Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of probabilistically linked data

Probabilistic matching of records from different data sets is often used to create linked data sets for use in research in health, epidemiology, economics, demography and sociology. Clearly, this type of matching can lead to linkage errors, which in turn can lead to bias and increased variability when standard statistical estimation techniques are used with the linked data. Recently, an inferential framework for statistical modelling using probabilistically linked data has been defined, which has then been used to develop modified estimation methods for regression models based on the assumption that the correctly linked records are mutually uncorrelated. In real life, however, measurements are usually made on clusters of correlated statistical units, such as people in a family, patients in a hospital or students in a school, and when analyzing such data, linear mixed models are often used. In this thesis we show how this inferential framework can be used to develop unbiased regression parameter estimates when fitting a linear mixed model to probabilistically linked data. Furthermore, since estimation of variance components is also an important objective when fitting a mixed model, we develop appropriate modifications to standard methods of variance components estimation in order to account for linkage error. In particular, we focus on three widely used methods of variance components estimation: analysis of variance (ANOVA), maximum likelihood (ML) and restricted maximum likelihood (REML). A simulation study investigates the bias and variability of parameter estimates obtained by methods developed in this work. Simulation results indicate that all methods developed here perform reasonably well. An application to longitudinal modeling is further investigated. In this situation, we focus on fitting linear mixed models to linked longitudinal registers. That is, more than two registers are linked and linkage errors occur across the entire registers. The results from a simulation study illustrate the performance of this approach, and show that although there is improved efficiency compared to the naive method which ignores the linkage errors, there are some issues that still need further investigation and improvement.
Optical signatures of momentum-dependent hybridization of the local moments and conduction electrons in kondo lattices

An analysis of the optical properties of heavy fermion compounds is reported. We focus on the 1-1-5 series, where strong deviations of the spectra are seen from the predictions of the periodic Anderson model. Specifically we demonstrate that the differences between the experimental results and the theoretical predictions can be explained by accounting for the momentum dependence of the hybridization between the local moments and the conducting carriers. Furthermore we find correlations between the hybridization strength on a particular band and some properties of the 1-1-5 compounds. These correlations suggest that the momentum dependence of the hybridization has to be taken into account, for an understanding of the electronic properties of these heavy fermion compounds.
Parameterized lossy compression of order-independent data

When dealing with extremely large quantities of data, it is sometimes necessary to make concessions in order to compress the data to a manageable size, a technique known as lossy compression. One example of such a concession is perfect knowledge of the order in which each data element was recorded. When sampling a random variable, it is often the case that the values measured are more important than the order in which they appear. We have designed a lossy compression scheme that capitalizes on this fact by representing the order in which a sequence of values was measured with less precision than the values themselves. That is, the compressed data is very accurate and efficiently compressed when order is disregarded. Our algorithm works by encoding the measured values as a non-decreasing sequence and their order of appearance as indices referencing contiguous subsequences or slices of the value list. By changing the criteria used to determine a slice, the recorded order may be made more or less accurate, increasing or decreasing compression ratios respectively. Moreover, values in special ranges can be treated specially; for instance, statistical outliers might be represented exactly, whereas mundane values might be recorded with less precision.
Crystallographic and NMR Analyses of UvsW and UvsW.1 from Bacteriophage T4*

The uvsWXY system is implicated in the replication and repair of the bacteriophage T4 genome. Whereas the roles of the recombinase (UvsX) and the recombination mediator protein (UvsY) are known, the precise role of UvsW is unclear. Sequence analysis identifies UvsW as a member of the monomeric SF2 helicase superfamily that translocates nucleic acid substrates via the action of two RecA-like motor domains. Functional homologies to Escherichia coli RecG and biochemical analyses have shown that UvsW interacts with branched nucleic acid substrates, suggesting roles in recombination and the rescue of stalled replication forks. A sequencing error at the 3′-end of the uvsW gene has revealed a second, short open reading frame that encodes a protein of unknown function called UvsW.1. We have determined the crystal structure of UvsW to 2.7Å and the NMR solution structure of UvsW.1. UvsW has a four-domain architecture with structural homology to the eukaryotic SF2 helicase, Rad54. A model of the UvsW-ssDNA complex identifies structural elements and conserved residues that may interact with nucleic acid substrates. The NMR solution structure of UvsW.1 reveals a dynamic four-helix bundle with homology to the structure-specific nucleic acid binding module of RecQ helicases.
Prolonged Thromboprophylaxis With Dalteparin After Surgical Treatment of Achilles Tendon Rupture: A Randomized, Placebo-Controlled Study

Objectives: Prophylaxis against thromboembolic complications has become routine after major orthopedic surgery. In contrast, it remains an issue for debate whether prophylaxis after minor surgery and immobilization is necessary, even though these treatments are well-known risk factors for deep-vein thrombosis (DVT). The objective of this study was to evaluate the efficacy of dalteparin during lower-limb immobilization after surgical treatment of Achilles tendon rupture. Design Setting, and Patients: Randomized, placebo-controlled, double-blind study of 105 consecutive patients surgically treated for Achilles tendon rupture in a trauma hospital. DVT screening with color duplex sonography was conducted 3 weeks and 6 weeks after surgery. All DVTs were confirmed with phlebography. Intervention was placebo or dalteparin (5000 U) given subcutaneously once daily for 6 weeks postoperatively. Main Outcome Measure: DVT incidence. Results: Primary endpoint analysis was available for 91 patients. DVT was diagnosed in 16 of 47 patients (34%) in the dalteparin group and in 16 of 44 patients (36%) in the placebo group. These figures are not significantly different (P = 0.8). Proximal DVT was diagnosed in 1 patient (2%) in the dalteparin group and in 3 patients (6%) in the placebo group (P = 0.6). No pulmonary emboli or major bleeding occurred in either of the groups. Conclusions: DVT is common after surgical treatment of Achilles tendon rupture, and therefore effective thromboprophylaxis is desirable. In our study, thromboprophylaxis with dalteparin, however, does not affect the incidence of DVT during immobilization after Achilles tendon rupture surgery. Long-term effects of immobilization, such as the risk for postthrombotic syndrome, need to be investigated further.
Statistical recombinant mapping in extended high‐risk Utah pedigrees narrows the 8q24 prostate cancer locus to 2.0 Mb

Chromosome 8q24 is a region of compelling interest for prostate cancer (PRCA). Linkage, association, and admixture analysis initially indicated the region. Subsequently, several variants at 8q24 have been found to independently associate with PRCA. One compelling hypothesis is allelic heterogeneity, whereby multiple variants affect the regulation of the same gene. In addition to potential allelic heterogeneity, 8q24 exhibits strong linkage disequilibrium over vast distances and is prone to chromosomal aberrations.
Improved Locally Linear Embedding by Using Adaptive Neighborhood Selection Techniques

Unsupervised learning algorithm locally linear embedding (LLE) is a typical technique which applies the preserving embedding method of high dimensional data to low dimension. The number of neighborhood nodes of LLE is a decisive parameter because the improper value will affect the manifold structure in the local neighborhood and lead to the lower computational efficiency. Based on the fact that the shortest path in low-density can be established easily, this paper proposes an improved LLE method by using the sparse matrix in combination with the weights related to each point used for the linear combination in local neighborhood. The correlation dimension between high and low dimension is used to estimate the proper number of the reduced dimension, thereby selecting the best upper bound for the non-uniform manifold. Finally, we provide the experimental evaluation to verify the effectiveness of the proposed algorithm.
Less stress during computer work: Survey on user preferences of stress measurement and notification methods

working with computer often experience work-related stress, which is unpleasant, unhealthy and unproductive, especially when experienced for prolonged periods. The aim of this paper is to indentify non intrusive ways to measure users' stress and inform users about their stress. A survey was completed to assess computer users' opinions on different ways used to measure their emotional state during work and on different methods used to inform them of their stress level. The conclusion is that the most preferred measuring method is a modified mouse: 89% of the people would not disagree or would accept this at work. The most preferred notification method is an MSN-like pop-up in the bottom right of the screen. Users expect that a pop-up with exercises is more effective to reduce stress than the MSN-like pop-up. Intrusion of privacy is a factor that correlated highly with disliking a measuring method. These findings can be applied in stress reducing software. Keywordsstress level, computer user, measuring stress, emotion recognition, affective computing, Stress recognition,, Notification methods.
Revolving multipinhole SPECT for small animal imaging

Multi-pinhole collimators are often used to obtain the detection sensitivity necessary for small animal SPECT with submillimeter spatial resolution. However, in comparison to pinhole collimators with single aperture, multipinhole acquisitions run the risk of yielding overlapping projection data, which can result in reconstructed images that exhibit multiplexing artifacts. In this work, we study the multiplexing artifacts produced by a nine-pinhole collimator in three different acquisition geometries: (1) circular multipinhole (CMP) in which the nine-pinhole collimator is rotated around the object with a simple circular gantry rotation, (2) helical multipinhole (HMP) that uses a circular gantry rotation combined with a table translation to produce a helical acquisition, and (3) revolving multipinhole (RMP) produced with a circular orbit of the gantry combined with a concurrent revolution of the nine-pinhole collimator. The pinhole configurations were simulated for a SPECT scanner with a 40 40 cm2 detector. The reconstructed images obtained using the different imaging geometries were compared by calculating the lesion detectability index, contrast-ratio, normalized standard deviation and percentage error using a series of simulation experiments. The improved sampling obtained with the RMP imaging geometry produced a faithful reconstruction of a larger FOV compared to the single pinhole (SP) case. For example, the contrast ratio for equivalent noise levels obtained from a Defrise phantom were approximately 98%, 92%, 75% and 35% for RMP, HMP, CMP and SP respectively. Results show that the improved angular sampling of the RMP imaging geometry diminishes the effects of multiplexing patterns thereby facilitating the accurate convergence of the resulting SPECT image.
False Discovery Rate and Correction for Multiple Comparisons in Association Genome Screens for Complex Disorders

There is great current interest in using linkage disequilibrium (LD)-based genome screens to localize genes responsible for common diseases. These screens involve many more markers than traditional linkage studies and therefore present the issue of defining an appropriate significance threshold that takes into account the consequent multiple comparisons. We explore the conceptual and practical implications of adopting the False Discovery Rate (FDR) as a measure of global error in multiple tests for LD-screening. Controlling FDR leads to an increased power to detect more than one locus, making this strategy particularly appealing for complex disease mapping. B ENJAMINI and HOCHBERG(1995) provided a step-wise rule for controlling FDR with independent tests and later proved that it works also for tests that are positive-dependent (B ENJAMINI and YEKUTIELI , 2001). We show analytically and through a simulation study that this rule also effectively controls the FDR for the dependent tests encountered in association mapping from case-control data. Our simulation also emphasizes the increase of power achieved with FDR based procedures over more traditional methods. We further demonstrate the utility of FDR with an example from a real data set from a genome-wide LD study.
Cardiac MRI: Recent progress and continued challenges

Cardiac MRI continues to develop and advance. MRI accurately depicts cardiac structure, function, perfusion, and myocardial viability with an overall capacity unmatched by any other single imaging modality. MRI is an accepted and widely utilized tool for cardiovascular research. Its clinical use has been limited, but is increasing because of its proven clinical efficacy, the proliferation of cardiac‐capable MRI systems, and the development of improved pulse sequences. The following article reviews the landmark developments in this field, with an emphasis on recent progress in the evaluation of ischemic or acquired heart disease. J. Magn. Reson. Imaging 2002;16:111–127. Published 2002 Wiley‐Liss, Inc.
Prospective randomized controlled clinical study comparing two dental implant types: volumetric soft tissue changes at 1 year of loading.

OBJECTIVE To evaluate the volumetric changes occurring from prosthesis insertion to the 1-year follow-up (FU) using one- and two-piece dental implants. METHODS Sixty patients were randomly assigned to receive one-piece or two-piece implants. Casts were obtained at baseline (insertion of final reconstruction) and at 1 year of loading. Finally, 33 pairs of casts (BRA = 18, STM = 15) were deemed appropriate for volumetric analysis of the peri-implant tissues. If the patients had more than one implant, one was randomly selected for analysis. Casts were scanned to obtain stereolithography (STL) files. Baseline and 1-year FU digital models were superimposed with an image analysis program. Linear and volumetric measurements were performed including (i) crown height changes (CHCs), (ii) volumetric changes, and (iii) changes in tissue thickness at three levels below the mucosal margin on the buccal side of the implants (at 1,3, and 5 mm). The Mann-Whitney U-test and the paired t-test were used to analyze the data between the two groups using the patient as the unit of analysis. RESULTS No significant baseline differences were observed between the one- and two-piece groups for the linear measurements. The mean CHCs in the two-piece group amounted to 0.02 mm (SD ± 0.32), whereas the one-piece group exhibited a change of -0.17 mm (±0.57). The mean volume changes (VCs) were -0.12 mm (±0.27) (two-piece group) and -0.03 mm (±0.29) (one-piece group). With regard to the changes in tissue thickness, the two-piece group presented a change of -0.15 mm (±0.20) at 1 mm, -0.06 mm (±0.20) at 3 mm, and -0.2 mm (±0.51) at 5 mm. The respective values for the one-piece group were -0.03 mm (±0.35), 0.01 mm (±0.28), and -0.01 mm (±0.51) at the three levels. None of the differences in linear measurements between baseline and the 1-year FU reached significance. Positive correlations were seen for tissue thickness changes at 1 and 3 mm for both groups (P < 0.05). Significant positive correlations were found for VCs and tissue thickness at 1 mm for the two-piece group and for VCs and tissue thickness at 1,3, and 5 mm for the one-piece group (P < 0.05). CONCLUSION Within the first year of loading, minimal changes occur with regard to tissue thickness, crown height, and facial volume for both implant types.
CAUTIONS ON DIRECT GENE FLOW ESTIMATION IN PLANT POPULATIONS

Abstract Through simulations we have investigated the statistical properties of two of the main approaches for directly estimating pollen gene flow (m) in plant populations: genotypic exclusion and mating models. When the assumptions about accurately known background pollen pool allelic frequencies are met, both methods provide unbiased results with comparable variances across a range of true m values. However, when presumed allelic frequencies differ from actual ones, which is more likely in research practice, both estimators are biased. We demonstrate that the extent and direction of bias largely depend on the difference (measured as genetic distance) between the presumed and actual pollen pools, and on the degree of genetic differentiation between the local population and the actual background pollen sources. However, one feature of the mating model is its ability to estimate pollen gene flow simultaneously with background pollen pool allelic frequencies. We have found that this approach gives nearly unbiased pollen gene flow estimates, and is practical because it eliminates the necessity of providing independent estimates of background pollen pool allelic frequencies. Violations of the mating model assumptions of random mating within local population affect the precision of the estimates only to a limited degree.
Assessment of cerebral blood flow in Alzheimer's disease by spin‐labeled magnetic resonance imaging

To evaluate the utility of arterial spin‐labeled blood flow magnetic resonance imaging for the detection of cerebral blood flow abnormalities in Alzheimer's disease, arterial spin‐labeled blood flow images in 16 contiguous 5‐mm axial sections were acquired in 18 patients diagnosed with probable Alzheimer's disease and 11 age‐matched controls. Blood flow images from all subjects were transformed to a standard anatomical space for voxel‐by‐voxel statistical analysis. High quality blood flow images were obtained from all but 1 subject. Statistical analysis demonstrated significant flow decreases relative to control subjects in temporal, parietal, frontal, and posterior cingulate cortices. Increased severity of disease, as measured by Mini‐Mental State Examination, correlated with posterior parietal and posterior cingulate decreases but not temporal decreases. Arterial spin‐labeled magnetic resonance imaging was found to be an effective tool for characterizing flow decreases accompanying Alzheimer's disease. The absence of ionizing radiation or injection and the ability to obtain high quality anatomical images within the same scanning session make arterial spin labeling an attractive technique for the study of Alzheimer's disease, for the evaluation of pharmacological therapies, and, possibly, for early diagnosis. Ann Neural 2000; 47:93–100
The Short Hairpin RNA Driven by Polymerase II Suppresses both Wild-Type and Lamivudine-Resistant Hepatitis B Virus Strains

Background Chronic infection with hepatitis B virus (HBV) is widespread because of the limited availability of therapeutic treatments. Although previous reports have suggested that RNA interference has promise as a treatment for HBV infection, further studies of long-term and off-target drug effects on HBV, especially on drug-resistant strains of HBV, are needed. Therefore, seven vectors that express short hairpin RNAs (shRNAs), driven by the polymerase II promoter, pSilencer4.1/HBV, were constructed to target open reading frames (ORFs) of the HBV C and S genes from wild-type and drug-resistant strains. Treatment efficiency was also assessed. Methods The pSilencer4.1/HBV vectors were investigated in HepG2.2. 15 cells and transgenic mice that consistently produce wild-type HBV. Additionally, vectors that produce a lamivudine-resistant strain of HBV were developed and cotransfected, along with pSilencer/HBV, into both HepG2 cells and mice. The effects of polymerase-II-driven pSilencer4.1/HBV were compared with those of polymerase-III-driven pSilencer3.1/HBV at both the gene and protein level. Results pSilencer4.1/HBV inhibited the expression of viral protein, DNA and HBV subtype ayw mRNA in both HepG2.2. 15 cells and transgenic mice. Toxicity, as well as off-target effects, did not occur after a short- to medium-term examination. Moreover, an HBV strain resistant to lamivudine, subtype adr, was suppressed by shRNA in both HepG2 cells and mice. In contrast to polymerase III, vectors that used polymerase II could drive efficient silencing without off-target effects. Conclusions Silencing by shRNA dramatically inhibited HBV expression and replication regardless of strain type. ShRNA could therefore be a promising treatment for HBV infection.
Development of a Chemically Defined Medium for the Growth of Leuconostoc mesenteroides

A chemically defined medium for the growth of Leuconostoc mesenteroides was developed. This medium contained lactose, Mn(sup2+), Mg(sup2+), 12 amino acids, eight vitamins, adenine, uracil, and Tween 80. We showed the beneficial effect of aerobic conditions on growth and that potassium phosphate (135 mM) is a suitable buffer. The growth rate in this medium was 0.85 (plusmn) 0.10 h(sup-1) for the six strains examined, and cell densities up to 3.5 x 10(sup9) CFU/ml were attained.
Variation in Shorebird Use of Diurnal, High-tide Roosts: How Consistently are Roosts Used?

Abstract In coastal environs during the non-breeding season, many shorebirds (suborder Charadrii) congregate at roosts, long considered to be traditional sites where flocks of individuals coalesce when high tides inundate feeding areas. Humboldt Bay, California was surveyed (9.5 months at roughly 10-d intervals) to assess temporal variation in incidence (proportion of 28 surveys birds used a roost), proportional abundance, concentrations, and repeatability (of seasonal average proportional abundances) of shorebird use of diurnal, high-tide roosts. Two hundred and forty roosting locations were identified and observations were made of 30 species. Fourteen species accounted for over 99% of observations. Shorebirds occurred at most roosts infrequently (<20% of surveys) and only 4% of roosts had roosting birds present on more than 80% of occasions. Abundant species occurred at more roosts (20-141 roosts per species) compared with less common species. Even at the most-used roosts, abundances at the species level varied greatly. Repeatability of roost use among seasons was high. At Humboldt Bay, roost use formed a continuum from ephemeral locations used by a few birds to sites used consistently by large numbers of individuals.