Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vivo SPECT Reporter Gene Imaging of Regulatory T Cells

Regulatory T cells (Tregs) were identified several years ago and are key in controlling autoimmune diseases and limiting immune responses to foreign antigens, including alloantigens. In vivo imaging techniques including intravital microscopy as well as whole body imaging using bioluminescence probes have contributed to the understanding of in vivo Treg function, their mechanisms of action and target cells. Imaging of the human sodium/iodide symporter via Single Photon Emission Computed Tomography (SPECT) has been used to image various cell types in vivo. It has several advantages over the aforementioned imaging techniques including high sensitivity, it allows non-invasive whole body studies of viable cell migration and localisation of cells over time and lastly it may offer the possibility to be translated to the clinic. This study addresses whether SPECT/CT imaging can be used to visualise the migratory pattern of Tregs in vivo. Treg lines derived from CD4+CD25+FoxP3+ cells were retrovirally transduced with a construct encoding for the human Sodium Iodide Symporter (NIS) and the fluorescent protein mCherry and stimulated with autologous DCs. NIS expressing self-specific Tregs were specifically radiolabelled in vitro with Technetium-99m pertechnetate (99mTcO4 −) and exposure of these cells to radioactivity did not affect cell viability, phenotype or function. In addition adoptively transferred Treg-NIS cells were imaged in vivo in C57BL/6 (BL/6) mice by SPECT/CT using 99mTcO4 −. After 24 hours NIS expressing Tregs were observed in the spleen and their localisation was further confirmed by organ biodistribution studies and flow cytometry analysis. The data presented here suggests that SPECT/CT imaging can be utilised in preclinical imaging studies of adoptively transferred Tregs without affecting Treg function and viability thereby allowing longitudinal studies within disease models.
An Empirical Study on Effects of Code Visibility on Code Coverage of Software Testing

Software testability is the degree of difficulty to test a program. Code visibility is important to support design principles, such as information hiding. It is widely believed that code visibility has effects on testability. However, little empirical evidence has been shown to clarify whether and how software testability is influenced by code visibility. We have performed an empirical study to shed light on this problem. Our study focuses on test code coverage, in particular that of automatic testing tools. Code coverage is commonly used for various purposes, such as evaluating test adequacy, assessing test quality, and analyzing testability. Our study uses code coverage as the concrete measurement of testability. By analyzing code coverage of two state-of-the-art tools, in comparison with that of developer-written tests, we have discovered that code visibility does not necessarily have effects on its code coverage, but significantly affects automatic testing tools. Low code visibility often leads to low code coverage for automatic tools. In addition, different treatments on code visibility can result in significant differences in overall code coverage for automatic tools. Using a tool enhancement specific to code visibility, we demonstrate the great potential to improve existing tools.
Zinc-finger protein-targeted gene regulation: Genomewide single-gene specificity

Zinc-finger protein transcription factors (ZFP TFs) can be designed to control the expression of any desired target gene, and thus provide potential therapeutic tools for the study and treatment of disease. Here we report that a ZFP TF can repress target gene expression with single-gene specificity within the human genome. A ZFP TF repressor that binds an 18-bp recognition sequence within the promoter of the endogenous CHK2 gene gives a >10-fold reduction in CHK2 mRNA and protein. This level of repression was sufficient to generate a functional phenotype, as demonstrated by the loss of DNA damage-induced CHK2-dependent p53 phosphorylation. We determined the specificity of repression by using DNA microarrays and found that the ZFP TF repressed a single gene (CHK2) within the monitored genome in two different cell types. These data demonstrate the utility of ZFP TFs as precise tools for target validation, and highlight their potential as clinical therapeutics.
Accurate Ensembles for Data Streams: Combining Restricted Hoeffding Trees using Stacking

The success of simple methods for classification shows that is is often not necessary to model complex attribute interactions to obtain good classification accuracy on practical problems. In this paper, we propose to exploit this phenomenon in the data stream context by building an ensemble of Hoeffding trees that are each limited to a small subset of attributes. In this way, each tree is restricted to model interactions between attributes in its corresponding subset. Because it is not known a priori which attribute subsets are relevant for prediction, we build exhaustive ensembles that consider all possible attribute subsets of a given size. As the resulting Hoeffding trees are not all equally important, we weigh them in a suitable manner to obtain accurate classifications. This is done by combining the log-odds of their probability estimates using sigmoid perceptrons, with one perceptron per class. We propose a mechanism for setting the perceptrons’ learning rate using the ADWIN change detection method for data streams, and also use ADWIN to reset ensemble members (i.e. Hoeffding trees) when they no longer perform well. Our experiments show that the resulting ensemble classifier outperforms bagging for data streams in terms of accuracy when both are used in conjunction with adaptive naive Bayes Hoeffding trees, at the expense of runtime and memory consumption.
Geometric bounds for stationary distributions of infinite Markov chains via Lyapunov functions

In this paper, we develop a systematic method for deriving bounds on the stationary distribution of stable Markov chains with a countably infinite state space. We assume that a Lyapunov function is available that satisfies a negative drift property (and, in particular, is a witness of stability), and that the jumps of the Lyapunov function corresponding to state transitions have uniformly bounded magnitude. We show how to derive closed form, exponential type, upper bounds on the steady-state distribution. Similarly, we show how to use suitably defined lower Lyapunov functions to derive closed form lower bounds on the steady-state distribution. We apply our results to homogeneous random walks on the positive orthant, and to multiclass single station Markovian queueing systems. In the latter case, we establish closed form exponential type bounds on the tail probabilities of the queue lengths, under an arbitrary work conserving policy.
The TIMI risk score for unstable angina/non-ST elevation MI: A method for prognostication and therapeutic decision making.

CONTEXT Patients with unstable angina/non-ST-segment elevation myocardial infarction (MI) (UA/NSTEMI) present with a wide spectrum of risk for death and cardiac ischemic events. OBJECTIVE To develop a simple risk score that has broad applicability, is easily calculated at patient presentation, does not require a computer, and identifies patients with different responses to treatments for UA/NSTEMI. DESIGN, SETTING, AND PATIENTS Two phase 3, international, randomized, double-blind trials (the Thrombolysis in Myocardial Infarction [TIMI] 11B trial [August 1996-March 1998] and the Efficacy and Safety of Subcutaneous Enoxaparin in Unstable Angina and Non-Q-Wave MI trial [ESSENCE; October 1994-May 1996]). A total of 1957 patients with UA/NSTEMI were assigned to receive unfractionated heparin (test cohort) and 1953 to receive enoxaparin in TIMI 11B; 1564 and 1607 were assigned respectively in ESSENCE. The 3 validation cohorts were the unfractionated heparin group from ESSENCE and both enoxaparin groups. MAIN OUTCOME MEASURES The TIMI risk score was derived in the test cohort by selection of independent prognostic variables using multivariate logistic regression, assignment of value of 1 when a factor was present and 0 when it was absent, and summing the number of factors present to categorize patients into risk strata. Relative differences in response to therapeutic interventions were determined by comparing the slopes of the rates of events with increasing score in treatment groups and by testing for an interaction between risk score and treatment. Outcomes were TIMI risk score for developing at least 1 component of the primary end point (all-cause mortality, new or recurrent MI, or severe recurrent ischemia requiring urgent revascularization) through 14 days after randomization. RESULTS The 7 TIMI risk score predictor variables were age 65 years or older, at least 3 risk factors for coronary artery disease, prior coronary stenosis of 50% or more, ST-segment deviation on electrocardiogram at presentation, at least 2 anginal events in prior 24 hours, use of aspirin in prior 7 days, and elevated serum cardiac markers. Event rates increased significantly as the TIMI risk score increased in the test cohort in TIMI 11B: 4.7% for a score of 0/1; 8.3% for 2; 13. 2% for 3; 19.9% for 4; 26.2% for 5; and 40.9% for 6/7 (P<.001 by chi(2) for trend). The pattern of increasing event rates with increasing TIMI risk score was confirmed in all 3 validation groups (P<.001). The slope of the increase in event rates with increasing numbers of risk factors was significantly lower in the enoxaparin groups in both TIMI 11B (P =.01) and ESSENCE (P =.03) and there was a significant interaction between TIMI risk score and treatment (P =. 02). CONCLUSIONS In patients with UA/NSTEMI, the TIMI risk score is a simple prognostication scheme that categorizes a patient's risk of death and ischemic events and provides a basis for therapeutic decision making. JAMA. 2000;284:835-842
Lipids-An Instrumental Excipient In Pharmaceutical Hot-Melt Coating

Coatings are widely used to provide drug protection, to increase aesthetic value of product (color, taste and texture), to reduces acidity if vitamins, to provide lubrication and modified drug release. Usually, coating agents are dissolved or dispersed in solvents (water or organic) prior to coating and glidants are commonly added to prevent particle agglomeration during coating. Lipids are the smart option to polymer coatings as they need melting before application directly on the substrate. As hot-melt coating (HMC) devoid of solvent use, solvent disposal, solvent evaporation and solvent treatment is not required; as a result powders with very high specific surface areas can be coated rapidly. Different lipids can be used in coating and selection of the right lipid for the application requires knowledge of their physico-chemical properties and its associated effect on drug release.
Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements

We present a boundary‐element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion‐exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix–vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near‐singular integrals over the curved boundary elements. Fourth, we present a general boundary‐integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite‐difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid‐binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved‐element BEM is important when more sophisticated techniques, such as nonrigid‐binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry, such as charge optimization or component analysis, can be computed to high accuracy using the presented BEM approach, in compute times comparable to traditional finite‐difference methods. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Interstitial thermometry in men undergoing electrovaporization of the prostate.

BACKGROUND AND OBJECTIVES Transurethral electrovaporization of the prostate (TVP) has been utilized increasingly in the therapeutic management of benign prostatic hyperplasia (BPH). The temperature profile within both prostatic and periprostatic tissue has been presented as a parameter of safety in various preliminary studies. This prospective study measured interstitial temperature during TVP in both the prostate and the surrounding tissue of 18 men. METHODS These 18 men undergoing TVP had three interstitial thermocouple probes placed under ultrasound guidance. Probes were positioned in the rectal wall and at the 5 and 7 o'clock position of the prostate capsule. A fourth probe was placed within 1 mm of the area of vaporization to determine "lesion" temperature. Temperature was measured at baseline and at 15-minute intervals as TVP was performed utilizing the VaporTrode at 240 to 280 W with a Valley Lab Force 40 generator. RESULTS The maximum temperature variability was 1.9 degrees C. The temperature within 0.5 mm of the area of vaporization was >100 degrees C. These results were independent of the temperature of the irrigating solution. CONCLUSIONS These results provide compelling evidence that high vaporization temperatures do not affect surrounding prostatic tissue. In theory, the risk of injury to either the rectum or the neurovascular bundle during TVP should be extremely low.
Synthesis of porous silicon carbide from cellulose fibre templates infiltrated with polycarbosilane

Abstract Amorphous silicon carbide (SiC) with a stable porous structure was synthesised using a cellulose fibre preform (ash less filter paper) infiltrated with poly(methyl-carbosilane) and heated to 1000°C, first under N2 and then air. Scanning electron microscopy and Hg porosimetry confirmed the structure and porosity of the preform was largely reproduced in the final material; the porosity of the untreated template (72·4%) decreased following pyrolysis (58·1%) and then increased after treatment in air (80·0%). The SiC yield, inferred from thermogravimetric analysis of the infiltrated template, was linearly correlated with the number of infiltration steps and ranged between 3 and 21 wt-% for one and five infiltrations respectively.
Effects of probiotics on atopic dermatitis: a randomised controlled trial

Background: The aim of the study was to investigate the effects of probiotics on moderate or severe atopic dermatitis (AD) in young children. Methods: Fifty six children aged 6–18 months with moderate or severe AD were recruited into a randomised double blind placebo controlled trial in Perth, Western Australia; 53 children completed the study. The children were given a probiotic (1×109Lactobacillus fermentum VRI-033 PCC; Probiomics) or an equivalent volume of placebo, twice daily for 8 weeks. A final assessment at 16 weeks was performed. Results: The main outcome measures were severity and extent of AD at the end of the study, as measured by the Severity Scoring of Atopic Dermatitis (SCORAD) index. The reduction in the SCORAD index over time was significant in the probiotic group (p = 0.03) but not the placebo group. Significantly more children receiving probiotics (n = 24, 92%) had a SCORAD index that was better than baseline at week 16 compared with the placebo group (n = 17, 63%) (p = 0.01). At the completion of the study more children in the probiotic group had mild AD (n = 14, 54%) compared to the placebo group (n = 8, 30%). Conclusion: Supplementation with probiotic L fermentum VRI-003 PCC is beneficial in improving the extent and severity of AD in young children with moderate or severe disease.
Reproducibilty test of ferrous xylenol orange gel dose response with optical cone beam CT scanning

Our previous studies of ferrous xylenol orange gelatin gel have revealed a spatial dependence to the dose response of samples contained in 10 cm diameter cylinders. Dose response is defined as change in optical attenuation coefficient divided by the dose (units cm−1 Gy−1). This set of experiments was conducted to determine the reproducibility of our preparation, irradiation and full 3D optical cone beam CT scanning. The data provided an internal check of a larger storage time-dose response dependence study.
Using bit-edge equalization in highspeed backplane data transmission

This paper presents an improved bit-edge equalization (BEE) method for mitigating intersymbol interference (ISI) in high-speed backplane applications. Using a least-mean-square (LMS) adaptive algorithm as a receiver (RX) error convergence engine, the proposed BEE method is based on equalizing only the edges of data bits with an adjustment of LMS error derivation points, which in turn changes the error information and affects filter coefficients for pulse amplitude modulation. As a result, the received channel far-end 3-level bit-edge eye diagrams can be optimized. This proposed BEE method employs a conventional symbol-spaced FIR (SSF) filter as transmitter (TX) pre-emphasis for bit-edge equalization. With TX data pre-coding, the received channel far-end 3-level signal to 2-level binary decoding only depends on the current received bit. No error propagation occurs. In this work, the proposed BEE method is compared with the conventional bit-center equalization (BCE) method and the duobinary signaling method. A typical Tyco 34-inch FR4 backplane channel is used as the comparison benchmark. A Matlab script based link simulation tool is used to evaluate the link performance. The simulation results demonstrate that the proposed BEE method is the most effective method for mitigation ISI in relatively high-loss channels.
Enhancement in Ti–6Al–4V sintering via nanostructured powder and spark plasma sintering

Studies are performed to enhance low temperature sintering of Ti–6Al–4V. High energy ball milling is found to be effective in lowering the sintering temperature through the mechanisms of particle size reduction and nanograin formation. The former reduces the diffusion distance for densification, whereas the latter introduces an additional densification mechanism allowing mass transport from the interior of the particle to the neck zone. Together, these two effects can reduce the onset temperature for densification by about 300°C. Spark plasma sintering can further improve low temperature sintering when compared with radiant heat sintering and microwave sintering. The enhanced densification is discussed on the basis of the applied pressure (50 MPa) and the intrinsic joule effect that leads to increase in the local temperature at the contact point between particles.
Resource-aware set-valued estimation for discrete-time linear systems

In this paper, we propose a self-triggered estimator for discrete-time linear systems subject to unknown but bounded disturbances affecting both the system states and outputs. The proposed self-triggered estimator is a set-valued estimator that employs rollout techniques to reduce the communication between the sensors and the estimator with respect to a periodic sampling strategy. Moreover, at each time instant it provides an estimate of the plant state and a guaranteed bound on the difference between the true plant state and the estimate.
Numerical Modeling, Thermomechanical Testing, and NDE Procedures for Prediction of Microcracking Induced Permeability of Cryogenic Composites

Reusable Space Vehicles will include light cryogenic composite fuel tanks that must not leak excessively even after multiple launches. Damage in cryogenic composite fuel tanks induced during manufacturing and advanced by thermomechanical cycling can accelerate leakage of the propellant. Whether the leakage exceeds tolerable levels depends on many factors, including pressure gradients, microcrack density, other damage such as delamination, connectivity of the cracks, residual stresses from manufacture, service-induced stresses from thermal and mechanical loads, and composite lay-up. Although it is critical to experimentally characterize permeability during various thermal and mechanical load histories, optimal design depends on having analytical models that can predict the effect of various parameters on performance. Our broad goal is to develop such models that are experimentally validated by destructive and non-destructive evaluation means.
Semantic Link Network-Based Model for Organizing Multimedia Big Data

Recent research shows that multimedia resources in the wild are growing at a staggering rate. The rapid increase number of multimedia resources has brought an urgent need to develop intelligent methods to organize and process them. In this paper, the semantic link network model is used for organizing multimedia resources. A whole model for generating the association relation between multimedia resources using semantic link network model is proposed. The definitions, modules, and mechanisms of the semantic link network are used in the proposed method. The integration between the semantic link network and multimedia resources provides a new prospect for organizing them with their semantics. The tags and the surrounding texts of multimedia resources are used to measure their semantic association. The hierarchical semantic of multimedia resources is defined by their annotated tags and surrounding texts. The semantics of tags and surrounding texts are different in the proposed framework. The modules of semantic link network model are implemented to measure association relations. A real data set including 100 thousand images with social tags from Flickr is used in our experiments. Two evaluation methods, including clustering and retrieval, are performed, which shows the proposed method can measure the semantic relatedness between Flickr images accurately and robustly.