Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time MRI-TRUS fusion for guidance of targeted prostate biopsies

Targeted prostate biopsy is challenging because no currently established imaging modality is both accurate for prostate cancer diagnosis and cost-effective for real-time procedure guidance. A system that fuses real-time transrectal ultrasound images with previously acquired endorectal coil MRI images for prostate biopsy guidance is presented here. The system uses electromagnetic tracking and intraoperative image registration to superimpose the MRI data on the ultrasound image. Prostate motion is tracked and compensated for without the need for fiducial markers. The accuracy of the system in phantom studies was shown to be 2.4 ± 1.2 mm. The fusion system has been used in more than 20 patients to guide biopsies with almost no modification of the conventional protocol. Retrospective clinical evaluation suggests that clinically acceptable spatial accuracy can be achieved.
Spleen Rupture in a Case of Untreated Plasmodium vivax Infection

1 Fundac¸a˜o de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil, 2Universidade do Estado do Amazonas, Manaus, Brazil, 3Barcelona Centre forInternational Health Research (CRESIB, Hospital Clinic–Universitat de Barcelona), Barcelona, Spain, 4 Laboratory of Pathology, Barcelona, Spain, 5 Institucio´ Catalana deRecerca I Estudis Avanc¸ats, Barcelona, Spain
Performance of Hybrid GANN in Comparison with Other Standalone Models on Dengue Outbreak Prediction

Early prediction of diseases especially dengue fever in the case of Malaysia, is very crucial to enable health authorities to develop response strategies and context preventive intervention programs such as awareness campaigns for the high risk population before an outbreak occurs. Some of the deficiencies in dengue epidemiology are insufficient awareness on the parameter as well as the combination among them. Most of the studies on dengue prediction use standalone models which face problem of finding the appropriate parameter since they need to apply try and error approach. The aim of this paper is to conduct experiments for determining the best network structure that has effective variable and fitting parameters in predicting the spread of the dengue outbreak. Four model structures were designed in order to attain optimum prediction performance. The best model structure was selected as predicting model to solve the time series prediction of dengue. The result showed that neighboring location of dengue cases was very effective in predicting the dengue outbreak and it is proven that the hybrid Genetic Algorithm and Neural Network (GANN) model significantly outperforms standalone models namely regression and Neural Network (NN).
ASIC for Small Angle Neutron Scattering Experiments at the SNS

We present an ASIC for a 3He gas detector to be used in small angle neutron scattering experiments at the Spallation Neutron Source in Oak Ridge. The ASIC is composed of 64 channels with low noise charge amplification, filtering, timing and amplitude measurement circuits, where an innovative current-mode peak-detector and digitizer (PDAD) is adopted. The proposed PDAD provides at the same time peak detection and A/D conversion in real time, at low power, and without requiring a clock signal. The channels share an efficient data sparsification and derandomization scheme, a 30-bit 256 deep FIFO, and low voltage differential signaling.
Greedy signal recovery and uncertainty principles

This paper seeks to bridge the two major algorithmic approaches to sparse signal recovery from an incomplete set of linear measurements - L1-minimization methods and iterative methods (Matching Pursuits). We find a simple regularized version of the Orthogonal Matching Pursuit (ROMP) which has advantages of both approaches: the speed and transparency of OMP and the strong uniform guarantees of the L1-minimization. Our algorithm ROMP reconstructs a sparse signal in a number of iterations linear in the sparsity, and the reconstruction is exact provided the linear measurements satisfy the Uniform Uncertainty Principle. In the case of inaccurate measurements and approximately sparse signals, the noise level of the recovery is proportional to &sqrt;log n parallel e parallel 2 where e is the error vector.
Can Pairwise Testing Perform Comparably to Manually Handcrafted Testing Carried Out by Industrial Engineers?

Testing is an important activity in engineering of industrial software. For such software, testing is usually performed manually by handcrafting test suites based on specific design techniques and domain-specific experience. To support developers in testing, different approaches for producing good test suites have been proposed. In the last couple of years combinatorial testing has been explored with the goal of automatically combining the input values of the software based on a certain strategy. Pairwise testing is a combinatorial technique used to generate test suites by varying the values of each pair of input parameters to a system until all possible combinations of those parameters are created. There is some evidence suggesting that these kinds of techniques are efficient and relatively good at detecting software faults. Unfortunately, there is little experimental evidence on the comparison of these combinatorial testing techniques with, what is perceived as, rigorous manually handcrafted testing. In this study we compare pairwise test suites with test suites created manually by engineers for 45 industrial programs. The test suites were evaluated in terms of fault detection, code coverage and number of tests. The results of this study show that pairwise testing, while useful for achieving high code coverage and fault detection for the majority of the programs, is almost as effective in terms of fault detection as manual testing. The results also suggest that pairwise testing is just as good as manual testing at fault detection for 64% of the programs.
The diameter of sparse random graphs

We derive an expression of the form c ln n + o(ln n) for the diameter of a sparse random graph with a specified degree sequence. The result holds asymptotically almost surely, assuming that certain convergence and supercriticality conditions are met, and is applicable to the classical random graph Gn,p with np = Θ(1) + 1, as well as certain random power law graphs. © 2007 Wiley Periodicals, Inc. Random Struct. Alg. , 2007
The tectonic setting of the eastern margin of the Sino-Korean Block inferred from detrital zircon U–Pb age and Nd isotope composition of the Pyeongan Supergroup (upper Palaeozoic – Lower Triassic), Korea

Abstract The upper Palaeozoic succession (Pyeongan Supergroup) in central eastern Korea is well correlated with the equivalent successions distributed in North China, suggestive of the Korean upper Palaeozoic being part of the Sino-Korean Block. Detrital zircon U–Pb ages and Sm–Nd isotope compositions of the Pyeongan Supergroup in the Samcheok coalfield of the Taebaeksan Basin were analysed. A single predominant zircon age peak at c. 1.9 Ga (> 70%) is marked in all sedimentary units, followed by varying amounts of minor late Palaeozoic grains (up to 30%). The rarity of Meso- to Neoproterozoic- and Silurian-aged zircons confirms that sediment influx from the South China and Qinling blocks was insignificant. The 2.0–1.8 Ga-dominated zircon age pattern and the Nd isotope composition (average εNd(0) = −15.5±4.0) of the Pyeongan Supergroup most closely reflect the signature of the Yeongnam Massif basements, which supports a previous hypothesis that the Pyeongan Supergroup was mostly derived from a palaeo-orogen located to the east–southeast. Relatively higher εNd(0) values (> −10.1) in the lowermost and the upper parts of the succession are closely matched by the increased occurrence of syn-depositional-aged zircons, which indicates considerable mixing of juvenile materials at c. 320 Ma and 260 Ma. Both arc-related magmatic events are interpreted to have been related to oceanic subduction, suggesting that the eastern margin of the Sino-Korean Block was an active continental margin during late Palaeozoic times.
Illness representations of cancer among healthy residents of Kolkata, India.

Cancer illness representations and screening history among residents of Kolkata, India, were investigated along with socio-demographic characteristics in an effort to understand possible motivations for health behavior. A total of 106 participants were recruited from community locations in Kolkata, India and completed surveys including demographics, the illness perception questionnaire-revised (IPQ-R), and previous experience with cancer and screening practices. Participants were 51.5% college educated, 57% female, 51.5% full-time employed with average age of 32.7 years (R: 18-60 years). Descriptive statistics were generated for the subscales of the IPQ-R, cancer-screening practices and cancer experience. Correlation analyses were conducted to investigate associations between cancer representations and socio-demographic variables. Univariate ANOVAs were calculated to determine gender differences in IPQ-R subscales and differences between participants who knew someone diagnosed with cancer versus those who did not. While 76% of participants knew someone with cancer, only 5% of the sample engaged in cancer screening. Participants perceived cancer as a serious illness with negative emotional valence. Younger age (r(100)=-. 36, p<0.001) and male gender (F(1, 98)=5.22, p=0.01, η2=0.05) were associated with better illness coherence. Males also reported greater personal control (F(1, 98)=5.34, p=0.02, η2=0.05) were associated with better illness coherence. Low screening rates precluded analyses of the relationship between illness representations and cancer screening. Cancer was viewed as a threatening and uncontrollable disease among this sample of educated, middle class Kolkata residents. This view may act as a barrier to seeking cancer screening. Public awareness campaigns aimed at improving understanding of the causes, symptoms and consequences of cancer might reduce misunderstandings and fear, especially among women and older populations, who report less comprehension of cancer.
Clinical neuropathology practice guide 1-2013: Molecular subtyping of glioblastoma: ready for clinical use?

Recently, integrated genome-wide analyses have revealed several glioblastoma (GB) subtypes, which differ in terms of key pathogenetic pathways and point to different cells of origin. Even though the proneural and mesenchymal GB signatures evolved as most robust, there is no consensus on the exact number of subtypes and defining criteria. Moreover, important issues concerning within-tumor heterogeneity and class-switching upon recurrence remain to be addressed. Early evidence indicates an association of different GB subtypes with patient outcome and response to therapy, which argues for the implementation of molecular GB subtyping, and consideration of GB subtypes in subsequent patient management. As genome-wide analyses are not routinely available to the majority of neuropathology laboratories, first attempts to implement immunohistochemical testing of surrogate markers are underway. However, so far, confirmatory studies are lacking and there is no consensus on which markers to use. Further, the rationale for testing is compromised from a clinical point of view by a lack of effective therapies for individual GB subtypes. Thus, incorporation of genomic research findings as a basis for GB patient management and clinical decision making currently remains a perspective for the future.
Spread of Avian Influenza Viruses by Common Teal (Anas crecca) in Europe

Since the recent spread of highly pathogenic (HP) H5N1 subtypes, avian influenza virus (AIV) dispersal has become an increasing focus of research. As for any other bird-borne pathogen, dispersal of these viruses is related to local and migratory movements of their hosts. In this study, we investigated potential AIV spread by Common Teal (Anas crecca) from the Camargue area, in the South of France, across Europe. Based on bird-ring recoveries, local duck population sizes and prevalence of infection with these viruses, we built an individual-based spatially explicit model describing bird movements, both locally (between wintering areas) and at the flyway scale. We investigated the effects of viral excretion duration and inactivation rate in water by simulating AIV spread with varying values for these two parameters. The results indicate that an efficient AIV dispersal in space is possible only for excretion durations longer than 7 days. Virus inactivation rate in the environment appears as a key parameter in the model because it allows local persistence of AIV over several months, the interval between two migratory periods. Virus persistence in water thus represents an important component of contamination risk as ducks migrate along their flyway. Based on the present modelling exercise, we also argue that HP H5N1 AIV is unlikely to be efficiently spread by Common Teal dispersal only.
Mechanical state, material properties and continuous description of an epithelial tissue

During development, epithelial tissues undergo extensive morphogenesis based on coordinated changes of cell shape and position over time. Continuum mechanics describes tissue mechanical state and shape changes in terms of strain and stress. It accounts for individual cell properties using only a few spatially averaged material parameters. To determine the mechanical state and parameters in the Drosophila pupa dorsal thorax epithelium, we severed in vivo the adherens junctions around a disc-shaped domain comprising typically a hundred cells. This enabled a direct measurement of the strain along different orientations at once. The amplitude and the anisotropy of the strain increased during development. We also measured the stress-to-viscosity ratio and similarly found an increase in amplitude and anisotropy. The relaxation time was of the order of 10 s. We propose a space–time, continuous model of the relaxation. Good agreement with experimental data validates the description of the epithelial domain as a continuous, linear, visco-elastic material. We discuss the relevant time and length scales. Another material parameter, the ratio of external friction to internal viscosity, is estimated by fitting the initial velocity profile. Together, our results contribute to quantify forces and displacements, and their time evolution, during morphogenesis.
Land use/cover changes and prediction of Dodoma, Tanzania

The primary objective of this paper is to analyze the past and present changes of Dodoma region and also predict the future changes using the Landsat satellite images of 1998, 2008 and 2018. In this study, land use and land cover change (LULC) is examined using remote sensing and Markov chains analysis. The study first uses remote sensing to detect LULC changes and then based on the result of classification images, predicts the 2030 LULC using Markov chains analysis. The results of the net change between 1998 and 2018 show that built-up land increased by 2221 ha, bare land by 15,737 ha and vegetation declined by 17,958 ha. Markov prediction to 2030 based on land use and land cover maps of 2008 and 2018 show that bare land has a high probability (0.61) of maintaining its current status in 2030. However, vegetation only has a probability of 0.41 for maintaining its current state, and it could convert to bare land at a probability of 0.43 and to built-up land at a probability of 0.015. The transition probabilities illustrate that most of the LULC are oriented towards the increase of the bare land and built-up land.
Surface Plasmon Resonance Analysis Shows an IgG-Isotype-Specific Defect in ABO Blood Group Antibody Formation in Patients with Common Variable Immunodeficiency

Background Common variable immunodeficiency (CVID) is the most common clinically severe primary immunodeficiency and comprises a heterogeneous group of patients with recurrent severe bacterial infections due to the failure to produce IgG antibodies after exposure to infectious agents and immunization. Diagnostic recommendations for antibody failure include assessment of isoagglutinins. We have readdressed this four decades old but still accepted recommendation with up to date methodology. Methods Anti-A/B IgM- and IgG-antibodies were measured by Diamed-ID Micro Typing, surface plasmon resonance (SPR) using the Biacore® device and flow cytometry. Results When Diamed-ID Micro Typing was used, CVID patients (n = 34) showed IgG- and IgM-isoagglutinins that were comparable to healthy volunteers (n = 28), while all XLA patients (n = 8) had none. Anti-A/B IgM-antibodies were present in more than 2/3 of the CVID patients and showed binding kinetics comparable to anti-A/B IgM-antibodies from healthy individuals. A correlation could be found in CVID patients between levels of anti-A/B IgM-antibodies and levels of serum IgM and PnP–IgM-antibodies. In contrast in CVID patients as a group ABO antibodies were significantly decreased when assessed by SPR, which correlated with levels of switched memory, non-switched memory and naïve B cells, but all CVID patients had low/undetectable anti-A/B IgG-antibodies. Conclusion These results indicate that conventional isoagglutinin assessment and assessment of anti-A/B IgM antibodies are not suited for the diagnosis of impaired antibody production in CVID. Examination of anti-A/B IgG antibodies by SPR provides a useful method for the diagnosis of IgG antibody failure in all CVID patients studied, thus indicating an important additional rationale to start immunoglobulin replacement therapy early in these patients, before post-infectious sequelae develop.
Human mesenchymal stem cell culture: rapid and efficient isolation and expansion in a defined serum‐free medium

Human mesenchymal stem cells (hMSCs) are typically obtained for research or therapeutic applications by isolating and subculturing adherent cells from bone marrow on tissue‐culture substrates using growth media. The purity and properties of the resulting populations can be affected greatly by the conditions under which they are cultured. Fetal bovine serum (FBS), although ill‐defined, has been widely used as a critical requirement for conventional hMSC culture. However, a defined serum‐free medium would greatly facilitate the development of robust, clinically acceptable bioprocesses for reproducibly generating quality‐assured cells. The present study provides evidence demonstrating that a defined serum‐free medium (PPRF‐msc6) shows several beneficial features over a conventional FBS‐containing medium for the production of hMSCs. When compared to control FBS‐based cultures, PPRF‐msc6 medium supported the derivation of hMSCs from primary cultures of bone marrow cells in a more rapid and consistent manner. Furthermore, hMSCs cultured in PPRF‐msc6 exhibited: (a) a greater colony‐forming capacity in primary as well as passaged cultures; (b) negligible lag phase and explicit exponential growth; (c) lower population doubling times (21–26 h vs 35–38 h between passage levels 1 and 10); (d) a greater number of population doublings (62 ± 4 vs 43 ± 2; over a 2 month period); and (e) a higher degree of homogeneity in size. Our data demonstrate that PPRF‐msc6 is an important development which opens the door for the rapid, efficient and reproducible production of hMSCs in clinical settings. Copyright © 2011 John Wiley & Sons, Ltd.
A Planar and a Volumetric Test for Stereoanomaly

Stereoanomaly is the failure to see differences in depth when the viewer is presented with stimuli having different magnitudes of stereoscopic disparity. In the absence of eye movements, everyone suffers from stereoanomaly for extremely large disparities. Typically, such disparities are seen at the same depth as monocular stimuli. However, about 30% of the population exhibit some form of stereoanomaly even for very small disparities, provided eye movements are avoided. In some cases, the sign of the disparity will be confused, and the perceived depth will be incorrectly seen as ‘behind’ rather than ‘in front of’ the fixation point, for example. Because anomalies provide useful information about perceptual mechanisms, tests that measure and quantify the extent of a blindness are important investigative tools for research. Here we offer two easy-to-administer tests for stereoanomaly. The first test is based on depth judgments of two bars relative to a fixation point. The second test involves judgments of volumetric stimuli, seen stereoscopically. In each case, subjects indicate depth by setting a rectangle (with fixed base) to match the perceived depth. Although both tests are correlated, some differences in stereo processing are seen, depending upon whether or not the stimuli are presented near the point of fixation.
A Mixed Value and Policy Iteration Method for Stochastic Control with Universally Measurable Policies

We consider stochastic optimal control models with Borel spaces and universally measurable policies. For such models the standard policy iteration is known to have difficult measurability issues and cannot be carried out in general. We present a mixed value and policy iteration method that circumvents this difficulty. The method allows the use of stationary policies in computing the optimal cost function in a manner that resembles policy iteration. It can also be used to address similar difficulties of policy iteration in the context of upper and lower semicontinuous models. We analyze the convergence of the method in infinite horizon total cost problems for the discounted case where the one-stage costs are bounded and for the undiscounted case where the one-stage costs are nonpositive or nonnegative. For undiscounted total cost problems with nonnegative one-stage costs, we also give a new convergence theorem for value iteration that shows that value iteration converges whenever it is initialized with a function that is above the optimal cost function and yet bounded by a multiple of the optimal cost function. This condition resembles Whittle’s bridging condition and is partly motivated by it. The theorem is also partly motivated by a result of Maitra and Sudderth that showed that value iteration, when initialized with the constant function zero, could require a transfinite number of iterations to converge. We use the new convergence theorem for value iteration to establish the convergence of our mixed value and policy iteration method for the nonnegative cost case.
Tropisetron and paracetamol association in post‐operative patients

Studies in animals and in healthy volunteers have demonstrated the central serotonergic analgesic mechanism of action of paracetamol involving the inhibition of this analgesia by tropisetron, a 5‐HT3 antagonist. This randomized, double‐blind, controlled study aims at studying this interaction in post‐operative patients after ear surgery. Thirty‐six patients are included in two parallel groups with intravenous paracetamol (1 g) and either tropisetron (T, 5 mg/mL) or placebo (c, NaCl 0.9%) administered at the end of surgery. Numerical pain evaluations are performed every 30 min, six times after awakening. The difference between the sums of numerical scales of both groups [9 ± 10 (T) vs. 6 ± 7 (c)] is not significant, but the tropisetron group displays higher pain scores despite additional rescue analgesia. The limits of this trial call for a much larger study to investigate further this pharmacodynamic interaction.