Miracle-dz/UniFAR-FTUs huggingface dataset:
Smoothing across time in repeated cross‐sectional data

Repeated cross‐sectional samples are common in national surveys of health like the National Health Interview Survey (NHIS). Because population health outcomes generally evolve slowly, pooling data across years can improve the precision of current‐year annual estimates of disease prevalence and other health outcomes. Pooling over time is particularly valuable in health disparities research, where outcomes for small groups are often of interest and pooling data across groups would bias disparity estimates. State‐space modeling and Kalman filtering are appealing choices for smoothing data across time. However, filtering can be problematic when few time points are available, as is common with annual cross‐sectional data. Problems arise because filtering relies on estimated variance components, which can be biased and imprecise when estimated with small samples, especially when estimated in tandem with linear trends. We conduct a simulation study showing that even when trends and variance components are estimated poorly, smoothing with these estimates can improve the mean squared error (MSE) of estimated health states for multiple racial/ethnic groups when the variance components are estimated with the pooled sample. We consider frequentist estimators with no trends, one common trend across groups, and separate trends for every group, as well as shrinkage estimators of trends through a Bayesian model. We show that the Bayesian model offers the greatest improvement in MSE, and that Bayesian Information Criterion (BIC)‐based model averaging of the frequentist estimators with different trend assumptions performs nearly as well. We present empirical examples using the NHIS data. Copyright © 2011 John Wiley & Sons, Ltd.
A complete estimate of the phylogenetic relationships in Ruminantia: a dated species‐level supertree of the extant ruminants

This paper presents the first complete estimate of the phylogenetic relationships among all 197 species of extant and recently extinct ruminants combining morphological, ethological and molecular information. The composite tree is derived by applying matrix representation using parsimony analysis to 164 previous partial estimates, and is remarkably well resolved, containing 159 nodes (>80% of the potential nodes in the completely resolved phylogeny). Bremer decay index has been used to indicate the degree of certainty associated with each clade. The ages of over 80 % of the clades in the tree have been estimated from information in the literature. The supertree for Ruminantia illustrates which areas of ruminant phylogeny are still only roughly known because of taxa with controversial relationships (e.g. Odocoileini, Antilopinae) or not studied in great detail (e.g. Muntiacus). It supports the monophyly of the ruminant families and Pecora. According to this analysis Antilocapridae and Giraffidae constitute the superfamily Giraffoidea, which is the sister group of a clade clustering Bovoidea and Cervoidea. The position of several taxa whose systematic positions have remained controversial in the past (Saiga, Pelea, Aepycerus, Pantholops, Ammotragus, Pseudois) is unambiguously established. Nevertheless, the position of Neotragus and Oreotragus within the original radiation of the non‐bovine bovids remains unresolved in the present analysis. It also shows that six successive rapid cladogenesis events occurred within the infraorder Pecora during the Oligocene to middle Pliocene, which coincided with periods of global climatic change. Finally, the presented supertree will be a useful framework for comparative and evolutionary biologists interested in studies involving the ruminants.
A luminescence assay for natural product inhibitors of the Mycobacterium tuberculosis proteasome.

INTRODUCTION Mycobacterium tuberculosis (Mtb) causes a large global burden of disease, with a high mortality rate in healthy and immuno-compromised patients. A number of molecular targets have been identified for treatment of this disease, including the Mtb proteasome. The Mtb proteasome enhances Mtb survival during nitrosative and oxidative stress in the latent, non-replicative phase. Therefore, Mtb proteasome inhibition could help to combat Mtb infections that do not respond to current therapies. OBJECTIVE To develop and validate a novel biochemical assay to assess Mtb proteasome activity in the presence of organic and aqueous plant test extracts. METHOD Fluorescence (photoluminescence) and luminescence (chemiluminescence) assays were investigated as potential methods to determine the robustness and repeatability for use in screening natural product extracts for Mtb proteasome inhibitors. RESULTS The fluorescence assay, used widely for Mtb proteasome activity assays, was subject to interference due to the natural fluorescence of compounds in many of the extracts; there is little interference with the luminescence approach. As proof of principle, we used the luminescence assay to screen a small set of plant test extracts. CONCLUSIONS Luminescence is the more suitable assay for assay of plant natural product extracts. The sensitivities of the luminescence and fluorescence assays are comparable. A Z'-factor of 0.58 for the luminescence assay makes it suitable for medium-to-high throughput screening efforts.
Nonnegative Matrix Factorization for Independent Component Analysis

In this paper, we develop a new algorithm with improved efficiency for nonnegative independent component analysis. This algorithm utilizes Kullback-Leibler divergence to generate nonnegative matrix factorization of the observation vectors. During the factorization, by pre-whitening the observations and orthonormalizing the mixing matrix, the independent components of sources are obtained. In the simulation, we successfully apply the developed algorithm to blind source separation of three images where sources are statistically independent.
Visible angiographic complications predict short and long‐term outcomes in patients with post‐procedural creatine‐phosphokinase elevation

Objectives: To assess whether visible angiographic complication is related to outcome in patients with elevated creatine phosphokinase (CK‐MB) following percutaneous coronary intervention (PCI). Background: Elevated biomarkers following PCI are associated with increased incidence of adverse events but the absolute risk of such events is low. A more specific marker of risk is needed. Methods: Consecutive patients with elevated post‐PCI CK‐MB were divided into two groups according to presence (n = 115, 43%) or absence (n = 150, 57%) of an angiographic complication. A control group (n = 250) was randomly chosen from 2,403 patients undergoing PCI during the same period without CK‐MB elevation. Major adverse cardiac events (MACE) were assessed at 30 days and 1 year. Results: Patients with an identifiable angiographic complication and elevated postprocedural CK‐MB had significantly worse outcomes at 30 days and 1 year compared with biomarker positive patients without an identifiable complication and control patients (30 day MACE rate: 8% vs 0% vs 0.4%, respectively, p < 0.001; 1 year MACE rate: 26% vs 11% vs 11%, respectively, p = 0.002, all p‐values for angiographic complication vs no angiographic complication and for angiographic complication vs control). Biomarker positive patients without identifiable angiographic complication had an excellent short and long term outcome, which was no different from biomarker negative patients (1 year MACE rate: 11% vs 11%, p = 0.53). Conclusion: Post‐PCI patients without visible angiographic complications have an excellent short and long term outcome. These findings call into question the need for routine CK‐MB monitoring after PCI in the absence of clinical symptoms or angiographic complication. © 2010 Wiley‐Liss, Inc.
Influence of DARPP-32 genetic variation on BOLD activation to happy faces

Abstract Dopaminergic pathways play a crucial role in reward processing, and advanced age can modulate its efficiency. DARPP-32 controls dopaminergic function and is a chemical nexus of reward processing. In 61 younger (20–30 years) and older adults (54% ♀) (65–74 years), we examined how blood–oxygen-level dependent (BOLD) activation to emotional faces, vary over genotypes at three single nucleotide polymorphism (SNPs), coding for DARPP-32 (rs879606; rs907094; 3764352). We also assessed age-magnification of DARPP-32 effects on BOLD activation. We found that major homozygote G, T or A genotypes, with higher cortical expression of DARPP-32, higher dopamine receptor efficacy, and greater bias toward positive cues, had increased functional connectivity in cortical–subcortical circuits in response to happy faces, engaging the dorsal prefrontal cortex (DLPFC), fusiform gyrus (FG) and the midbrain (MB). Local BOLD response to happy faces in FG, and MB was age-dependent, so that older carriers of the major G, T or A alleles showed lesser activation than minor genotypes. These genetic variants of DARPP-32 did not modulate BOLD response to angry faces, or engagement of the inferior occipital gyrus, to happy or angry faces. Taken together our results lend support for a potential role of DARPP-32 genetic variants in neural response to potential reward triggering cues.
Porting Hyperkernel to the ARM Architecture

This work describes the porting of Hyperkernel, an x86 kernel, to the ARMv8-A architecture. Hyperkernel was created to demonstrate various OS design decisions that are amenable to push-button verification. Hyperkernel simplifies reasoning about virtual memory by separating the kernel and user address spaces. In addition, Hyperkernel adopts an exokernel design to minimize code complexity, and thus its required proof burden. Both of Hyperkernel’s design choices are accomplished through the use of x86 virtualization support. After developing an x86 prototype, advantageous design differences between x86 and ARM motivated us to port Hyperkernel to the ARMv8-A architecture. We explored these differences and benchmarked aspects of the new interface Hyperkernel provides on ARM to demonstrate that the ARM version of Hyperkernel should be explored further in the future. We also outline the ARMv8-A architecture and the various design challenges overcome to fit Hyperkernel within the ARM programming model.
Whole-Body Gallium-67 Scintigraphic Findings in IgG4-Related Disease

Purpose: To clarify the features of gallium-67 (Ga-67) imaging typical of IgG4-related disease. Methods: We retrospectively investigated 14 patients diagnosed with IgG4-related disease who underwent Ga-67 scintigraphy in our hospital between January 2005 and May 2010. Of these, 13 patients who underwent gallium scintigraphy before steroid therapy were enrolled in this study. The patient population comprised 11 men and 2 women with age ranging from 47 to 76 years (mean age, 61.9 years). Results: Among the 13 patients, significant accumulation of Ga-67 was detected in the bilateral pulmonary hila in 10 patients (77%), pancreas in 10 (77%), salivary glands in 7 (54%), lacrimal glands in 7 (54%), periaortic lesions in 2 (15%), and lung parenchyma in 1 (8%) patient. High accumulation of Ga-67 in the salivary glands was observed in the parotid glands in 3 cases and in the submandibular glands in 6 cases, with the following pattern: normal parotid gland uptake and symmetrical submandibular gland uptake in 2 cases; symmetrical high accumulation in both parotid and submandibular glands in 1 case; symmetrical high accumulation in parotid glands and normal submandibular gland uptake in 1 case; symmetrical uptake by parotid glands and asymmetric uptake by submandibular glands in 1 case; normal parotid gland uptake and asymmetric submandibular gland uptake in 1 case; and asymmetric parotid gland uptake and symmetrical parotid gland uptake in 1 case. Conclusion: Characteristic patterns of gallium uptake would be helpful for diagnosis, detection of involved lesions, and differential diagnosis in patients with IgG4-related disease to avoid unnecessary surgery.
Dimensional Analysis Using Toric Ideals: Primitive Invariants

Classical dimensional analysis in its original form starts by expressing the units for derived quantities, such as force, in terms of power products of basic units etc. This suggests the use of toric ideal theory from algebraic geometry. Within this the Graver basis provides a unique primitive basis in a well-defined sense, which typically has more terms than the standard Buckingham approach. Some textbook examples are revisited and the full set of primitive invariants found. First, a worked example based on convection is introduced to recall the Buckingham method, but using computer algebra to obtain an integer matrix from the initial integer matrix holding the exponents for the derived quantities. The matrix defines the dimensionless variables. But, rather than this integer linear algebra approach it is shown how, by staying with the power product representation, the full set of invariants (dimensionless groups) is obtained directly from the toric ideal defined by . One candidate for the set of invariants is a simple basis of the toric ideal. This, although larger than the rank of , is typically not unique. However, the alternative Graver basis is unique and defines a maximal set of invariants, which are primitive in a simple sense. In addition to the running example four examples are taken from: a windmill, convection, electrodynamics and the hydrogen atom. The method reveals some named invariants. A selection of computer algebra packages is used to show the considerable ease with which both a simple basis and a Graver basis can be found.
Hand Motion and Image Stabilization in Hand-held Devices

The mobile imaging market is a rapidly developing market, and has outgrown the traditional imaging market. This market is dominated by CMOS sensors, with pixels getting small and smaller. As pixel size is reduced, the sensitivity is lowered and must be compensated by longer exposure times. However, in the mobile market, this amount to increased motion blur. We characterize the hand motion with a typical shooting scenario. This data can be used to create an evaluation procedure for image stabilization solutions, and we indeed present one such procedure.
Comparison of supervised and semi-supervised beamformers using real audio recordings

In this contribution two different disciplines for designing microphone array beamformers are explored. On the one hand a fixed beamformer based on numerical near field optimization is employed. On the other hand an adaptive beamformer algorithm based on the linearly constrained minimum variance (LCMV) method is applied. For the evaluation, an audio-database for microphone array impulse responses and audio recordings (speech and noise) was created. Different acoustic scenarios were constructed, consisting of various audio sources (desired speaker, interfering speaker and directional noise) distributed around the microphone array at different angles and distances. The algorithms were compared based on both objective measure (signal-to-noise, signal-to-interference and speech distortion, and subjective tests (assessment of sonograms and informal listening tests).
Efficient Subcarrier Allocation for Stable Services in Multi-user OFDM Systems

Adaptive resource allocation is a method of allocation for utilizing limited resources effectively in multi-user orthogonal frequency division multiplexing (OFDM) systems. In this paper, the allocation method in two steps that adaptively allocate subcarrier to every user is proposed. It makes use of bit-error rate (BER), user's minimum data rate requirement and channel state information for maximizing spectral efficiency while satisfying every user's quality of service (QoS). As the result, the proposed subcarrier allocation method is adaptable for more users in comparison with the conventional the algorithm method and improves performance of spectral efficiency.
An Efficient Training Strategy for Face Detector in Specific Scenes

Face detection has been well studied and widely applied in a variety of fields including online education, computer-aided medicine, and video surveillance, etc. Unfortunately, directly applying the algorithm trained on public wild face benchmarks to unconstrained scenes fails to obtain satisfactory performance. To solve this problem, we first propose an automatic data annotation method, and then propose a simple but efficient self-adapted training strategy for the face detector based on aggregate channel features and the boosting classifier. Experiments show that the self-adapted detector outperforms several other state-of-the-art approaches on our challenging test set.
Human Transforming Growth Factor-β Activates a Receptor Serine/Threonine Kinase from the Intravascular ParasiteSchistosoma mansoni *

The biology of the helminth parasiteSchistosoma mansoni is closely integrated with that of its mammalian host. SmRK1, a divergent type I transforming growth factor-β (TGF-β) receptor of unknown ligand specificity, was previously identified as a candidate for a receptor that allows schistosomes to respond to host-derived growth factors. The TGF-β family includes activin, bone morphogenetic proteins (BMPs), and TGF-β, all of which can play crucial roles in metazoan development. The downstream signaling protein of receptors that respond to TGF-β and activin is Smad2, whereas the receptors that respond to BMPs signal via Smad1. When a constitutively active mutant of SmRK1 was overexpressed with either schistosome Smad1 (SmSmad1) or SmSmad2, a receptor-dependent modulation of SmSmad phosphorylation and luciferase reporter activity occurred only with SmSmad2. To evaluate potential ligand activators of SmRK1, a chimeric receptor containing the extracellular domain of SmRK1 joined to the intracellular domain of the human type I TGF-β receptor was used. The chimeric receptor bound radiolabeled TGF-β and could activate a luciferase reporter gene in response to both TGF-β1 and TGF-β3 but not BMP7. Confirmatory results were obtained using full-length SmRK1. These experiments implicate TGF-β as a ligand for SmRK1 and as a potential host-derived regulator of parasite growth and development.
The Public Health Approach to TBI.

I 1996, CONGRESS PASSED PUBLIC LAW 104166 mandating the Centers for Diseases Control and Prevention (CDC) to engage in work focused on reducing the incidence of traumatic brain injury (TBI) in the United States. The TBI Act, which has been amended and renewed 3 times since then, specifies certain activities around which the TBI work at the CDC should be focused. The CDC’s National Center for Injury Prevention and Control has remained responsive to Congress by conducting surveillance to better understand the burden of TBI, conducting research to better explore the full range of TBI outcomes, identifying prevention strategies, implementing education initiatives, and providing technical assistance to states and other key partners. As the field evolved, new priorities emerged and the CDC revised its strategic plan for measuring and reducing the public health burden of TBI in the United States. The articles included in this special issue fit within this newly developed strategic plan. The public health model emphasizes a framework by which a health condition of interest is defined and systematically studied to describe the overall public health burden, identify modifiable risk and protective factors, implement effective prevention strategies, and carry out widespread dissemination to increase adoption of evidence-based practices. The CDC’s strategic plan for TBI aims to anchor work to the public health model with the intent of achieving maximum impact in reducing TBI-related morbidity and mortality. The CDC’s strategic plan for TBI is organized into 4 pillars: (1) improving the understanding of the public health burden of TBI; (2) reducing the incidence of TBI through primary prevention; (3) improving the recognition and management of mild TBI; and (4) promoting healthy lifestyles and improving health outcomes for persons living with TBI. Surveillance is the cornerstone of all epidemiologic work and primary prevention activities at the CDC. Improving TBI surveillance is essential to determining
A Serologic Survey for Some Bacterial and Viral Zoonoses in Game Animals in the Czech Republic

Between 1986 and 1991, sera were collected from 33 roe deer (Capreolus capreolus), 24 red deer (Cervus elaphus), four fallow deer (Dama dama), two mouflon (Ovis musimon), 34 wild boars (Sus scrofa), and 48 hares (Lepus europaeus) shot in two areas of the Czech Republic. Collectively, the sera contained antibodies to Coxiella burnetii (prevalence of 12%), Francisella tularensis (4%), Brucella spp. (2%), Central European tick-borne encephalitis virus (8%), Ťahyňa (California serogroup) virus (36%), and Čalovo (=Batai) virus (23%). We propose that these mammals may play a role in maintaining natural foci of Q-fever, Ťahyňa fever and Čalovo virus infection.
Exposure-response relationship between hand-arm vibration and vibrotactile perception sensitivity.

BACKGROUND The objectives of the study were to examine whether occupational use of vibrating hand-held tools was associated with an impaired vibrotactile perception, whether any exposure-response relationship exists, and whether the different populations of mechano-receptive afferent units are equally affected. METHODS Vibrotactile perception thresholds have been measured at seven frequencies (8-500 Hz) and evaluated among 125 vibration-exposed and 45 non-exposed male employees in a heavy engineering production workshop. Vibration exposure measurements were assessed on tools in accordance with ISO 5349. Vibrotactile perception thresholds have been individually graded in stages and placed in relation to individual vibration exposure. RESULTS The outcome did not reveal a clear relationship between vibration exposure and reduced vibrotactile sensitivity on an individual basis. There was a clear tendency on a group basis towards elevated thresholds when the study population was divided into three exposure categories. A fourfold increase in relative risk of reduced vibrotactile sensitivity for test frequencies above 40 Hz was observed between the highest exposure category compared to the non-exposed. CONCLUSIONS It was concluded that reduced tactile sensitivity is related to the degree of vibration exposure but it is not at present possible to delineate an exposure-response relationship.
Smoking increases conversion of lactate to glucose during submaximal exercise.

We examined the hypotheses that 1) smoking acutely before exercise (AS) results in a higher rate of lactate production during exercise compared with chronic smoking with preexercise abstinence (CS) and 2) smokers have a higher rate of lactate conversion to glucose during exercise compared with nonsmokers (NS). To test our hypotheses, seven male smokers and seven nonsmokers were studied by using a primed continuous infusion of [3-13C]lactate during 90 min of rest and 60 min of exercise on a cycle ergometer at 50% peak O2 consumption; smokers were studied twice: once after an overnight smoking abstinence and once after smoking three cigarettes before exercise. The rates of lactate appearance and conversion to glucose were increased markedly with exercise compared with rest in all groups (P < 0.05); the rate of lactate appearance for AS was significantly greater (7.87 +/- 0.77 mg.kg-1.min-1) than for both CS (4.64 +/- 0.33 mg.kg-1.min-1) and NS (5.57 +/- 0.60 mg.kg-1.min-1) (P < 0.05). The rate of lactate conversion to glucose was similar between CS and AS (6.49 +/- 1.82 and 6.30 +/- 1.69 mg.kg-1.min-1, respectively) during exercise; NS had a significantly lower rate (3.31 +/- 0.90 mg.kg-1.min-1) compared with CS and AS (P < 0.05). In summary, acute smoking increases lactate flux during exercise; in addition, smokers have a higher rate of lactate to glucose conversion during exercise compared with nonsmokers, which may indicate an increased glucose dependency.