquely stimulate DCs to produce high levels of CCL19 through tumor necrosis factor α (TNFα) and interferon γ (IFNγ), a process that relies on secondary NK-cell activation by additional inflammatory signals including IFNα, IL-15, IL-12 and IL-2. DCs activated by helper NK cells not only promote the efficient CCR7-mediated recruitment of naïve CD8+ T cells, but also stimulate their expansion and expression of granzyme B. Using an ex vivo explant culture system based on LNs isolated from colorectal cancer patients, we found that CCL19 is upregulated in human tumor-associated lymphoid tissues treated with helper NK cell-stimulating factors. Our findings demonstrate the ability of 2 signal-activated helper NK cells to promote the production of the DC- and naïve/memory T cell-attracting chemokine CCL19 in LNs, and provide a rationale for the therapeutic application of IL-18-containing ‘combinatorial adjuvants’ to facilitate the induction of antitumor immune responses.
Role of herpes simplex and cytomegalo viruses in recalcitrant oral lesions of pemphigus vulgaris

, 256–257 © 2004 The International Society of Dermatology 256 Propafenone-induced acute generalized exanthematous pustulosis An 85-year-old man was hospitalized as a result of a generalized cutaneous eruption. He had a history of chronic obstructive pulmonary disease treated with oral and inhalation bronchodilators, including procaterol, salmeterol, aminophylline and the inhalation corticosteroid budesonide for more than 15 years. In addition, he had been on oral digoxin 0.25 mg per day for impaired cardiac function routinely for about 10 years. Seven days prior to admission, he was given propafenone 75 mg three times daily for paroxysmal atrial fibrillation. Five days after taking propafenone, multiple erythematous papules and pustules developed, and he was therefore hospitalized. On physical examination, confluent papules and some targetoid erythema multiforme-like plaques (Fig. 1a) were seen on the trunk and lower extremities. Many distinctive nonfollicular pustules coalescing to produce extensive separation of the epidermis were also found on the groin and thighs (Fig. 1b). No oral, conjunctival mucosa or genital lesions were noted. He denied any personal history of psoriasis or contact with mercury. His white blood cell count was elevated to 18,000 cells/mm 3 with 96% neutrophils on admission. Bacterial and fungal cultures of pustules were negative. Histology of a biopsy (Fig. 2) taken from pustular lesions on the right thigh showed intraepidermal spongiosis and microabscess formation with prominent neutrophil aggregations. Furthermore, lymphocytes and occasional neutrophils were found to scatter through the edematous papillary dermis involved. Based on the clinicopathological findings, acute generalized exanthematous pustulosis was diagnosed. The patient was then treated with intravenous hydrocortisone 100 mg four times a day. After discontinuing all his oral medications, the acute eruption dramatically resolved within 3 days, followed by postinflammatory desquamations. There has been no recurrence at 6 months follow-up. Acute generalized exanthematous pustulosis (AGEP) is a cutaneous reaction pattern, exclusively accompanied by fever with neutrophilia and characterized by the acute onset of eruption with numerous small nonfollicular sterile pustules overlying an erythematous and edematous background. 2
Perceptual Importance of the Phase Related Information in Speech

The importance of phase information in the perceptual quality of the speech signals is studied in this paper. Many speech synthesisers do not use the original phase information of the signals assuming their contribution is almost inaudible. The Relative Phase Shift (RPS) representation of the phase allows straightforward phase structure analysis, manipulation and resynthesis, and we use these features to do a comparative evaluation of some phase modifications usually found in speech models. The final intention of this study is to get an answer to the question of whether phases deserve elaborate models to get high quality synthetic speech, or their subtle effects justify overlooking them.
Social Integration, Social Support and Mortality in the US National Health Interview Survey

Background Social relationship quantity and quality are associated with mortality, but it is unclear whether each relationship dimension is equally important for longevity and whether these associations are sensitive to baseline health status. Methods This study examined the individual and joint associations of relationship quantity (measured using a social integration score) and quality (measured by perceived social support) with mortality in a representative US sample (n = 30,574). The study also evaluated whether these associations were consistent across individuals with and without diagnosed chronic illness and whether they were independent of socioeconomic status (SES; education, income, employment, and wealth). Baseline data were collected in 2001 and were linked to vital status records 5 years later (1836 deaths). Results Both social integration and social support were individually related to mortality (hazard ratios [HRs] = 0.83 [95% confidence interval {CI} = 0.80–0.85] and HR = 0.94 [95% CI = 0.89–0.98], respectively). However, in multivariate models including demographic and SES variables, social integration (HR = 0.86, 95% CI = 0.83–0.89) but not social support (HR = 1.03, 95% CI = 0.98–1.08) was associated with mortality. The social integration association was linear and consistent across baseline health status and men and women. Conclusions Social integration but not social support was independently associated with mortality in the US sample. This association was consistent across baseline health status and not accounted for by SES.
Normalization and Differential Gene Expression Analysis of Microarray Data

DNA microarray technologies have the capability of simultaneously measuring the abundance of thousands of mRNA-sequences. Analysis of microarray data involves many different steps such as image analysis, background correction, and normalization, but also more classical statistical analysis such as testing for significant differences between groups of arrays. The work presented in this thesis is focused on Affymetrix GeneChip arrays and deals with normalization and the problem of finding differentially expressed genes. Normalization of microarray data is essential to allow between-array comparisons. A procedure called Contrast Normalization is proposed and compared with existing methods together with two additional presented methods, Cyclic-Loess and Quantile Normalization. All three presented methods improve on the performance of the existing methods with a slight edge for Quantile Normalization. The quality of microarray data often varies between arrays. A model called WAME has been proposed, using a global covariance matrix to account for differing variances and array-to-array correlations, and thus WAME defines a weighted analysis for finding differentially expressed genes. This thesis presents two new methods for estimating the covariance matrix. Both methods show superior computer run-time over the existing method. Moreover, the second proposed method greatly reduces the bias of the existing method when used on simulated data with regulated genes, although to a less degree for real data with many regulated genes. Microarray data frequently shows a dependency between variability and intensity level which is ignored by the majority of moderated t-tests. The WAME model is extended to incorporate this dependency, and two locally moderated t-tests are proposed, Probe level Locally moderated Weighted median-t (PLW), and Locally Moderated Weighted-t (LMW). When compared with 12 existing methods on 5 spike-in data sets, the PLW method produces the most accurate ranking of regulated genes in 4 out of the 5 data sets, whereas LMW consistently performs better than all (globally) moderated t-tests.
Creating Resilient IT: How the Sign-Out Sheet Shows Clinicians Make Healthcare Work

Information technology (IT) systems have been described as brittle and prone to automation surprises. Recent reports of information system failure, particularly computerized physician order entry (CPOE) systems, shows the result of such IT failure in actual practice. Such mismatches with healthcare work requirements require improvement to IT research and development. Resilience is the feature of some systems that makes it possible for them to respond to sudden, unanticipated demands for performance and return to normal operation quickly, with minimum decrement in performance. Workers create resilience at healthcare's sharp end by daily confronting constraints and obstacles that need to be surmounted in order to accomplish results. The resident sign-out sheet is described as an example of resilience. Efforts to develop successful IT systems for healthcare's sharp end must incorporate properties that reflect work domain traits, as the sign-out sheet shows.
Effect of CPPU on Carbohydrate and Endogenous Hormone Levels in Young Macadamia Fruit

N-(2-Chloro-4-pyridyl)-N′-phenylurea (CPPU) is a highly active cytokinin-like plant growth regulator that promotes chlorophyll biosynthesis, cell division, and cell expansion. It also increases fruit set and accelerates fruit enlargement. However, there has been no report about the effect of CPPU on fruit development and its physiological mechanism in macadamia. In this study, we investigated the effect of CPPU treatment at early fruit development via foliar spray or raceme soaking at 20 mg·L-1 on fruit set and related physiology in macadamia. Changes in carbohydrate contents and endogenous hormones in leaves, bearing shoots and fruit were also examined. Results showed that CPPU significantly reduced young fruit drop and delayed the wave of fruit drop by 1–2 weeks. The treatment significantly decreased the contents of total soluble sugars and starch in the leaves, but increased them in the bearing shoots and total soluble sugars in the husk (pericarp) and seeds. These findings suggested that CPPU promoted carbohydrate mobilization from the leaves to the fruit. In addition, CPPU increased the contents of indole-3-acetic acid (IAA), gibberellin acid (GA3), and zeatin riboside (ZR) and decreased the abscisic acid (ABA) in the husk. Therefore, CPPU treatment reduced the early fruit drop by increasing carbohydrate availability and by modifying the balance among endogenous hormones.
Differential expression of miRNAs in response to salt stress in maize roots.

BACKGROUND AND AIMS Corn (Zea mays) responds to salt stress via changes in gene expression, metabolism and physiology. This adaptation is achieved through the regulation of gene expression at the transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) have been found to act as key regulating factors of post-transcriptional gene expression. However, little is known about the role of miRNAs in plants' responses to abiotic stresses. METHODS A custom microparaflo microfluidic array containing release version 10.1 plant miRNA probes (http://microrna.sanger.ac.uk/) was used to discover salt stress-responsive miRNAs using the differences in miRNA expression between the salt-tolerant maize inbred line 'NC286' and the salt-sensitive maize line 'Huangzao4'. Key Results miRNA microarray hybridization revealed that a total of 98 miRNAs, from 27 plant miRNA families, had significantly altered expression after salt treatment. These miRNAs displayed different activities in the salt response, and miRNAs belonging to the same miRNA family showed the same behaviour. Interestingly, 18 miRNAs were found which were only expressed in the salt-tolerant maize line, and 25 miRNAs that showed a delayed regulation pattern in the salt-sensitive line. A gene model was proposed that showed how miRNAs could regulate the abiotic stress-associated process and the gene networks coping with the stress. CONCLUSIONS Salt-responsive miRNAs are involved in the regulation of metabolic, morphological and physiological adaptations of maize seedlings at the post-transcriptional level. The miRNA genotype-specific expression model might explain the distinct salt sensitivities between maize lines.
Customizable gradual polymorphic effects for Scala

Despite their obvious advantages in terms of static reasoning, the adoption of effect systems is still rather limited in practice. Recent advances such as generic effect systems, lightweight effect polymorphism, and gradual effect checking, all represent promising steps towards making effect systems suitable for widespread use. However, no existing system combines these approaches: the theory of gradual polymorphic effects has not been developed, and there are no implementations of gradual effect checking. In addition, a limiting factor in the adoption of effect systems is their unsuitability for localized and customized effect disciplines. This paper addresses these issues by presenting the first implementation of gradual effect checking, for Scala, which supports both effect polymorphism and a domain-specific language called Effscript to declaratively define and customize effect disciplines. We report on the theory, implementation, and practical application of the system.
Impact of Student Achievement Goals on CS1 Outcomes

Achievement goals are cognitively-represented end states that individuals strive to reach in competence situations. Well-studied by educational psychologists, achievement goals are robust predictors of grades, interest, and motivation of students. In this paper, we apply achievement goal theory to measure CS1 students' achievement goals and consequent interest in CS and final exam grade. We find that students aiming for topic mastery become interested in CS and, contrary to theoretical expectations, perform well on the exam. A more complex pattern of results surrounds students who orient toward competence demonstration or normative comparison, and the link between such performance goals and outcomes is less clear. We argue for the continued appropriation of educational theory to inform our studies of CS success.
The role of laccase in prostaglandin production by Cryptococcus neoformans

Recently, it has been demonstrated that the opportunistic fungal pathogen Cryptococcus neoformans can synthesize authentic immunomodulatory prostaglandins. The mechanism by which this takes place is unclear as there is no cyclooxygenase homologue in the cryptococcal genome. In this study, we show that cryptococcal production of both PGE2 and PGF2α can be chemically inhibited by caffeic acid, resveratrol and nordihydroguaiaretic acid. These polyphenolic molecules are frequently used as inhibitors of lipoxygenase enzymes; however, blast searches of the cryptococcal genome were unable to identify any homologues of mammalian, plant or fungal lipoxygenases. Next we investigated cryptococcal laccase, an enzyme known to bind polyphenols, and found that either antibody depletion or genetic deletion of the primary cryptococcal laccase (lac1Δ) resulted in a loss of cryptococcal prostaglandin production. To determine how laccase is involved, we tested recombinant laccase activity on the prostaglandin precursors, arachidonic acid (AA), PGG2 and PGH2. Using mass spectroscopy we determined that recombinant Lac1 does not modify AA or PGH2, but does have a marked activity toward PGG2 converting it to PGE2 and 15‐keto‐PGE2. These data demonstrate a critical role for laccase in cryptococcal prostaglandin production, and provides insight into a new and unique fungal prostaglandin pathway.
Update on the Equilibrium between Liquid Fe‐Ti‐O Slags and Metallic Iron

The current work is an update on the equilibrium between a synthetic high titania slag and metallic iron at temperatures above the slag melting point. The experimental setup is essentially the same as previously shown in the literature, thus employing a cold crucible in a high frequency induction furnace. A new addition to the experimental setup is the temperature measurement by a spectropyrometer. The temperature measurements will give the liquidus temperature for the slags. This temperature shows a decreasing trend as the FeO content in the slag increases. 24 slags have been successfully produced with iron saturation with a FeO content ranging from 6 to 33 wt%. The slags show a clear trend and provide a solid foundation to the location of the slag‐metal equilibrium line in the investigated area. The experiments are in agreement with previously published experimental data but not with previously calculated results using thermodynamical software.
Mesoscale circulation and the surface distribution of copepods near the south Florida keys

Near-surface zooplankton samples were collected during an interdisciplinary study of biological responses to oceanographic circulation south of Looe Reef in the southern Straits of Florida (SSF) in late May 1994. Surface currents in the sampling region were monitored during the study with the University of Miami's high frequency (HF) Ocean Surface Current Radar (OSCR). HF-radar was highly effective in resolving submesoscale (<30 km) circulation patterns that would have been difficult to discern using conventional current meters and shipboard surveys, particularly in this coastal region where local circulation patterns undergo rapid temporal transitions. The present study focused on the surface abundance and distribution of copepod nauplii and copepodites. These groups generally remain in the near-surface layer, tend to behave as passive drifting particles and in the case of nauplii, are good indicators of recent egg production. Copepod nauplii and juveniles were found to be most abundant in cyclonic submesoscale eddies (SMEs; 10-12 km) that traversed the frontal-mixing zone between the Florida Current and nearshore coastal water during the field study. The region of greatest zooplankton abundance was also associated with elevated pigment fluorescence. These data suggest that the SMEs in the SSF may enhance biological productivity, probably through a combination of accumulation and retention of zooplankton and upwelling of nutrients. General distribution patterns of numerically dominant copepod taxa were determined and linked with water of Florida Current origin or nearshore coastal water.
Comparison of Statistical Population Reconstruction Using Full and Pooled Adult Age-Class Data

Background Age-at-harvest data are among the most commonly collected, yet neglected, demographic data gathered by wildlife agencies. Statistical population construction techniques can use this information to estimate the abundance of wild populations over wide geographic areas and concurrently estimate recruitment, harvest, and natural survival rates. Although current reconstruction techniques use full age-class data (0.5, 1.5, 2.5, 3.5, … years), it is not always possible to determine an animal's age due to inaccuracy of the methods, expense, and logistics of sample collection. The ability to inventory wild populations would be greatly expanded if pooled adult age-class data (e.g., 0.5, 1.5, 2.5+ years) could be successfully used in statistical population reconstruction. Methodology/Principal Findings We investigated the performance of statistical population reconstruction models developed to analyze full age-class and pooled adult age-class data. We performed Monte Carlo simulations using a stochastic version of a Leslie matrix model, which generated data over a wide range of abundance levels, harvest rates, and natural survival probabilities, representing medium-to-big game species. Results of full age-class and pooled adult age-class population reconstructions were compared for accuracy and precision. No discernible difference in accuracy was detected, but precision was slightly reduced when using the pooled adult age-class reconstruction. On average, the coefficient of variation increased by 0.059 when the adult age-class data were pooled prior to analyses. The analyses and maximum likelihood model for pooled adult age-class reconstruction are illustrated for a black-tailed deer (Odocoileus hemionus) population in Washington State. Conclusions/Significance Inventorying wild populations is one of the greatest challenges of wildlife agencies. These new statistical population reconstruction models should expand the demographic capabilities of wildlife agencies that have already collected pooled adult age-class data or are seeking a cost-effective method for monitoring the status and trends of our wild resources.