Miracle-dz/UniFAR-FTUs huggingface dataset:
Diffusional kurtosis imaging: The quantification of non‐gaussian water diffusion by means of magnetic resonance imaging

A magnetic resonance imaging method is presented for quantifying the degree to which water diffusion in biologic tissues is non‐Gaussian. Since tissue structure is responsible for the deviation of water diffusion from the Gaussian behavior typically observed in homogeneous solutions, this method provides a specific measure of tissue structure, such as cellular compartments and membranes. The method is an extension of conventional diffusion‐weighted imaging that requires the use of somewhat higher b values and a modified image postprocessing procedure. In addition to the diffusion coefficient, the method provides an estimate for the excess kurtosis of the diffusion displacement probability distribution, which is a dimensionless metric of the departure from a Gaussian form. From the study of six healthy adult subjects, the excess diffusional kurtosis is found to be significantly higher in white matter than in gray matter, reflecting the structural differences between these two types of cerebral tissues. Diffusional kurtosis imaging is related to q‐space imaging methods, but is less demanding in terms of imaging time, hardware requirements, and postprocessing effort. It may be useful for assessing tissue structure abnormalities associated with a variety of neuropathologies. Magn Reson Med 53:1432–1440, 2005. © 2005 Wiley‐Liss, Inc.
Improved sensitivity of 3.0 Tesla susceptibility-weighted imaging in detecting traumatic bleeds and its use in predicting outcomes in patients with mild traumatic brain injury

Background The efficacy of susceptibility-weighted imaging (SWI) for detecting intracranial bleeds (ICBs) in patients with mild traumatic brain injury (MTBI) has not been directly compared to that of T2*-weighted gradient-recalled-echo imaging (T2*WI). Further, its prognostic value for MTBI patients remains unproven. Purpose To compare the sensitivity of ICB identification between SWI and T2*WI and examine the prognostic value of SWI for MTBI patients. Material and Methods T2*WI, SWI, and clinical information of 63 MTBI patients were collected. Sensitivity was compared between T2*WI and SWI for ICB identification, and statistical analysis was conducted to understand the correlations between SWI and clinical characteristics. Results ICBs were detected in more patients (47 vs. 35, P < 0.001) and more ICBs were detected (276 vs. 147, P < 0.001) on SWI than T2*WI. On SWI, patients with conscious disturbance showed higher ICBs prevalence (84.6% vs. 58.3%, P = 0.020), and more patients from the post-concussive syndrome (PCS)(+) group than the PCS(−)group were ICBs positive (86.1% vs. 59.3%, P = 0.015). The numbers of ICBs were significantly higher in the PCS(+) group than the PCS(−) group (P < 0.001). Significant correlation was found between PCS and ICBs number (r = 0.510, P < 0.001). Multiple logistic regression analysis showed that ICB number was an independent variable predicting occurrence of PCS. Conclusion SWI is more sensitive than T2*WI in detecting hemorrhagic foci in MTBI patients and may offer valuable prognostic information regarding these patients, for example, information on PCS. Further, cerebral parenchymal hemorrhage may affect long-term outcomes in MTBI patients.
Rare variants contribute disproportionately to quantitative trait variation in yeast

A detailed understanding of the sources of heritable variation is a central goal of modern genetics. Genome-wide association studies (GWAS) in humans1 have implicated tens of thousands of DNA sequence variants in disease risk and quantitative trait variation, but these variants fail to account for the entire heritability of diseases and traits. GWAS have by design focused on common DNA sequence variants; however, recent studies underscore the likely importance of the contribution of rare variants to heritable variation2. Further, finding the genes that underlie the GWAS signals remains a major challenge. Here, we use a unique model system to disentangle the contributions of common and rare variants to a large number of quantitative traits. We generated large crosses among 16 diverse yeast strains and identified thousands of quantitative trait loci (QTLs) that explain most of the heritable variation in 38 traits. We combined our results with sequencing data for 1,011 yeast isolates3 to decouple variant effect size estimation from allele frequency and showed that rare variants make a disproportionate contribution to trait variation as a consequence of their larger effect sizes. Evolutionary analyses revealed that this contribution is driven by rare variants that arose recently, that such variants are more likely to decrease fitness, and that negative selection has shaped the relationship between variant frequency and effect size. Finally, we leveraged the structure of the crosses to resolve hundreds of QTLs to single genes. These results refine our understanding of trait variation at the population level and suggest that studies of rare variants are a fertile ground for discovery of genetic effects.
Characterization of melanocyte‐specific inducible Cre recombinase transgenic mice

Conditional Cre‐mediated recombination has emerged as a robust method of introducing somatic genetic alterations in an organ‐specific manner in the mouse. Here, we generated and characterized mice harboring a 4‐hydroxytamoxifen (OHT)‐inducible Cre recombinase‐estrogen receptor fusion transgene under the control of the melanocyte‐specific tyrosinase promoter, designated Tyr::CreERT2. Cre‐mediated recombination was induced in melanocytes in a spatially and temporally controlled manner upon administration of OHT and was documented in embryonic melanoblasts, follicular bulb melanocytes, dermal dendritic melanocytes, epidermal melanocytes of tail skin, and in putative melanocyte stem cells located within the follicular bulge. Functional evidence suggestive of recombination in follicular melanocyte stem cells included the presence of Cre‐mediated recombination in follicular bulb melanocytes 1 year after topical OHT administration, by which time several hair cycles have elapsed and the melanocytes residing in this location have undergone multiple rounds of apoptosis and replenishment. These Tyr:: CreERT2 transgenic mice represent a useful resource for the evaluation of melanocyte developmental genetics, the characterization of melanocyte stem cell function and dynamics, and the construction of refined mouse models of malignant melanoma. genesis 44:262–267, 2006. Published 2006 Wiley‐Liss, Inc.
Correlated Fluctuations of Daytime Skin Temperature and Vigilance

Skin temperature shows spontaneous ultradian fluctuations during everyday-life wakefulness. Previous work showed that mild manipulations of skin temperature affect human sleep and vigilance, presumably by influencing neuronal systems involved in both thermal sensing and arousal regulation. We therefore examined whether fluctuations in skin temperature are associated with those in vigilance level under conditions similar to everyday-life situations requiring sustained attention. Eight healthy participants (30.1 ± 8.1 years, M ± SD) participated in a 2-day protocol, during which vigilance and skin temperature were assessed 4 times per day in a silent, dimly lit, temperature-controlled room. Vigilance was assessed by measuring reaction speed and lapses on a novel sustained vigilance task specifically designed to increase lapse rate and range of reaction times. Skin temperature was sampled at 30-second intervals from 3 locations: distal, intermediate, and proximal temperatures were obtained from the middle finger (Tfinger ), the wrist (Twrist), and the infraclavicular area (Tchest), respectively. Furthermore, 3 distal to proximal gradients were calculated. Mixed-effect regression analyses were used to evaluate the association of the fluctuations in temperatures and gradients and those in response speed and lapse probability. Especially the spontaneous fluctuations in proximal temperature were negatively associated with fluctuations in response speed and positively with lapse rate. If individual Tchest temperature ranges were classified into 10 deciles, they accounted for 23% of the variance in response speed and 11% of the variance in lapse rate. The findings indicate coupling between the spontaneous fluctuations in skin temperature and vigilance during the day and are compatible with the hypothesis of overlap in brain networks involved in the regulation of temperature and vigilance. From an applied point of view, especially proximal skin temperature assessment may be of use in vigilance monitoring.
Integration of Heterogeneous Data Sources with Limited Capabilities in the Object-Oriented Mediator Engine AMOSII

Information becomes a more and more valuable asset in today’s organizations. Therefore the need of creating an integrated view over all available data sources arises. Several technical problems must be overcome in the design and implementation of a system for integrating different data sources. To the main obstacles count autonomy, data heterogeneity and different query capabilities of the repositories. This thesis presents the data integration system AMOS II , which is based on the wrapper-mediator approach. The main focus of this work lies on data model transformation and query processing. The following extensions to the AMOS II system are described in this thesis: • A framework for transforming various data models into the objectoriented model of AMOS II is presented. • The roles and tasks of wrappers are described. In particular their participation in query processing and query optimization is discussed. • A way for describing and utilizing the query capabilities of the different data sources is proposed. • Two different approaches to query processing over external data sources are developed and analyzed. All the proposed techniques are implemented in the AMOS II system, which runs on a Windows NT platform.
Seroprevalence of Hepatitis B Surface Antigen and Anti Hepatitis C Antibody in Zahedan City, Iran: A Population-Based Study

Background There have been studies regarding the prevalence of hepatitis B surface antigen (HBsAg) and anti-hepatitis C antibody (HCVAb) in Iran. However, the majority of these have reported a variety of rates, depending on their study population, which limits the generalizability of their results to the general population. On the other hand, cultural diversity in the different provinces of Iran also necessitates the performing separate population-based studies in the various regions. Objectives To evaluate the population-based prevalence of HBsAg and HCVAb and their correlates in Zahedan City, Iran. Patients and Methods Included in this study were 2587 individuals, using a random and cluster sampling approach. The participants were drawn from the Family Registry of the public health centers in Zahedan City, Iran, from 2008 to 2009. Following data collection from the interviews, subjects were assessed for seropositivity of HBsAg and HCVAb. We then calculated the prevalence of HBsAg and HCVAb, and evaluated these viral markers for an association with; age, sex and potential risk factors. Results Weighted seroprevalence of HBsAg and HCVAb was 2.5% (CI 95% : 1.9 to 3.3 %) and 0.5% (CI 95% : 0.27 to 0.9 %), respectively. Prevalence of HBsAg increased significantly with age (P value < 0.001), but this was not true for HCVAb (P value: 0.67). We observed no sex dominance in the prevalence of HBsAg (3.2% and 2.2% for males and females, respectively, P value: 0.15) or HCVAb (0.4% and 0.7% for males and females, respectively, P value: 0.27). In a multivariate regression analysis, every additional year in age resulted in a 2% increment in the odds of HBsAg seropositivity. HBsAg was also three times more prevalent among married, than single subjects (with a P value reaching toward significance: 0.065) in multivariate analysis. Prevalence of HCVAb did not differ with respect to any of the potential risk factors. Conclusions This is the first population-based study on the prevalence of HCVAb and one of the few population based studies on HBsAg in Zahedan City. We detected lower prevalence rates of HBsAg and HCVAb than in previous studies conducted in Zahedan City. In addition to improvements in social awareness and general health elements, we think that the observed low prevalence rates have been achieved due to the efficiency of mass vaccination projects, implemented against HBV infection in Iran.
Structure-Dependent Sequence Alignment, a hybrid Iterative-Parametric approach to suboptimal alignment, and the amino acid property-based Proximity Correlation Matrix

Introduction The rate at which new protein sequences are discovered has long outpaced the rate at which those proteins are experimentally assigned functions. To speed the process of function assignment, protein sequences with unknown functions can be compared to sequences with known functions. If two protein sequences are shown to be highly related, then it follows that the protein functions may be closely related as well (Domingues et. al 2000). Early sequence alignment algorithms such as Smith-Waterman and BLAST focused on comparing the residue sequences only in making alignments. However, function may be conserved even in sequences that appear to have diverged. Much recent effort has been devoted to developing algorithms that align distantly related proteins, also known as remote homologues. The three algorithms discussed in this paper consider three separate approaches to this alignment problem. The three algorithms are the Structure-Dependent Sequence Alignment, a hybrid Iterative-Parametric approach to suboptimal alignment, and the amino acid property-based Proximity Correlation Matrix alignment.
Carboxyl-Terminal Cleavage of Apolipoprotein A-I by Human Mast Cell Chymase Impairs Its Anti-Inflammatory Properties

Objective— Apolipoprotein A-I (apoA-I) has been shown to possess several atheroprotective functions, including inhibition of inflammation. Protease-secreting activated mast cells reside in human atherosclerotic lesions. Here we investigated the effects of the neutral proteases released by activated mast cells on the anti-inflammatory properties of apoA-I. Approach and Results— Activation of human mast cells triggered the release of granule-associated proteases chymase, tryptase, cathepsin G, carboxypeptidase A, and granzyme B. Among them, chymase cleaved apoA-I with the greatest efficiency and generated C-terminally truncated apoA-I, which failed to bind with high affinity to human coronary artery endothelial cells. In tumor necrosis factor-&agr;–activated human coronary artery endothelial cells, the chymase-cleaved apoA-I was unable to suppress nuclear factor-&kgr;B–dependent upregulation of vascular cell adhesion molecule-1 (VCAM-1) and to block THP-1 cells from adhering to and transmigrating across the human coronary artery endothelial cells. Chymase-cleaved apoA-I also had an impaired ability to downregulate the expression of tumor necrosis factor-&agr;, interleukin-1&bgr;, interleukin-6, and interleukin-8 in lipopolysaccharide-activated GM-CSF (granulocyte-macrophage colony-stimulating factor)– and M-CSF (macrophage colony-stimulating factor)–differentiated human macrophage foam cells and to inhibit reactive oxygen species formation in PMA (phorbol 12-myristate 13-acetate)–activated human neutrophils. Importantly, chymase-cleaved apoA-I showed reduced ability to inhibit lipopolysaccharide-induced inflammation in vivo in mice. Treatment with chymase blocked the ability of the apoA-I mimetic peptide L-4F, but not of the protease-resistant D-4F, to inhibit proinflammatory gene expression in activated human coronary artery endothelial cells and macrophage foam cells and to prevent reactive oxygen species formation in activated neutrophils. Conclusions— The findings identify C-terminal cleavage of apoA-I by human mast cell chymase as a novel mechanism leading to loss of its anti-inflammatory functions. When targeting inflamed protease-rich atherosclerotic lesions with apoA-I, infusions of protease-resistant apoA-I might be the appropriate approach.
Brief Report: Intravital Imaging of Cancer Stem Cell Plasticity in Mammary Tumors

It is widely debated whether all tumor cells in mammary tumors have the same potential to propagate and maintain tumor growth or whether there is a hierarchical organization. Evidence for the latter theory is mainly based on the ability or failure of transplanted tumor cells to produce detectable tumors in mice with compromised immune systems; however, this assay has lately been disputed to accurately reflect cell behavior in unperturbed tumors. Lineage tracing experiments have recently shown the existence of a small population of cells, referred to as cancer stem cells (CSCs), that maintains and provides growth of squamous skin tumors and intestinal adenomas. However, the lineage tracing techniques used in these studies provide static images and lack the ability to study whether stem cell properties can be obtained or lost, a process referred to as stem cell plasticity. Here, by intravital lineage tracing, we report for the first time the existence of CSCs in unperturbed mammary tumors and demonstrate CSC plasticity. Our data indicate that existing CSCs disappear and new CSCs form during mammary tumor growth, illustrating the dynamic nature of these cells. STEM CELLS2013;31:602–606
A Motion Tracking Method for the Modeling and Simulation of Human Movement in 3D

Interest in computer models of the human musculoskeletal system is increasing amongst clinic ians and movement scientists as tools to analyze muscle and joint function in ways that are both non-invasive and inexpensive. Quantifying internal loads resulting from muscles and external forces is necessary to understand and treat movement pathologies. Current simulation methods, however, fall short of accurately reproducing observed human performance when compared to observations made during movement experiments. It is a minimal requirement that models closely reproduce external observations before considering them to answer questions about severity of a disorder and possible treatments. Given this underl ying requirement, a dynamical motion-tracking method was developed to leverage experimental observations directly to guide forward simulations and provide simulations that are more accurate. In the present study, we demonstrate how tracking can provide joint-moment information that produce accurate forward simulations in minutes using a detailed 23 degree-of- freedom human model and 3D motion-capture data.
Thermal biology of the sub-polar–temperate estuarine crab Hemigrapsus crenulatus (Crustacea: Decapoda: Varunidae)

ABSTRACT Optimum temperatures can be measured through aerobic scope, preferred temperatures or growth. A complete thermal window, including optimum, transition (Pejus) and critical temperatures (CT), can be described if preferred temperatures and CT are defined. The crustacean Hemigrapsus crenulatus was used as a model species to evaluate the effect of acclimation temperature on: (i) thermal preference and width of thermal window, (ii) respiratory metabolism, and (iii) haemolymph proteins. Dependant on acclimation temperature, preferred temperature was between 11.8°C and 25.2°C while CT was found between a minimum of 2.7°C (CTmin) and a maximum of 35.9°C (CTmax). These data and data from tropical and temperate crustaceans were compared to examine the association between environmental temperature and thermal tolerance. Temperate species have a CTmax limit around 35°C that corresponded with the low CTmax limit of tropical species (34–36°C). Tropical species showed a CTmin limit around 9°C similar to the maximum CTmin of temperate species (5–6°C). The maximum CTmin of deep sea species that occur in cold environments (2.5°C) matched the low CTmin values (3.2°C) of temperate species. Results also indicate that the energy required to activate the enzyme complex (Ei) involved in respiratory metabolism of ectotherms changes along the latitudinal gradient of temperature. Summary: The preferred temperature of the intertidal temperate crab Hemigrapsus crenulatus was determined to be between 12°C and 25°C. Oceanic warming would trap this species between tropical and polar temperatures, causing increasing population stress with unknown ecological consequences.
Brainstem Auditory Responses to Resolved and Unresolved Harmonics of a Synthetic Vowel in Quiet and Noise

Objectives: This study investigated speech auditory brainstem responses (speech ABR) with variants of a synthetic vowel in quiet and in background noise. Its objectives were to study the noise robustness of the brainstem response at the fundamental frequency F0 and at the first formant F1, evaluate how the resolved/unresolved harmonics regions in speech contribute to the response at F0, and investigate the origin of the response at F0 to resolved and unresolved harmonics in speech. Design: In total, 18 normal-hearing subjects (11 women, aged 18–33 years) participated in this study. Speech ABRs were recorded using variants of a 300 msec formant-synthesized /a/ vowel in quiet and in white noise. The first experiment employed three variants containing the first three formants F1 to F3, F1 only, and F2 and F3 only with relative formant levels following those reported in the literature. The second experiment employed three variants containing F1 only, F2 only, and F3 only, with the formants equalized to the same level and the signal-to-noise ratio (SNR) maintained at –5 dB. Overall response latency was estimated, and the amplitude and local SNR of the envelope following response at F0 and of the frequency following response at F1 were compared for the different stimulus variants in quiet and in noise. Results: The response at F0 was more robust to noise than that at F1. There were no statistically significant differences in the response at F0 caused by the three stimulus variants in both experiments in quiet. However, the response at F0 with the variant dominated by resolved harmonics was more robust to noise than the response at F0 with the stimulus variants dominated by unresolved harmonics. The latencies of the responses in all cases were very similar in quiet, but the responses at F0 due to resolved and unresolved harmonics combined nonlinearly when both were present in the stimulus. Conclusions: Speech ABR has been suggested as a marker of central auditory processing. The results of this study support earlier work on the differential susceptibility to noise of the F0 and F1 components of the evoked response. In the case of F0, the results support the view that in speech, the pitch of resolved harmonics and that of unresolved harmonics are processed in different but interacting pathways that converge in the upper brainstem. Pitch plays an important role in speech perception, and speech ABR can offer a window into the neural extraction of the pitch of speech and how it may change with hearing impairment.
Improved Rear-Side Passivation by Atomic Layer Deposition  ${\rm Al}_{2}{\rm O}_{3}/{\rm SiN}_{x}$ Stack Layers for High  $V_{\rm OC}$ Industrial $p$-Type Silicon Solar Cells

This research develops high open-circuit voltage (VOC) p-type industrial screen-printed silicon solar cells using improved rear surface passivation. It shows a significant improvement in the minority carrier lifetime by low temperature thermal atomic layer deposition of Al2O3 layers and plasma-enhanced chemical vapor deposition of SiNx passivation layers. An increase in the VOC and the short-circuit current (JSC) due to an improved long-wavelength response are also demonstrated. With the optimized stack layers, a high efficiency of 19.2% across a large area (156 cm2) is seen. Furthermore, the rear-side passivation scheme can be easily integrated into the conventional screen-printed process. This is very promising for in-line solar cell manufacturing.