Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression of functional neurokinin-1 receptors in regenerative glands during gastric wound healing in rodents.

BACKGROUND & AIMS Although functions of the neurokinin-1 receptor have been well explored in neurogenic inflammation and immunoinflammatory responses, little is known about neurokinin-1 receptors during gastric wound healing. The aim of this study was to assess whether neurokinin-1 receptors play a role in gastric wound healing. METHODS In vitro neurokinin-1 receptor autoradiography and immunohistochemistry were performed to identify, locate, and quantify neurokinin-1 receptors during wound healing in rodents with cryoulcers in the gastric corpus and antrum. Moreover, to assess the functionality of these receptors, the effect of the neurokinin-1 receptor antagonist NKP608 on gastric wound healing was quantified in vivo in wild-type and cyclooxygenase-2(-/-) mice. RESULTS Regenerative glands of the mucosal ulcer margin of rat cryoulcers of the gastric corpus showed strong expression of neurokinin-1 receptors in binding studies between days 3 and 22, with little expression on days 29-84. In addition, strong immunoreactivity for neurokinin-1 receptors was detected on the cell membrane of these regenerative glands. Expression of neurokinin-1 receptors in regenerative glands was confirmed in the rat antrum and the mouse gastric corpus. Moreover, in vivo functional tests during gastric ulcer healing showed that cell proliferation in the regenerative epithelia of the ulcer margin was significantly decreased by NKP608 compared with placebo; furthermore, gastric ulcer healing was significantly delayed by NKP608 both in wild-type and cyclooxygenase-2(-/-) mice. CONCLUSIONS This report shows the time-limited overexpression of neurokinin-1 receptors in the mucosal repair tissue of the corpus and antrum. Our in vitro and in vivo data suggest that neurokinin-1 receptors are involved in gastric wound healing.
Negation Detection in Swedish Clinical Text

NegEx, a rule-based algorithm that detects negations in English clinical text, was translated into Swedish and evaluated on clinical text written in Swedish. The NegEx algorithm detects negations through the use of trigger phrases, which indicate that a preceding or following concept is negated. A list of English trigger phrases was translated into Swedish, taking grammatical differences between the two languages into account. This translation was evaluated on a set of 436 manually classified sentences from Swedish health records. The results showed a precision of 70% and a recall of 81% for sentences containing the trigger phrases and a negative predictive value of 96% for sentences not containing any trigger phrases. The precision was significantly lower for the Swedish adaptation than published results on the English version, but since many negated propositions were identified through a limited set of trigger phrases, it could nevertheless be concluded that the same trigger phrase approach is possible in a Swedish context, even though it needs to be further developed.
High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers.

BACKGROUND To distinguish new primary breast cancers from true recurrences, pangenomic analyses of DNA copy number alterations (CNAs) using single-nucleotide polymorphism arrays have proven useful. METHODS The pangenomic profiles of 22 pairs of primary breast carcinoma (ductal or lobular) and ipsilateral breast cancers from the same patients were analyzed. Hierarchical clustering was performed using CNAs and DNA breakpoint information. A partial identity score developed using DNA breakpoint information was used to quantify partial identities between two tumors. The nature of ipsilateral breast cancers (true recurrence vs new primary tumor) as defined using the clustering methods and the partial identity score was compared with that based on clinical characteristics. Metastasis-free survival was compared among patients with primary tumors and true recurrences as defined using the partial identity score and by clinical characteristics. All statistical tests were two-sided. RESULTS All methods agreed on the nature of ipsilateral breast cancers for 14 pairs of samples. For five pairs, the clinical definition disagreed with both clustering methods. For three pairs, the two clustering methods were discordant and the one using DNA breakpoints agreed with the clinical definition. The partial identity score confirmed the nature of ipsilateral breast cancers as defined by clustering of DNA breakpoints in 21 of 22 pairs. The difference in metastasis-free survival of patients with new primary tumors and those with true recurrences was not statistically significant when tumors were defined based on clinical and histologic characteristics (5-year metastasis-free survival: 76%, 95% confidence interval [CI] = 52% to 100% for new primary tumors and 38%, 95% CI = 17% to 83% for true recurrences; P = .18; new primary tumor vs true recurrence, hazard ratio = 2.8, 95% CI = 0.6 to 13.7), but the difference was statistically significant when tumors were defined using the partial identity score (5-year metastasis-free survival: 100% for new primary tumors and 29%, 95% CI = 11% to 78% for true recurrences; P = .01). CONCLUSIONS DNA breakpoint information more often agreed with the clinical determination than CNAs in this population. The partial identity score, which was calculated based on DNA breakpoints, allows statistical discrimination between new primary tumors and true recurrences that could outperform the clinical determination in terms of prognosis.
Tilt menu: using the 3D orientation information of pen devices to extend the selection capability of pen-based user interfaces

We present a new technique called 'Tilt Menu' for better extending selection capabilities of pen-based interfaces. The Tilt Menu is implemented by using 3D orientation information of pen devices while performing selection tasks. The Tilt Menu has the potential to aid traditional one-handed techniques as it simultaneously generates the secondary input (e.g., a command or parameter selection) while drawing/interacting with a pen tip without having to use the second hand or another device. We conduct two experiments to explore the performance of the Tilt Menu. In the first experiment, we analyze the effect of parameters of the Tilt Menu, such as the menu size and orientation of the item, on its usability. Results of the first experiment suggest some design guidelines for the Tilt Menu. In the second experiment, the Tilt Menu is compared to two types of techniques while performing connect-the-dot tasks using freeform drawing mechanism. Results of the second experiment show that the Tilt Menu perform better in comparison to the Tool Palette, and is as good as the Toolglass.
GeneXpert for TB diagnosis: planned and purposeful implementation

Xpert MTB/RIF is a major advance for TB diagnostics, especially for multidrug-resistant (MDR) TB and HIV-associated TB. But implementation concerns including cost, technical support requirements, and challenging demands of providing second-line TB drugs for diagnosed MDR-TB cases call for gradual, careful introduction based on country circumstances. Xpert MTB/RIF is a major advance for TB diagnostics, especially for multidrug-resistant (MDR) TB and HIV-associated TB. But implementation concerns including cost, technical support requirements, and challenging demands of providing second-line TB drugs for diagnosed MDR-TB cases call for gradual, careful introduction based on country circumstances.
Improving Cloud Security using Secure Enclaves

Internet services can provide a wealth of functionality, yet their usage raises privacy, security and integrity concerns for users.This is caused by a lack of guarantees about what is happening on the server side.As a worst case scenario, the service might be subjected to an insider attack.This dissertation describes the \emph{unalterable secure service} concept for trustworthy cloud computing.Secure services are a powerful abstraction that enables viewing the cloud as a true extension of local computing resources.Secure services combine the security benefits one gets locally with the manageability and availability of the distributed cloud.Secure services are implemented using secure enclaves.Remote attestation of the server is used to obtain guarantees about the programming of the service.This dissertation addresses concerns related to using secure enclaves such as providing data freshness and distributing identity information.Certificate Transparency is augmented to distribute information about which services exist and what they do.All combined, this creates a platform that allows legacy clients to obtain security guarantees about Internet services.
Correcting susceptibility-induced distortion in diffusion-weighted MRI using constrained nonrigid registration

Echo Planar Imaging (EPI) is the standard pulse sequence used in fast diffusion-weighted magnetic resonance imaging (MRI), but is sensitive to susceptibility-induced inhomogeneities in the main B0 magnetic field. In diffusion MRI of the human head, this leads to geometric distortion of the brain in reconstructed diffusion images and a resulting lack of correspondence with the high-resolution MRI scans that are used to define the subject anatomy. In this study, we propose and test an approach to estimate and correct this distortion using a non-linear registration framework based on mutual-information. We use an anatomical image as the registration-template and constrain the registration using spatial regularization and physics-based information about the characteristics of the distortion, without requiring any additional data collection. Results are shown for simulated and experimental data. The proposed method aligns diffusion images to the anatomical image with an error of 1-3 mm in most brain regions.
Improving the Accuracy of Incremental Decision Tree Learning Algorithm via Loss Function

Hoeffding's bound (HB) has been widely used for node splitting in incremental decision tree algorithms. Many decision-tree algorithms adopt a sliding-window technique to detect concept drift when mining changing data streams. This paper presents a novel node-splitting approach that replaces the traditional HB with a new measure. The new measure is derived from a loss function applied in a cache-based classifier within a sliding window during incremental decision tree learning. Replacing the use of HB with this new bound is proposed for growing a Hoeffding decision tree that adapts to concept drifts detected in the data stream, thus improving the accuracy of prediction. The experimental results show that this new method has the potential to achieve better performance with fine tuning of the sliding window size.
Mesoscopic simulation of two-dimensional grain growth with anisotropic grain-boundary properties

Abstract Grain-boundary (GB) properties in a polycrystalline system are generally anisotropic; in particular, both the GB energy and the mobility depend on the GB misorientation. Here the effect of anisotropic GB properties on two- dimensional grain growth is investigated by computer simulation. A stochastic velocity Monte Carlo algorithm based on a variational formulation for the dissipated power is implemented. The simulations show that grain growth leads to an increase in the fraction of small-angle GBs during the growth process. The average grain area is found to grow with a smaller exponent than in a system with isotropic GB properties. An extended von Neumann-Mullins relation based on averaged GB properties is proposed.
Species–genus ratios reflect a global history of diversification and range expansion in marine bivalves

The distribution of marine bivalve species among genera and higher taxa takes the form of the classic hollow curve, wherein few lineages are species rich and many are species poor. The distribution of species among genera (S/G ratio) varies with latitude, with temperate S/G's falling within the null expectation, and tropical and polar S/G's exceeding it. Here, we test several hypotheses for this polar overdominance in the species richness of small numbers of genera. We find a significant positive correlation between the latitudinal range of a genus and its species richness, both globally and within regions. Genus age and species richness are also positively related, but this relationship breaks down when the analysis is limited to genera endemic to climate zones or with narrow latitudinal ranges. The data suggest a link between speciation and range-expansion, with genera expanding out of the tropical latitudinal bins tending to speciate more prolifically, both globally and regionally. These genera contain more species within climate zones than taxa endemic to that zone. Range expansion thus appears to be fundamentally coupled with speciation, producing the skewed distribution of species among genera, both globally and regionally, whereas clade longevity is achieved through extinction—resistance conferred by broad geographical ranges.
Intelligent Agent Based RFID System for on Demand Bus Scheduling and Ticketing

The public transportation system needs some change for satisfying the commuting needs of the general public. These systems are operated by state run authorities or by private parties. The commuters face challenges as far as accessing the public transportation facility as needed. This is mostly attributed to the static scheduling of bus trips, within some pattern, regardless of fluctuations in commuters demand. This is very common in many countries and Jamaica is not exception in this respect. There has been quite an amount of research work carried out in using Radio Frequency Identification (RFID) technology in public transportation system towards tracking of passengers while they board and exit the bus. Research has also been carried out on tracking passengers possessing RFID enabled Smart card and store in central locations for future viewing if need be, which a privacy concern is really. Also research has been carried out in using RFID technology towards tracking of buses by deploying RFID sensors at traffic stop lights, intersections, etc., for updating bus arrival time which user can view in his cell phone. In addition research is being conducted in using mobile agents with RFID technology towards passenger demand and carrying capacity. It is therefore clear from literature available on the subject that there has been no work reported so far in dynamic scheduling of buses based on passenger demand by means of RFID usage. So our proposed research work would be on dynamic scheduling of buses from the point of view of passenger tracking pattern, which would be noted and included in planning and scheduling by means of intelligent agents.
Missense Mutations in the MEFV Gene Are Associated with Fibromyalgia Syndrome and Correlate with Elevated IL-1β Plasma Levels

Background Fibromyalgia syndrome (FMS), a common, chronic, widespread musculoskeletal pain disorder found in 2% of the general population and with a preponderance of 85% in females, has both genetic and environmental contributions. Patients and their parents have high plasma levels of the chemokines MCP-1 and eotaxin, providing evidence for both a genetic and an immunological/inflammatory origin for the syndrome (Zhang et al., 2008, Exp. Biol. Med. 233: 1171–1180). Methods and Findings In a search for a candidate gene affecting inflammatory pathways, among five screened in our patient samples (100 probands with FMS and their parents), we found 10 rare and one common alleles for MEFV, a gene in which various compound heterozygous mutations lead to Familial Mediterranean Fever (FMF). A total of 2.63 megabases of genomic sequence of the MEFV gene were scanned by direct sequencing. The collection of rare missense mutations (all heterozygotes and tested in the aggregate) had a significant elevated frequency of transmission to affecteds (p = 0.0085, one-sided, exact binomial test). Our data provide evidence that rare missense variants of the MEFV gene are, collectively, associated with risk of FMS and are present in a subset of 15% of FMS patients. This subset had, on average, high levels of plasma IL-1β (p = 0.019) compared to FMS patients without rare variants, unaffected family members with or without rare variants, and unrelated controls of unknown genotype. IL-1β is a cytokine associated with the function of the MEFV gene and thought to be responsible for its symptoms of fever and muscle aches. Conclusions Since misregulation of IL-1β expression has been predicted for patients with mutations in the MEFV gene, we conclude that patients heterozygous for rare missense variants of this gene may be predisposed to FMS, possibly triggered by environmental factors.
Does late childbearing increase the risk for behavioural problems in children? A longitudinal cohort study.

BACKGROUND This study aimed to examine the relationship between advanced parental age and behavioural outcomes in offspring in a longitudinal cohort of children in Western Australia. METHODS The Western Australian Pregnancy Cohort (Raine) is a prospective study of 2900 pregnancies. Offspring were followed up at ages 2, 5, 8, 10, 14, and 17 years, and 1754 adolescents were available for follow-up at 17 years. The Child Behaviour Checklist was used to measure child behaviour, including internalising (e.g. anxious/withdrawn) and externalising (e.g. aggressive/destructive) behaviours. RESULTS There was a significant linear relationship between maternal age and total internalising and externalising behaviour outcomes, but not paternal age. Increasing maternal age was associated with decreasing risk for problem behaviours in offspring. In the categorical models, young maternal age (20-24 years) was associated with significantly increased risk for problem behaviours in offspring relative to offspring of parents in the reference group (25-29 years), and a paternal age of 35-39 years was associated with decreased risk for total behaviour morbidity in offspring. CONCLUSIONS This study showed no evidence that late fatherhood is associated with adverse behavioural outcomes in offspring. Increasing maternal age was found to be a protective factor for child behaviour morbidity.
Spoof Fingerprint Detection based on Co-occurrence Matrix

Fingerprint-based recognition systems have been widely deployed in numerous civilian and government applications. However, the fingerprint recognition systems can be deceived by commonly used sensors with the artificially fake fingerprint made using materials like gelatin or silicon. In this paper, spoof fingerprint detection is considered as a two-class classification problem and co-occurrence matrix is constructed from image gradients to extract features. In feature extraction process, the quantization operation is firstly applied with the fingerprint images. Secondly, the horizontal and vertical differences at each pixel are calculated. Thirdly, the differences of large absolute values are truncated into a reduced range. Finally, the co-occurrence matrix is constructed from the truncated differences, and the elements of the co-occurrence matrix are directly used as features. The features are separately utilized to train support vector machine classifiers on two databases. The experimental results have demonstrated that the proposed method outperform the state-of-the-arts.
A framework for estimating NBTI degradation of microarchitectural components

Degradation of device parameters over the lifetime of a system is emerging as a significant threat to system reliability. Among the aging mechanisms, wearout resulting from NBTI is of particular concern in deep submicron technology generations. To facilitate architectural level aging analysis, a tool capable of evaluating NBTI vulnerabilities early in the design cycle has been developed. The tool includes workload-based temperature and performance degradation analysis across a variety of technologies and operating conditions, revealing a complex interplay between factors influencing NBTI timing degradation.
Using the GPU to Green an Intensive and Massive Computation System

In this paper, we present the early results of an ongoing project aimed at giving an existing software system a more eco-sustainable lease of life. We defined a strategy and a process for migrating a subject system that performs intensive and massive computation to a Graphics Processing Unit (GPU) based architecture. We validated our solutions on a software system for path finding robot simulations. An initial comparison on the energy consumption of the original system and the greened one has been also executed. The obtained results suggested that the application of our solution produced more eco-sustainable software.
Conditional stochastic simulation for character animation

In a context of interactive applications, adapting motion capture data to new situations or producing variants of them are known as non trivial tasks. We propose an original method that produces motions that preserve the statistical properties of a reference motion while ensuring some constraints. This method uses principles of conditional stochastic simulation to achieve this goal. Notably, a new real time algorithm, performing sequentially and producing the desired motion is introduced. Possible applications of our method are numerous and several examples are given, along with results. Copyright © 2010 John Wiley & Sons, Ltd.
Solving QBF by Clause Selection

Algorithms based on the enumeration of implicit hitting sets find a growing number of applications, which include maximum satisfiability and model based diagnosis, among others. This paper exploits enumeration of implicit hitting sets in the context of Quantified Boolean Formulas (QBF). The paper starts by developing a simple algorithm for QBF with two levels of quantification, which is shown to relate with existing work on enumeration of implicit hitting sets, but also with recent work on QBF based on abstraction refinement. The paper then extends these ideas and develops a novel QBF algorithm, which generalizes the concept of enumeration of implicit hitting sets. Experimental results, obtained on representative problem instances, show that the novel algorithm is competitive with, and often outperforms, the state of the art in QBF solving.
Gradual Typing for Functional Languages

Static and dynamic type systems have well-known strengths and weaknesses, and each is better suited for different programming tasks. There have been many efforts to integrate static and dynamic typing and thereby combine the beneﬁts of both typing disciplines in the same language. The ﬂexibility of static typing can be improved by adding a type Dynamic and a typecase form. The safety and performance of dynamic typing can be improved by adding optional type annotations or by performing type inference (as in soft typing). However, there has been little formal work on type systems that allow a programmer-controlled migration between dynamic and static typing. Thatte proposed Quasi-Static Typing, but it does not statically catch all type errors in completely annotated programs. Anderson and Drossopoulou deﬁned a nominal type sys-tem for an object-oriented language with optional type annotations. However, developing a sound, gradual type system for functional languages with structural types is an open problem. In this paper we present a solution based on the intuition that the structure of a type may be partially known/unknown at compile-time and the job of the type system is to catch incompatibilities between the known parts of types. We deﬁne the static and dynamic semantics of a λ -calculus with optional type annotations and we prove that its type system is sound with respect to the simply-typed λ -calculus for fully-annotated terms. We prove that this calculus is type safe and that the cost of dynamism is “pay-as-you-go”.