Miracle-dz/UniFAR-FTUs huggingface dataset:
The Metabolic Syndrome as a Risk Factor for Venous and Arterial Thrombosis

The metabolic syndrome is a cluster of risk factors for atherosclerosis. Although a universally accepted deﬁnition is still lacking because available classiﬁcations present slightly different diagnostic criteria, the metabolic syndrome is now recognized as a serious public health problem that affects up to 45% of the population > 50 years of age in the United States and (cid:1) 20 to 25% of the adult population in Europe. To diagnose the metabolic syndrome, the concomitant presence of at least three components, among them visceral obesity deﬁned by the measurement of the waist circumference, elevated blood pressure, hyperglycemia, hypertriglyceridemia, or reduced high-density lipoprotein cholesterol levels, is required. The concomitant presence of these risk factors, and thus the presence of the metabolic syndrome, is associated with inﬂammatory and hypercoagulable states that through increased levels of coagulation factors, reduction in ﬁbrinolysis, endothelial dysfunction, and platelet hyperreactivity may predispose patients to develop cardiovascular events. Several studies have consistently shown that patients with the metabolic syndrome are at signiﬁcantly increased risk of diabetes, coronary artery disease, and ischemic stroke. A few recent studies suggest that the metabolic syndrome may also play a role in the pathogenesis of venous thromboembolism, but this latter ﬁnding needs conﬁrmation by large clinical studies.
An Unfitted Discontinuous Galerkin Scheme for Micro-scale Simulations and Numerical Upscaling

The aim of this thesis is the development of a new discretization method for solving partial differential equations on complex shaped domains. Many biological, physical, and chemical applications involve processes on such domains and the numerical treatment of such processes is a challenging task. The proposed method offers a higher-order discretization where the mesh is not required to resolve the complex shaped boundary. The method combines the Unfitted Finite Element method with a Discontinuous Galerkin discretization. Trial and test functions are defined on a structured grid and their support is restricted according to the domain boundary. Essential boundary conditions are imposed weakly via the Discontinuous Galerkin formulation. Thus, the mesh is not required to resolve the domain boundary but higher-order ansatz functions can still be used. Hence it is possible to vary the size of the ansatz space independently of the geometry. For an elliptic test problem, stability and convergence properties of the method are analyzed numerically. Even though some assumptions of the underlying Discontinuous Galerkin method regarding the finite element mesh cannot be guaranteed, the method is stable in all tests and converges optimally. The control over the size of the approximation space is especially attractive for applications like numerical upscaling and multi-scale simulations. In this thesis the method is successfully applied to numerical upscaling of a stationary flow problem and to a time-dependent transport problem, where the complex domains used are artificially generated as well as experimentally measured structures, obtained from micro X-ray CT scans.
The Importance of De-escalating Antimicrobial Therapy in Patients with Ventilator-Associated Pneumonia

The management of ventilator-associated pneumonia (VAP) requires a strategy for antibiotic use that achieves prompt and accurate empirical therapy without overusing antibiotics. Although, efforts at better diagnosis and antibiotic restriction have been attempted, ‘‘de-escalation’’ may be a more useful and effective strategy, and one that can achieve these goals while improving patient outcomes. The centerpiece of this approach is to initiate empirical therapy with a broad-spectrum treatment regimen, based on knowledge of local patterns of microbiology and antimicrobial resistance. Prior to therapy, patients require collection of a lower respiratory tract sample for culture. After 2 to 3 days, the clinical course can be assessed and the culture data reviewed, and in responding patients, efforts can be made to change the initial broad-spectrum therapy. This de-escalation can involve focusing to a more narrow spectrum agent, reducing the number of antibiotics, stopping therapy altogether in patients not likely to have infection, and making efforts to reduce duration of therapy. When this strategy has been used, outcomes such as the frequency of secondary infection, antimicrobial resistance, and mortality have improved. Additional information is needed to apply this approach more widely, especially in patients infected with multidrug-resistant organisms and in those with negative lower respiratory tract cultures.
The Prothrombin Gene and Its Liver-Specific Expression

Prothrombin and its enzymatically active form thrombin play a key role in a number of biologic events. Prothrombin is activated by Factor Xa in the presence of a negatively charged phospholipid cell surface, calcium, and Factor Va to thrombin, an enzyme with serine pro­ tease activity. Thrombin proteolytically removes fibrin-opeptides A and B from fibrinogen to form a fibrin clot. Thrombin also activates Factor XIII, which is involved in cross-linking fibrin to form an insoluble fibrin clot. Fac­ tors V and VIII, cofactors required in the coagulation process, are also activated by thrombin. Thrombin is also involved in the inhibition of the clotting reaction by acti­ vating protein C in the presence of thrombomodulin. Activated protein C inactivates Factor Villa. 1-3 Besides its central role in several aspects of blood coagulation, thrombin is also involved in the stimulation of shape change in platelets, causes mitogenesis in fibroblasts, is chemotactic for macrophages, and is involved in the reg­ ulation of proliferation of endothelial cells and possibly other cell types. 4-7 In fact, a receptor specific for throm­
MR Imaging of Tendons and Ligaments of the Midfoot

Disorders of ligaments and tendons at the midfoot are less common than those around the ankle and at the hindfoot. Nevertheless, disorders of the distal portions of the anterior and posterior tibialis tendons (ATT and PTT) and the spring ligament complex have an important clinical impact and can be treated with surgery. In this article, we discuss important factors for the magnetic resonance (MR) protocol and review the normal MR anatomy and MR ﬁndings in disorders of the distal ATT and PTT as well as of the spring ligament complex. In addition, we discuss clinical aspects of these disorders.
Exploring the Regulatory Mechanism of Stress Responses in the Paraventricular Nucleus of the Hypothalamus: Backgrounds and Future Perspectives of Corticotropin-Releasing Factor-Modified Yellow Fluorescent Protein-Knock-In Mouse

Corticotropin-releasing factor (CRF) plays a central role in the stress response by regulating the hypothalamic- pituitary-adrenal axis. In order to unravel unsolved issues underlying the regulatory mechanisms for CRF neurons, modiﬁed yellow ﬂuorescent protein (Venus) gene was inserted into the CRF gene in frame, and CRF neurons were visualized by the Venus ﬂuorescence. Venus expression is overlapped with CRF expression in most brain regions, including the paraventricular nucleus of the hypothalamus (PVH). This mouse is a useful tool especially for conducting electrophysiological recordings from CRF neurons. In the ﬁrst half of the present review, the backgrounds of the generation of the mouse are described based on the previous literature: ﬁrst, the anatomical distribution of CRF-immunoreactive neurons in the rat brain is overviewed, and then the knowledge on the electrophysiological properties of the parvocellular neuroendocrine neurons that constitute a subpopulation of neurons in the PVH (including PVH-CRF neurons) is described. These sections may help the readers in understanding the purpose of generating the CRF-Venus mouse. In the second half of the manuscript, the distribution of Venus-expressing neurons is characterized in the CRF-Venus mouse, and preliminary results of electrophysiological recordings from the Venus-expressing neurons are shown. CRF driver mouse lines are also referred to as a means for the CRF neuron-selective gene transfer or targeting. Novel mouse lines may serve as tools for disclosing the regulatory mechanisms for CRF neurons in the PVH, as well as other brain regions.
Controversies in Lung Transplantation: Are Two Lungs Better Than One?

Lung transplantation is commonly used for patients with end-stage lung disease. However, there is continuing debate on the optimal operation for patients with chronic obstructive pulmonary disease (COPD) and pulmonary ﬁbrosis. Single-lung transplantation (SLT) provides equivalent short-and medium-term results compared with bilateral lung transplantation (BLT), but long-term survival appears slightly better in BLT recipients (especially in patients with COPD). The number of available organs for lung transplantation also inﬂuences the choice of operation. Recent developments suggest that the organ donor shortage is not as severe as previously thought, making BLT a possible alternative for more patients. Local expertise and waiting list issues are important in inﬂuencing the choice of SLT versus BLT. Most of the data support the use of BLT for the majority of COPD patients when available, and the use of SLT for the majority of idiopathic pulmonary ﬁbrosis (IPF) patients. The ultimate choice of operation will depend on donor and recipient characteristics and local expertise and waiting list issues.
New Treatments of Hepatorenal Syndrome

Hepatorenal syndrome (HRS) is a common complication of advanced cirrhosis, characterized by renal failure and major abnormalities in the systemic circulatory function. Renal failure is caused by intense vasoconstriction of the renal circulation. The syndrome is probably the ﬁnal consequence of an extreme underﬁlling of the arterial circulation, secondary to vasodilatation in the splanchninc vascular bed and a decrease in cardiac output due to central hypovolemia. The diagnosis of HRS is based on the exclusion of other causes of renal failure. The survival of patients with HRS is very short, particularly when there is rapidly progressive renal failure (type-1 HRS). Liver transplantation is the best therapeutic option but its applicability is low. During the past few years effective treatment for HRS, such as vasoconstrictor drugs (vasopressin analogues, / -adrenergic agonists) associated with intravenous albumin infusion and transjugular intrahepatic portosystemic shunts (TIPS), have been introduced. They improve circulatory function, normalize serum creatinine, and may improve survival. Sequential treatment with vaso-constrictors plus albumin and TIPS is an attractive therapeutic possibility. Plasma volume expansion with albumin at infection diagnosis in patients with spontaneous bacterial peritonitis and the administration of pentoxiphilline in patients with severe alcoholic hepatitis signiﬁcantly reduce the development of type-1 HRS.
Robust control for uncertain linear delay systems via sliding mode control

In this paper, a novel discontinuous control strategy for robust stabilization of a class of uncertain multivariable linear time‐delay systems with delays in both the state and control variables is proposed. Two predictors are first designed to compensate the delay effect in the control input, and then an integral sliding mode control technique is applied to compensate partially the effect of the perturbation term. Finally, a nominal delay‐free component of the full control input is designed to stabilize the sliding mode dynamics. Conditions for the stability of the closed‐loop perturbed system are then derived. The proposed framework is then extended to the class of systems modeled in regular form. Some examples illustrate the feasibility of the proposed scheme. Copyright © 2017 John Wiley & Sons, Ltd.
Pulmonary Pathology of the Rheumatic Diseases

Thoracic manifestations of the rheumatic diseases (RDs) are a signiﬁcant cause of morbidity and mortality worldwide. The ﬁve RDs most frequently associated with pleuropulmonary disease are (1) rheumatoid arthritis (RA), (2) systemic lupus erythema-tosus (SLE), (3) progressive systemic sclerosis (PSS), (4) polymyositis/dermatomyositis (PM/DM), and (5) Sjo¨gren syndrome (SS). The clinical presentation is highly variable, ranging from pleuritic pain alone to slowly progressive breathlessness accompanied by cough. On occasion RD may present acutely with overwhelming respiratory failure as the ﬁrst pulmonary manifestation. In all of the RDs, the pathology is dominated by either or both inﬂammation and ﬁbrosis, but the anatomical distribution in each varies somewhat. For example, airway-associated lymphoid hyperplasia is a common manifestation of SS, PM/DM preferentially involves the alveolar parenchyma, and pleural inﬂammation is most commonly seen in RA. Such changes may be detected radiologically as peribronchovascular disease in SS, ground-glass inﬁltrates in PM/DM, and pleural disease with effusion in RA. Some RDs are more commonly associated with distinctive histopathology, such as rheumatoid nodules in RA, or lymphoid hyperplasia in both RA and SS. Patients with PSS are at particular risk for pulmonary hypertension when the lung is involved. Also, statistically, acute lung injury occurs more commonly in some, such as SLE and PM/DM. The very common use of immunosuppressive agents in the treatment of RD creates additional diagnostic problems related to drug toxicity and infection. Finally, a major confounding factor occurs when preclinical RD presents ﬁrst as pulmonary disease (particularly PM/DM), an occurrence that may invoke one of the so-called idiopathic interstitial pneumonias. The most common pleuropulmonary pathological manifestations of the ﬁve major RDs are presented and discussed with brief radiological correlations.
Muscle Injury of the Chest Wall and Upper Extremity

Most muscle trauma more commonly involves the lower extremity, but injury to the chest wall, particularly the pectoralis major, is well recognized. Trauma to the upper limb muscle-tendon unit is preserved. Development of complications from muscle injury is also discussed. This article systematically reviews the clinical features, pathogenesis, imaging ﬁndings, and management for upper limb and chest wall muscle injuries. Imaging modalities focus on magnetic resonance imaging and ultrasound, highlighting their advantages and disadvantages in speciﬁc situations
Progress in Respiratory Virus Vaccine Development

Viral respiratory infections continue to cause signiﬁcant morbidity and mortality in infants and young children as well as in at-risk adults and the elderly. Although many viral pathogens are capable of causing acute respiratory disease, vaccine development has to focus on a limited number of pathogens (i.e., agents that commonly cause serious lower respiratory disease). Inactivated and, more recently, live attenuated inﬂuenza virus vaccines are the mainstay of interpandemic inﬂuenza prevention, but vaccines are not available yet for other important viruses such as respiratory syncytial virus, metapneumovirus, the parainﬂuenza viruses, and avian inﬂuenza viruses with pandemic potential. Reverse genetics systems that allow rational vaccine development are now widely used, and considerable progress has been made in preclinical and clinical development of novel respiratory virus vaccines.
New Concepts in the Radiological Assessment of COPD

Chronic obstructive pulmonary disease (COPD) is a complex genetic disorder in which environmental factors, such as tobacco smoke, interact with genetic susceptibility to cause disease. Airway obstruction in COPD is due to an exaggerated inﬂammatory response that ultimately destroys the lung parenchyma (emphysema) and increases airway resistance by remodeling the airway wall. Until recently, assessment of these disease processes required the examination of resected tissue. However, computed tomography (CT) now allows researchers to measure the structure of the lung parenchyma and airway wall without having to remove the tissue. This review describes some of the new CT techniques for quantitative assessment of lung structure. These techniques are extremely important to study the pathogenesis of COPD as well as differentiate patients with predominantly emphysema disease from those with airway wall remodeling, and to assess the effects of therapeutic interventions.
Mechanisms of Thrombospondin-1-Mediated Metastasis and Angiogenesis

The major route of tumor spread is through the bloodstream. Once in circulation, the tumor cells aggregate in clumps with platelets, which enhances the tumor cell survival. The tumor emboli will then adhere to the endothelium and by the release of proteases extravasation of the cells will occur. One of the platelet-secreted proteins is thrombospondin-1. In this article, thrombospondin-1 will be described as a modulator of angiogenesis through its role in regulating endothelial cell apoptosis, protease expression, and vascular endothelial growth factor expression. We hope to convey the idea that activity of thrombospondin-1 in tumor progression is dependent upon its interaction with several host-and tumor-associated proteins.
Method of Statistical Testing

By Y. A. Shreider Essex: Elsevier Publishing Co. Ltd. 1964. Pp. 303. Price 90s. Statistical methods may be used to study both stochastic and deterministic problems. The term 'Monte Carlo method ' is usually used for the second type of problem and it is fitting that one of the main fields of application of this method is in particle physics where the distinction between the two types of problem becomes somewhat blurred.
Bronchiolar Complications of Connective Tissue Disorders

A spectrum of inflammatory and fibrotic disorders involving the small air ways (i.e., respiratory and terminal bronchioles) may complicate connective tissue disor ders (CTDs). Obliterative (constrictive) bronchiolitis (OB) is a well-recognized, albeit rare, complication of rheumatoid arthritis, and occasional cases have been described in other CTDs. Bronchiolitis obliterans with organizing pneumonia (BOOP), also termed crypto genic organizing pneumonia, is a rare complication of CTDs. Clinical, radiographic, histo logical features and prognosis differ markedly between these entities. Clinical features are nonspecific, and the diagnosis (particularly OB) may be difficult. High resolution thin section computed tomographic (HRCT) scans are useful in detecting bronchiolar pathol ogy, even when symptoms are minimal or absent. Surgical (open or thoracoscopic) lung biopsies can substantiate the diagnosis, but in some cases, the diagnosis can be affirmed less aggressively by appropriate imaging studies (e.g., HRCT) and transbronchial lung biopsies. Corticosteroids are highly efficacious for BOOP, but therapeutic options for OB are disappointing.
Category theory in Coq 8.5: Extended version

We report on our experience implementing category theory in Coq 8.5. Our work formalizes most of basic category theory, including concepts not covered by existing formalizations, in a library that is fit to be used as a general-purpose category-theoretical foundation. Our development particularly takes advantage of two features new to Coq 8.5: primitive projections for records and universe polymorphism. Primitive projections allow for well-behaved dualities while universe polymorphism provides a relative notion of largeness and smallness. The latter is one of the main contributions of this paper. It pushes the limits of the new universe polymorphism and constraint inference algorithm of Coq 8.5. In this paper we present in detail smallness and largeness in categories and the foundation they are built on top of. We furthermore explain how we have used the universe polymorphism of Coq 8.5 to represent smallness and largeness arguments by simply ignoring them and entrusting them to the universe inference algorithm of Coq 8.5. We also discuss our experience throughout this implementation, discuss concepts formalized in this development and give a comparison with a few other developments of similar extent. Furthermore, we discuss (future) works on top of or related to this development including our experience regarding our ongoing effort of porting a version of this development on top of the HoTT library. Category Theory in Coq 8.5: Extended Version Amin Timany Bart Jacobs iMinds-DistriNet – KU Leuven firstname.lastname@cs.kuleuven. be
Comparative study of worm‐like chain models for collagen molecules

Collagen is the main structural protein in various biological tissues and of high interest for microstructural multi‐scale models due to its load bearing functionality. The worm‐like chain (WLC) model [4] with its approximation [6] is a widely used approach for the modeling of DNA, which has a helical structure similar to tropocollagen. However, the classical WLC is suitable only for the entropic deformation regime of collagen. By modeling the extension behavior, it fails to give accurate predictions when the helical structure of the molecule starts twisting under higher loads.
Exploring Vulnerabilities of the Internet of Things Devices

We introduce in this thesis a ranking list of the ten most common vulnerabilities in Internet of Things devices. The main aim was to provide ranking lists created from public data with a transparent creation methodology because ranking lists with these requirements currently do not exist. For example, the popular project OWASP published the most recent ranking list in 2018, and other existing up-to-date ranking lists do not provide a transparent creation methodology and used data sources. We introduce in this thesis a ranking list of the ten most common vulnerabilities in Internet of Things devices. Furthermore, we propose a similar ranking list only for camera devices. Also, we present the most common vulnerability for different smart device categories. In addition, the scraping tool for vulnerability collection was implemented in the framework Scrapy, and an analysis of three vulnerabilities in the context of the Internet of Things devices was performed. The selected vulnerability categories are Access Control, Overflow, and Password Management.
Fitting Longitudinal Mixed Effect Logistic Regression Models with the NLMIXED Procedure

The NLMIXED procedure fits nonlinear mixed models; it is also useful for fitting linear mixed models having non-Gaussian error distributions. We recently used the NLMIXED procedure to perform longitudinal logistic regressions in which a random intercept was included to induce a compound symmetry covariance structure for repeated measures on individual subjects. We devised a macro to automate fitting this model. The NLMIXED procedure requires writing out regression equations, declaring parameter names, and providing initial parameter estimates. To get accurate initial parameter estimates for our NLMIXED models we fit Generalized Estimating Equations (GEE) models with the GENMOD procedure. Our macro automates the procedure of fitting GEE models, entering their parameter estimates as the initial values for NLMIXED models, and then fitting the NLMIXED models. The macro does this recursively so that for most multivariable models only one new parameter estimate is entered into an NLMIXED model at a time. This step-by-step approach to model fitting increases the probability of successful convergence of the optimization procedure; however, it also means that fitting a model with, for example, five variables requires ten regression models—five GEE and five NLMIXED models. The macro makes this work simpler and more user-friendly.