Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics

Proteomic and lipidomic profiling was performed over a time course of acute hepatitis C virus (HCV) infection in cultured Huh-7.5 cells to gain new insights into the intracellular processes influenced by this virus. Our proteomic data suggest that HCV induces early perturbations in glycolysis, the pentose phosphate pathway, and the citric acid cycle, which favor host biosynthetic activities supporting viral replication and propagation. This is followed by a compensatory shift in metabolism aimed at maintaining energy homeostasis and cell viability during elevated viral replication and increasing cellular stress. Complementary lipidomic analyses identified numerous temporal perturbations in select lipid species (e.g. phospholipids and sphingomyelins) predicted to play important roles in viral replication and downstream assembly and secretion events. The elevation of lipotoxic ceramide species suggests a potential link between HCV-associated biochemical alterations and the direct cytopathic effect observed in this in vitro system. Using innovative computational modeling approaches, we further identified mitochondrial fatty acid oxidation enzymes, which are comparably regulated during in vitro infection and in patients with histological evidence of fibrosis, as possible targets through which HCV regulates temporal alterations in cellular metabolic homeostasis.
Biomechanical regulation of vascular smooth muscle cell functions: from in vitro to in vivo understanding

Vascular smooth muscle cells (VSMCs) have critical functions in vascular diseases. Haemodynamic factors are important regulators of VSMC functions in vascular pathophysiology. VSMCs are physiologically active in the three-dimensional matrix and interact with the shear stress sensor of endothelial cells (ECs). The purpose of this review is to illustrate how haemodynamic factors regulate VSMC functions under two-dimensional conditions in vitro or three-dimensional co-culture conditions in vivo. Recent advances show that high shear stress induces VSMC apoptosis through endothelial-released nitric oxide and low shear stress upregulates VSMC proliferation and migration through platelet-derived growth factor released by ECs. This differential regulation emphasizes the need to construct more actual environments for future research on vascular diseases (such as atherosclerosis and hypertension) and cardiovascular tissue engineering.
On the Calculation of the Hilbert Transform From Interpolated Data

This correspondence studies the calculation of the Hilbert transform of continuous functions f with continuous conjugate f from a finite set of sampling points. It shows that there exists no linear operator which approximates f arbitrary well in the uniform norm from a finite number of sampling points for all possible continuous function f with continuous conjugate f. However for smooth functions such linear approximation operators exist and sufficient conditions on the smoothness of the functions are presented. The correspondence also examines the robustness of the calculation of the Hilbert transform from interpolated data and it gives explicit error bounds. It is shown that for a large class of algorithms the error grows at least proportional to the logarithm of the number of sampling points.
Management of Bile Duct Injuries: Treatment and Long-Term Results

Only a few years after the introduction of laparoscopic cholecystectomy in the late 1980s, surgeons declared the laparoscopic procedure as the gold standard for symptomatic gallstone disease. Several studies have shown the efficacy and safety of the procedure as well as the advantages such as reduced hospital stay, earlier recovery, less intraabdominal adhesions and a better cosmetic outcome [1– 3]. More recently it has been shown that the procedure can also be performed safely as a day-care procedure [4]. There has been extensive controversy about the increased incidence of bile duct injury (BDI) after laparoscopic cholecystectomy. Injury rates as high as 2% were reported in the early ‘learning’ phase and more recently a decrease in BDI has been reported from different countries [5–7]. Remarkably, other papers suggested that the majority of BDI was due to surgeons who were far beyond the learning curve, as was reported many years ago for open surgery. It has therefore also been suggested that the learning curve is not only relevant for the occurrence of BDI, but that accidental injuries are partly due to failure of the technique [8]. Different mechanisms of injury have been described in the past but more recently, Cuschieri [9] preferred a more practical approach and he identified two major groups of errors, namely (1) misidentification of the anatomy of the biliary tract as being the dominant factor in around 70% of the injuries and (2) technical errors leading to bleeding and subsequent clipping of the bile duct/artery or leading to bile leakage by inadequate clipping or traction and subsequent lateral wall injuries. Prevention of injuries is most important and different measurements have been advocated as for example the use of routine operative cholangiography [3]. Inadequate management of BDI may lead to severe complications, such as biliary peritonitis leading to sepsis and multiple organ failure in the early phase, and biliary cirrhosis during long-term follow-up, eventually leading to the need for liver transplantation [10]. Not all forms of diagnostic work-up and treatment are available in all hospitals and there should be a low barrier for referral. The management of these patients should ideally be performed/discussed in a multidisciplinary team consisting of gastroenterologists, radiologists and surgeons. Unfortunately, lesions will occur, but suboptimal treatment of BDI is not acceptable nowadays. The Academic Medical Center (AMC) is a referral center for HPB surgery and in this review several aspects of BDI, treatment and long-term outcome will be discussed.
Impact of Climate Change on Ambient Ozone Level and Mortality in Southeastern United States

There is a growing interest in quantifying the health impacts of climate change. This paper examines the risks of future ozone levels on non-accidental mortality across 19 urban communities in Southeastern United States. We present a modeling framework that integrates data from climate model outputs, historical meteorology and ozone observations, and a health surveillance database. We first modeled present-day relationships between observed maximum daily 8-hour average ozone concentrations and meteorology measured during the year 2000. Future ozone concentrations for the period 2041 to 2050 were then projected using calibrated climate model output data from the North American Regional Climate Change Assessment Program. Daily community-level mortality counts for the period 1987 to 2000 were obtained from the National Mortality, Morbidity and Air Pollution Study. Controlling for temperature, dew-point temperature, and seasonality, relative risks associated with short-term exposure to ambient ozone during the summer months were estimated using a multi-site time series design. We estimated an increase of 0.43 ppb (95% PI: 0.14–0.75) in average ozone concentration during the 2040’s compared to 2000 due to climate change alone. This corresponds to a 0.01% increase in mortality rate and 45.2 (95% PI: 3.26–87.1) premature deaths in the study communities attributable to the increase in future ozone level.
Existence and Limiting Behavior of a Non--Interior-Point Trajectory for Nonlinear Complementarity Problems Without Strict Feasibility Condition

For P0-complementarity problems, most existing non--interior-point path-following methods require the existence of a strictly feasible point. (For a P*-complementarity problem, the existence of a strictly feasible point is equivalent to the nonemptyness and the boundedness of the solution set.) In this paper, we propose a new homotopy formulation for complementarity problems by which a new non--interior-point continuation trajectory is generated. The existence and the boundedness of this non--interior-point trajectory for P0-complementarity problems are proved under a very mild condition that is weaker than most conditions used in the literature. One prominent feature of this condition is that it may hold even when the often-assumed strict feasibility condition fails to hold. In particular, for a P*-problem it turns out that the new non--interior-point trajectory exists and is bounded if and only if the problem has a solution. We also study the convergence of this trajectory and characterize its limiting point as the parameter approaches zero.
Epidemiology of Sexually Transmitted Infections among Human Immunodeficiency Virus Positive United States Military Personnel

Background. Minimal data exist that describe the epidemiology of sexually transmitted infections (STI) in human immunodeficiency virus (HIV) positive populations across the pre- and post-diagnosis periods for HIV. Purpose. The purpose of this study was to identify and describe the epidemiology of gonorrhea, chlamydia, syphilis, herpes simplex virus, and human papillomavirus in an HIV-positive population. Methods. All 1,961 HIV seropositive United States active duty military personnel from 2000–2010 were identified. STI diagnoses relative to HIV diagnosis from 1995, which was the earliest electronic medical record available, to 2010 were examined. Results. The incidence diagnosis rates of STI generally increased during the period leading up to eventual HIV diagnosis. The rates of STI during the post-HIV diagnosis period fluctuated, but remained elevated compared to pre-HIV diagnosis period. Approximately 45%–69% with an STI in the HIV seropositive military population were diagnosed with their first STI greater than one year after their HIV diagnosis. Of those who were diagnosed with an STI in the post-HIV diagnosis period, 70.6% had one STI diagnosis, 23.5% had two STI diagnoses, and 5.8% had three or more STI diagnoses. Conclusions. Despite aggressive counseling, high-risk sexual behavior continues to occur in the HIV-positive military population.
RNA–Mediated Epigenetic Heredity Requires the Cytosine Methyltransferase Dnmt2

RNA–mediated transmission of phenotypes is an important way to explain non-Mendelian heredity. We have previously shown that small non-coding RNAs can induce hereditary epigenetic variations in mice and act as the transgenerational signalling molecules. Two prominent examples for these paramutations include the epigenetic modulation of the Kit gene, resulting in altered fur coloration, and the modulation of the Sox9 gene, resulting in an overgrowth phenotype. We now report that expression of the Dnmt2 RNA methyltransferase is required for the establishment and hereditary maintenance of both paramutations. Our data show that the Kit paramutant phenotype was not transmitted to the progeny of Dnmt2−/− mice and that the Sox9 paramutation was also not established in Dnmt2−/− embryos. Similarly, RNA from Dnmt2-negative Kit heterozygotes did not induce the paramutant phenotype when microinjected into Dnmt2-deficient fertilized eggs and microinjection of the miR-124 microRNA failed to induce the characteristic giant phenotype. In agreement with an RNA–mediated mechanism of inheritance, no change was observed in the DNA methylation profiles of the Kit locus between the wild-type and paramutant mice. RNA bisulfite sequencing confirmed Dnmt2-dependent tRNA methylation in mouse sperm and also indicated Dnmt2-dependent cytosine methylation in Kit RNA in paramutant embryos. Together, these findings uncover a novel function of Dnmt2 in RNA–mediated epigenetic heredity.
Spectrum-based vibrotactile footstep-display for crinkle of fragile structures

This study developed a vibrotactile display method for the crinkle/scrunch of fragile structures. For such structures, tactile stimuli are more easily perceived by humans than the very small reaction forces that occur during a crinkle. The developed method synthesizes vibrotactile acceleration stimuli for a crinkle based on the preliminarily measured acceleration spectra. We developed a footstep display that presents the synthesized stimuli to human soles in response to the humans' foot speed. The display presents the sensations acquired by stepping on fragile structures. Experimental participants identified the types of materials of cylindrical fragile structures among paper, aluminum foil, and polypropylene film, at probabilities significantly higher than the chance level.
Second-order cone programming approach for elliptically distributed joint probabilistic constraints with dependent rows

In this paper, we investigate the problem of linear joint probabilistic constraints. We assume that the rows of the constraint matrix are dependent and the dependence is driven by a convenient Archimedean copula. Further we assume the distribution of the constraint rows to be elliptically distributed, covering normal, t, or Laplace distributions. Under these and some additional conditions, we prove the convexity of the investigated set of feasible solutions. We also develop two approximation schemes for this class of stochastic programming problems based on second-order cone programming, which provides lower and upper bounds. Finally, a computational study on randomly generated data is given to illustrate the tightness of these bounds.
An introduction to ghost imaging: quantum and classical

Ghost imaging has been a subject of interest to the quantum optics community for the past 20 years. Initially seen as manifestation of quantum spookiness, it is now recognized as being implementable in both single- and many-photon number regimes. Beyond its scientific curiosity, it is now feeding novel imaging modalities potentially offering performance attributes that traditional approaches cannot match. This article is part of the themed issue ‘Quantum technology for the 21st century’.
Fitting Prony-Series Viscoelastic Models with Power-Law Presmoothing

An efficient method of fitting Prony-series models to viscoelastic experimental data with power-law presmoothing is presented. A direct fitting of a Prony-series function to experimental data without appropriate presmoothing is difficult when the data have significant variance. A power-law series comprising multiple power-law terms is found capable of portraying a globally smooth, broadband viscoelastic behavior with minimal impact from local variance in the data. However, from a computational point of view, a Prony series representation is preferred to a power-law series representation because of the computational efficiency associated with the exponential basis functions of a Prony series. In this paper, a procedure involving presmoothing of experimental data via power-law-series representation followed by fitting of a Prony-series model to the presmoothed data is discussed and illustrated. Discussion focuses on how experimental data with significant variance can be effectively presmoothed through power.
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

Development of high throughput analytical methods has given physicians the potential access to extensive and patient-specific data sets, such as gene sequences, gene expression profiles or metabolite footprints. This opens for a new approach in health care, which is both personalized and based on system-level analysis. Genome-scale metabolic networks provide a mechanistic description of the relationships between different genes, which is valuable for the analysis and interpretation of large experimental data-sets. Here we describe the generation of genome-scale active metabolic networks for 69 different cell types and 16 cancer types using the INIT (Integrative Network Inference for Tissues) algorithm. The INIT algorithm uses cell type specific information about protein abundances contained in the Human Proteome Atlas as the main source of evidence. The generated models constitute the first step towards establishing a Human Metabolic Atlas, which will be a comprehensive description (accessible online) of the metabolism of different human cell types, and will allow for tissue-level and organism-level simulations in order to achieve a better understanding of complex diseases. A comparative analysis between the active metabolic networks of cancer types and healthy cell types allowed for identification of cancer-specific metabolic features that constitute generic potential drug targets for cancer treatment.
Characterization of the components of urban particulate matter mediating impairment of nitric oxide‐dependent relaxation in intrapulmonary arteries

We have previously shown that exposure to urban particulate matter (UPM) impairs endothelial nitric oxide (NO) bioactivity in intrapulmonary arteries. As UPM is composed of heterogeneous constituents, the aim of this study was to clarify the class of pollutants responsible for such effect. Extracts (aqueous, acidic or organic) were prepared from SRM1648, an UPM sample collected in St. Louis (MO, USA). The metal composition of extracts as well as endotoxin content was determined. The effects of each extract, metal mixture and endotoxin were evaluated on endothelium‐dependent relaxation to acetylcholine (reflecting endothelial NO production) in rat isolated intrapulmonary arteries. Aqueous or organic SRM1648 pretreatment altered acetylcholine‐induced relaxation, similar to that induced by native SRM1648. Organic extract induced similar attenuation of acetylcholine relaxation than organic‐treated SRM1648, whereas aqueous extract had no effect. Acidic pretreatment, which impoverished metal and endotoxin content of SRM1648, prevented the impairment of acetylcholine‐induced relaxation. However, neither the acidic extract enriched in metals, nor a metal mixture representative of SRM1648 content, modified acetylcholine relaxation, while endotoxin impaired it. Polymyxin B, which chelates endotoxin, prevented SRM1648‐induced decrease in relaxation to acetylcholine. It is concluded that SRM1648‐induced impairment of endothelial NO‐dependent relaxation in intrapulmonary arteries unlikely involved a soluble factor released by vascular cells during UPM exposure, but rather an organic extractible and acidic‐sensitive constituents of UPM. Endotoxin, but not metals, may be responsible for UPM‐induced impairment of endothelial NO‐dependent relaxation. Copyright © 2013 John Wiley & Sons, Ltd.
Comparison of Open-Graded Friction Course Mix Design Procedures in the United States

This research compares the open graded friction course (OGFC) mix design methods which are currently being used in the United States. OGFC is a type of porous pavement that has been used in the United States since 1944, but has provided inconsistent and highly variable performance results. The design procedures of several agencies were obtained, and then compared for similarities. Fourteen mix design methods were then conducted to determine the optimum binder contents (OBC) using two aggregate sources and a single aggregate gradation. The design methods which are currently used fall into three categories. The first is a property and performance specification where samples are compacted at various binder contents and tested for certain criteria to determine the OBC. The second is an oil absorption method where the oil absorption of the aggregate is used in a series of empirical calculations to determine the OBC. The final method is a visual determination where binder draindown is visually analyzed to determine the optimum binder content. The design methods produced optimum binder contents which had high variability. The oil absorption and visual determination methods all produced a single optimum binder content which varied over 0.5%. The property and performance specification results showed a range of results which were only capped by the binder content range used in research.
Lasers and Electro-optics: Fundamentals and Engineering

1. Spontaneous and stimulated transitions 2. Optical frequency amplifiers 3. Introduction to two practical laser systems 4. Passive optical resonators 5. Optical resonators containing amplifying media 6. Laser radiation 7. Control of laser oscillators 8. Optically pumped solid state lasers 9. Gas lasers 10. Molecular gas lasers I 11. Molecular gas lasers II 12. Tunable lasers 13. Semiconductor lasers 14. Analysis of optical systems I 15. Analysis of optical systems II 16. Optics of Gaussian beams 17. Optical fibers and waveguides 18. Optics of anisotropic media 19. The electro-optic and acousto-optic effects and modulation of light beams 20. Introduction to non-linear processes 21. Wave propagation in non-linear media 22. Detection of optical radiation 23. Coherence theory 24. Laser applications Appendices Index.
Outcomes of 3 or 4 Horizontal Muscles Surgery in Large-Angle Exotropia

PurposeTo evaluate motor and sensory outcomes of 3 or 4 horizontal muscles surgery for the treatment of large-angle exotropia and to evaluate factors influencing the success rate and the relationship between initial postoperative and final motor outcomes. DesignA retrospective analytical study. MethodsMedical records of patients with primary large-angle exotropia [>50 prism diopters (PD)] who had 3 or 4 horizontal muscles surgery were reviewed. Motor outcomes were categorized as successful (esotropia 1–8 PD, orthotropia or exotropia 1–10 PD), acceptable (exotropia 11–20 PD), and poor (esotropia >8 PD or exotropia >20 PD). Results were evaluated only at the last follow-up visit if patients were followed up for less than 2 years. Those who were followed up for more than 2 years were evaluated at both the 2-year and final follow-up visits. Factors influencing the success rate and the relationship between initial postoperative and final motor outcomes were analyzed. ResultsA total of 36 patients were enrolled in this study. The median follow-up time was 18 months (range, 3–60 months). The success rate was 69% at the last follow-up and 75% at the follow-up at 2 years, respectively. Stereopsis improved in 43% at the last follow-up and 56% at 2 years. Initial postoperative deviation was found to correlate with the success rate at the last follow-up (P = 0.018). Initial postoperative overcorrection of 8 to 14 PD had the highest possibility of gaining successful final motor outcomes. ConclusionsThree or 4 horizontal muscles surgery in large-angle exotropia can achieve successful motor outcomes and improve stereopsis. Surgeons should aim for initial overcorrection in order to maximize long-term success.