Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplex Real-Time PCR Assay for Simultaneous Quantification of BK Polyomavirus, JC Polyomavirus, and Adenovirus DNA

ABSTRACT In recent years, virus-induced nephropathy caused mainly by BK polyomavirus (BKPyV), JC polyomavirus (JCPyV), and adenovirus has emerged as a problem in renal transplant patients. In the present study, we developed a multiplex real-time PCR assay to quantify the viral load of BKPyV, JCPyV, and adenovirus simultaneously. The dynamic range covered at least 6 orders of magnitude. This system was specific and reproducible, even in the presence of large amounts of DNA of other viruses. To validate this assay, urine samples from 124 renal transplant patients and serum samples from 18 hemorrhagic cystitis patients after hematopoietic stem cell transplantation were examined. In the urine samples from renal transplant patients, BKPyV was detected in 28 patients (22.6%), JCPyV was detected in 51 patients (41.1%), and adenovirus was detected in 2 patients (1.6%). The maximum amounts of each virus detected were 2.7 × 109, 8.7 × 108, and 1.2 × 102 copies/ml, respectively. Decoy cells were observed in 31 patients. The quantities of both BKPyV and JCPyV DNA were greater in samples with decoy cells. Two patients whose BKPyV viral loads exceeded 108 copies/ml had elevated serum creatinine levels and were diagnosed with BKPyV nephropathy based on graft biopsies. In serum samples from hemorrhagic cystitis patients, BKPyV, JCPyV, and adenovirus was detected in six, two, and three patients, respectively. Strong correlations were observed between the viral DNA copy numbers determined in the multiplex assays and those determined in single assays. Since this new assay is rapid, sensitive, and specific, it can be used for quantitative analyses of viruses in urine and serum samples after transplantation.
Effects of castration on the expression of the NGF and TrkA in the vas deferens and accessory male genital glands of the rat

Nerve Growth Factor (NGF) is a member of the neurotrophin family. Neurotrophins exert their effects by binding to corresponding receptors, which are formed by the tyrosine protein kinases TrkA, TrkB, and TrkC, and the low affinity p75NTR receptor. The role of neurotrophins in the biology of male genital organs is far from clear. In particular, little is known about the influence of sex hormones on the expression of neurotrophins and their receptors. In the present study, using immunohistochemistry and real time RT-PCR, we investigated the expression of NGF and TrkA in the vas deferens and accessory male genital glands in normal and castrated rats. In normal rats, both NGF- and TrkA-immunoreactivities (IR) were localized in the epithelial layer of the vas deferens. NGF-IR was also found in the stroma and epithelium of the vesicular gland and prostate. TrkA-IR was distributed in the epithelial cells of vesicular and prostate glands. The nerves were weakly immunoreactive in all the examined organs. After castration the immunoreactivities increased. Real-time RT-PCR experiments indicated that NGF and TrkA mRNA levels increased significantly after castration. These results suggest that NGF and TrkA are expressed in the internal male genital organs of the rat and that their expression is downregulated by androgen hormones. We hypothesize NGF and TrkA play a role in the processes that regulate the involution of these organs under conditions of androgen deprivation.
Physical Activity and All-cause Mortality in Japan:  The Jichi Medical School (JMS) Cohort Study

Background In April 2008, a new health check-up and health guidance system was introduced by the Japanese Government to promote increased physical activity. However, few studies have documented the health benefits of physical activity in Asian populations. We examined the association between all-cause mortality and level of physical activity in a Japanese multicommunity population-based study. Methods The Jichi Medical School Cohort Study is a multicommunity, population-based study based in 12 districts in Japan. Baseline data from 4222 men and 6609 women (mean age, 54.8 and 55.0 years, respectively) were collected between April 1992 and July 1995. The participants were followed for a mean duration of 11.9 years. To determine the association between all-cause mortality and level of physical activity, crude mortality rates per 1000 person-years and hazard ratios (HRs) with 95% confidence intervals (CI) were determined using the Cox proportional hazards model. Physical activity was categorized by using physical activity index (PAI) quartiles. The lowest (first) PAI quartile was defined as the HR reference. Results In men, the lowest mortality rate was observed in the third quartile, with 95 deaths and a crude mortality rate of 7.6; the age- and area-adjusted HR was 0.59 (95% CI, 0.45–0.76), and the mortality curve had a reverse J shape. In women, the lowest mortality rate was observed in the highest PAI quartile, with 69 deaths and a crude mortality rate of 3.5; the HR was 0.81 (95% CI, 0.58–1.12). Conclusion Our results suggest that increased physical activity lowers the risk for all-cause death in Japanese.
Model reduction by moment matching, steady-state response and projections

The model reduction problem by moment matching for linear systems is revisited and connections between projection based methods and the notion of steady-state response are established. A systems theoretic interpretation of the (oblique) projectors used in Krylov methods is derived and a new family of reduced order models achieving moment matching is given. Finally, the equivalence between various families of reduced order models, all achieving moment matching, is established.
Social Event Detection at MediaEval 2012: Challenges, Dataset and Evaluation

This paper provides an overview of the Social Event Detection (SED) task, which is organized as part of the MediaEval 2012 benchmarking activity and examines how social events can be detected by automatically analyzing social multimedia content. The 2012 edition of the SED task follows the successful completion of the flrst edition of SED, in 2011. This paper discusses the challenges set as part of SED 2012, the dataset, and the process of evaluating the submissions.
Cross-Reactive Anti-Viral T Cells Increase Prior to an Episode of Viral Reactivation Post Human Lung Transplantation

Human Cytomegalovirus (CMV) reactivation continues to influence lung transplant outcomes. Cross-reactivity of anti-viral memory T cells against donor human leukocyte antigens (HLA) may be a contributing factor. We identified cross-reactive HLA-A*02:01-restricted CMV-specific cytotoxic T lymphocytes (CTL) co-recognizing the NLVPMVATV (NLV) epitope and HLA-B27. NLV-specific CD8+ T cells were expanded for 13 days from 14 HLA-A*02:01/CMV seropositive healthy donors and 11 lung transplant recipients (LTR) then assessed for the production of IFN-γ and CD107a expression in response to 19 cell lines expressing either single HLA-A or -B class I molecules. In one healthy individual, we observed functional and proliferative cross-reactivity in response to B*27:05 alloantigen, representing approximately 5% of the NLV-specific CTL population. Similar patterns were also observed in one LTR receiving a B27 allograft, revealing that the cross-reactive NLV-specific CTL gradually increased (days 13–193 post-transplant) before a CMV reactivation event (day 270) and reduced to basal levels following viral clearance (day 909). Lung function remained stable with no acute rejection episodes being reported up to 3 years post-transplant. Individualized immunological monitoring of cross-reactive anti-viral T cells will provide further insights into their effects on the allograft and an opportunity to predict sub-clinical CMV reactivation events and immunopathological complications.
A signal processing approach to fair surface design

In this paper we describe a new tool for interactive free-form fair surface design. By generalizing classical discrete Fourier analysis to two-dimensional discrete surface signals - functions defined on polyhedral surfaces of arbitrary topology -, we reduce the problem of surface smoothing, or fairing, to low-pass filtering. We describe a very simple surface signal low-pass filter algorithm that applies to surfaces of arbitrary topology. As opposed to other existing optimization-based fairing methods, which are computationally more expensive, this is a linear time and space complexity algorithm. With this algorithm, fairing very large surfaces, such as those obtained from volumetric medical data, becomes affordable. By combining this algorithm with surface subdivision methods we obtain a very effective fair surface design technique. We then extend the analysis, and modify the algorithm accordingly, to accommodate different types of constraints. Some constraints can be imposed without any modification of the algorithm, while others require the solution of a small associated linear system of equations. In particular, vertex location constraints, vertex normal constraints, and surface normal discontinuities across curves embedded in the surface, can be imposed with this technique.
Deconvolution of dynamic contrast‐enhanced MRI data by linear inversion: Choice of the regularization parameter

Truncated singular value decomposition (TSVD) is an effective method for the deconvolution of dynamic contrast‐enhanced MRI. Two robust methods for the selection of the truncation threshold on a pixel‐by‐pixel basis—generalized cross validation (GCV) and the L‐curve criterion (LCC)—were optimized and compared to paradigms in the literature. The methods lead to improvements in the estimate of the residue function and of its maximum and converge properly with SNR. The oscillations typically observed in the solution vanish entirely and perfusion is more accurately estimated at small mean transit times. This results in improved image contrast and increased sensitivity to perfusion abnormalities, at the cost of 1–2 min in calculation time and isolated instabilities in the image. It is argued that the latter problem may be resolved by optimization. Simulated results for GCV and LCC are equivalent in terms of performance, but GCV is faster. Magn Reson Med 52:209–213, 2004. © 2004 Wiley‐Liss, Inc.
Bridging the Gap Between Basic and Clinical Electrophysiology:

Monophasic Action Potentials. With rapid advances occuring in both basic and clinical electrophysiology, the gap between the two disciplines appears to be widening rather than narrowing. In most instances, we cannot apply the knowledge derived from cellular studies directly to clinical practice. Monophasic action potential (MAP) recording by contact electrode technique allows us in measure basic electrophysiological phenomena in the human heart and thus provides an important bridge between basic and clinical electrophysiology. MAP recordings produce the lime course of cellular repolarization during cycle length changes and antiarrhythmic drug administration, lending insights into use dependency and reverse use dependency of antiarrhythmic drug effects in the clinical electrophsiology laboratory. The ability to deliver electrical stimuli at the MAI recording site further allows one to investigate drug‐induced postrepolarization refractoriness. MAP recordings provide precise local activation times, important for mapping of abnormal ventricular activation, and detect areas of abnormal repolarization due to ischemia or scarring. MAP recordings are uniquely suited to detect early and delayed afterdepolarizations in the human heart, thereby helping to unravel the arrhythmia mechanisms in the long QT syndrome. By embedding the MAP electrode in a radiofrequency electrode, arrhythmogenic foci may be both detected and ablated. In many instances, MAP recordings are more accurate than KCG tracings in defining and distinguishing ventricular fibrillation and ventricular tachycardia. This can he of clinical importance during testing of the implantable cardioverler/delibrillator. An area of growing interest is stretch‐activated arrhythmias. Here, MAP recordings are of particular value because no other method is available to record mechanically induced electrophysiological changes in the vigorously beating heart. It can be expected that MAP recordings will, in the future, provide this important bridge between “cell and bedside” also in atrial tachyarrhythmias, such as in atrial fibrillation and flutter.
Manin Pairs and Moment Maps

A Lie group $G$ in a group pair ($D, G$), integrating the Lie algebra $\mathfrak{g}$ in a Manin pair ($\mathfrak{d,g}$), has a quasi-Poisson structure. We define the quasi-Poisson actions of such Lie groups $G$, and show that they generalize the Poisson actions of Poisson Lie groups. We define and study the moment maps for those quasi-Poisson actions which are hamiltonian. These moment maps take values in the homogeneous space $D/G$. We prove an analogue of the hamiltonian reduction theorem for quasi-Poisson group actions, and we study the symplectic leaves of the orbit spaces of hamiltonian quasi-Poisson spaces.
Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

The multidrug-resistant Streptococcus pneumoniae Taiwan19F-14, or PMEN14, clone was first observed with a 19F serotype, which is targeted by the heptavalent polysaccharide conjugate vaccine (PCV7). However, “vaccine escape” PMEN14 isolates with a 19A serotype became an increasingly important cause of disease post-PCV7. Whole genome sequencing was used to characterize the recent evolution of 173 pneumococci of, or related to, PMEN14. This suggested that PMEN14 is a single lineage that originated in the late 1980s in parallel with the acquisition of multiple resistances by close relatives. One of the four detected serotype switches to 19A generated representatives of the sequence type (ST) 320 isolates that have been highly successful post-PCV7. A second produced an ST236 19A genotype with reduced resistance to β-lactams owing to alteration of pbp1a and pbp2x sequences through the same recombination that caused the change in serotype. A third, which generated a mosaic capsule biosynthesis locus, resulted in serotype 19A ST271 isolates. The rapid diversification through homologous recombination seen in the global collection was similarly observed in the absence of vaccination in a set of isolates from the Maela refugee camp in Thailand, a collection that also allowed variation to be observed within carriage through longitudinal sampling. This suggests that some pneumococcal genotypes generate a pool of standing variation that is sufficiently extensive to result in “soft” selective sweeps: The emergence of multiple mutants in parallel upon a change in selection pressure, such as vaccine introduction. The subsequent competition between these mutants makes this phenomenon difficult to detect without deep sampling of individual lineages.
On the stability of planar randomly switched systems

Consider the random process (Xt) t>0 solution of u Xt = AItXt where (It) t>0 is a Markov process on f 0;1g and A0 and A1 are real Hurwitz matrices on R 2 . Assuming that there exists � 2 (0;1) such that (1 − � )A0 + �A 1 has a positive eigenvalue, we establish that k Xtk may converge to 0 or +1 depending on the the jump rate of the process I. An application to product of random matrices is studied. This paper can be viewed as a probabilistic counterpart of the paper [2] by Balde, Boscain and Mason.
POSTERIOR CONSISTENCY OF BAYESIAN NONPARAMETRIC MODELS USING LÉVY RANDOM FIELD PRIORS

Department of Statistical Science, Duke University March 24, 2008 We show the posterior consistency of certain nonparametric regression models using Lévy Random field priors. An easily verifiable sufficient condition is derived for the posterior consistency to hold in popular models which use Lévy random fields for regression and function estimation. We apply our results to a Poisson regression model. Our calculations on the Poisson regression model are of independent interest.
Prospective Evaluation of the Effect of an Aminoglycoside Dosing Regimen on Rates of Observed Nephrotoxicity and Ototoxicity

ABSTRACT The nephrotoxicity and ototoxicity associated with once-daily versus twice-daily administration of aminoglycosides was assessed in patients with suspected or proven gram-negative bacterial infections in a randomized, double-blind clinical trial. Patients who received therapy for ≥72 h were evaluated for toxicity. Patients also received concomitant antibiotics as deemed necessary for treatment of their infection. Plasma aminoglycoside concentrations, prospective aminoglycoside dosage adjustment, and serial audiologic and renal status evaluations were performed. The probability of occurrence of a nephrotoxic event and its relationship to doses and daily aminoglycoside exposure served as the main outcome measurement. One hundred twenty-three patients were enrolled in the study, with 83 patients receiving therapy for at least 72 h. For 74 patients plasma aminoglycoside concentrations were available for analysis, and the patients formed the group evaluable for toxicity. The primary infectious diagnosis for the patients who were enrolled in the study were bacteremia or sepsis, respiratory infections, skin and soft tissue infections, or urosepsis or pyelonephritis. Of the 74 patients evaluable for toxicity, 39 received doses twice daily and 35 received doses once daily and a placebo 12 h later. Nephrotoxicity occurred in 6 of 39 (15.4%) patients who received aminoglycosides twice daily and 0 of 35 patients who received aminoglycosides once daily. The schedule of aminoglycoside administration, concomitant use of vancomycin, and daily area under the plasma concentration-time curve (AUC) for the aminoglycosides were found to be significant predictors of nephrotoxicity by multivariate logistic regression analysis (P ≤ 0.001). The time to a nephrotoxic event was significantly influenced by vancomycin use and the schedule of administration, as assessed by Cox proportional hazards modeling (P ≤ 0.002). The results of the multivariate logistic regression analysis and the Cox proportional hazards modeling demonstrate that both the probability of occurrence and the time to occurrence of aminoglycoside nephrotoxicity are influenced by the schedule on which the aminoglycoside is administered as well as by the concomitant use of vancomycin. Furthermore, this risk of occurrence is modulated by the daily AUC for aminoglycoside exposure. These data suggest that once-daily administration of aminoglycosides has a predictably lower probability of causing nephrotoxicity than twice-daily administration.
Catalytic Upgrading of Biomass-Derived Furfuryl Alcohol to Butyl Levulinate Biofuel over Common Metal Salts

Levulinate ester has been identified as a promising renewable fuel additive and platform chemical. Here, the use of a wide range of common metal salts as acid catalysts for catalytic upgrading of biomass-derived furfuryl alcohol to butyl levulinate was explored by conventional heating. Both alkali and alkaline earth metal chlorides did not lead effectively to the conversion of furfuryl alcohol, while several transition metal chlorides (CrCl3, FeCl3, and CuCl2) and AlCl3 exhibited catalytic activity for the synthesis of butyl levulinate. For their sulfates (Cr(III), Fe(III), Cu(II), and Al(III)), the catalytic activity was low. The reaction performance was correlated with the Bronsted acidity of the reaction system derived from the hydrolysis/alcoholysis of cations, but was more dependent on the Lewis acidity from the metal salts. Among these investigated metal salts, CuCl2 was found to be uniquely effective, leading to the conversion of furfuryl alcohol to butyl levulinate with an optimized yield of 95%. Moreover, CuCl2 could be recovered efficiently from the resulting reaction mixture and remained with almost unchanged catalytic activity in multiple recycling runs.
Ti-doped ZnO Thin Films Prepared at Different Ambient Conditions: Electronic Structures and Magnetic Properties

We present a comprehensive study on Ti-doped ZnO thin films using X-ray Absorption Fine Structure (XAFS) spectroscopy. Ti K edge XAFS spectra were measured to study the electronic and chemical properties of Ti ions in the thin films grown under different ambient atmospheres. A strong dependence of Ti speciation, composition, and local structures upon the ambient conditions was observed. The XAFS results suggest a major tetrahedral coordination and a 4+ valence state. The sample grown in a mixture of 80% Ar and 20% O2 shows a portion of precipitates with higher coordination. A large distortion was observed by the Ti substitution in the ZnO lattice. Interestingly, the film prepared in 80% Ar, 20% O2 shows the largest saturation magnetic moment of 0.827 ± 0.013 µB/Ti.
Dynamic Copula Networks for Modeling Real-valued Time Series

Probabilistic modeling of temporal phenomena is of central importance in a variety of elds ranging from neuroscience to economics to speech recognition. While the task has received extensive attention in recent decades, learning temporal models for multivariate real-valued data that is non-Gaussian is still a formidable challenge. Recently, the power of copulas, a framework for representing complex multi-modal and heavy-tailed distributions, was fused with the formalism of Bayesian networks to allow for exible modeling of highdimensional distributions. In this work we introduce Dynamic Copula Bayesian Networks (DCBNs), a generalization aimed at capturing the distribution of rich temporal sequences. We apply our model to three markedly dierent real-life domains and demonstrate substantial quantitative and qualitative advantages.
Effects of Compressing Pressure on Briquettes Made from Woody Biomass

Biomass, in particular wood, has become a fundamental renewable energy source that can replace fossil fuels in many applications, from eating to electricity production. Wood chips are one of the most popular biomass fuel in latest cogenerating plants and in small heating systems. This fuel has low bulk density and needs large volumes in handling and transport operations. These obstacles, common to many biological residues, can be overcome by densification. This study reports the effects of the compressing pressure on the demand of energy required in briquetting, final bulk density and durability of briquettes manufactured from wood chips. An hydraulic press was used to produce briquettes in controlled conditions. Five pressure levels (20, 30, 50, 80 and 110 MPa) and three different types of wood chips (PC hybrid poplar, CC chestnut, and MC mixture of spruce white pine) were investigated. The study shows that the different pressures adopted significantly affect the specific compression energy, the final density and the durability of the compacted samples. Equations were developed to predict compact density and the specific compression energy required by the densification process. The specific compression energy values obtained in this study (18-58 kJ kg) were significantly lower than the specific energy required to manufacture pellets made from biomass feedstock (typically 19-90 kJ kg). Furthermore, chestnut wood chips with pressure at 110 MPa resulted in the maximum briquettes bulk density and durability.