Miracle-dz/UniFAR-FTUs huggingface dataset:
Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces.

The patterns of synonymous codon choices of the completely sequenced genome of the bacterium Chlamydia trachomatis were analysed. We found that the most important source of variation among the genes results from whether the sequence is located on the leading or lagging strand of replication, resulting in an over representation of G or C, respectively. This can be explained by different mutational biases associated to the different enzymes that replicate each strand. Next we found that most highly expressed sequences are located on the leading strand of replication. From this result, replicational-transcriptional selection can be invoked. Then, when the genes located on the leading strand are studied separately, the correspondence analysis detects a principal trend which discriminates between lowly and highly expressed sequences, the latter displaying a different codon usage pattern than the former, suggesting selection for translation, which is reinforced by the fact that Ks values between orthologous sequences from C. trachomatis and Chlamydia pneumoniae are much smaller in highly expressed genes. Finally, synonymous codon choices appear to be influenced by the hydropathy of each encoded protein and by the degree of amino acid conservation. Therefore, synonymous codon usage in C.trachomatis seems to be the result of a very complex balance among different factors, which rises the problem of whether the forces driving codon usage patterns among microorganisms are rather more complex than generally accepted.
An accretion disc origin for the ‘X-ray broad-line region’ in 1H0707-495

We use a 380-ks X-ray Multi-Mirror Mission–Newton (XMM–Newton) high-resolution Reflection Grating Spectrometer (RGS) spectrum to look for narrow spectral features from the nuclear environment of 1H0707-495. We do not find any evidence of a line-of-sight ionized wind (warm absorber). We do, however, detect broad emission lines, of width ∼5000 km s−1, consistent with O viii Lyα, N vii Lyα, C vi Lyα and an Fe xix/Fe xx/Ne ix Heα blend. Intriguingly, these lines have both blueshifted and redshifted components, whose velocity shifts are consistent with an origin in an accretion disc at ∼1600 Rg from the black hole. The features can be interpreted as the narrow-line cores of the disc reflection spectrum, thus providing independent support for the discline interpretation of the X-ray spectrum of 1H0707-495. We discuss the relevance of our findings for the ‘X-ray broad-line region’ in other Seyferts, and for the origins of the optical broad-line region itself.
THE EFFECTS OF INTELLECTUAL PROPERTY PROTECTION ON GROWTH IN TRANSITION ECONOMIES

Recent research has suggested that stronger intellectual property protection affects the composition of foreign direct investment in transition economies but has not addressed the impact that it might have on the per capita growth rate. This paper seeks to answer that question, empirically exploring the effect that stronger intellectual property rights have on the growth rate. First, it estimates the effect of intellectual property protection on the per capita growth rate using panel data from 1994-2004. Next, the paper surveys output in a variety of sectors, in an attempt to explain where the changes in growth take place when IPR protection changes. Stronger IPR protection appears to have a strong positive effect on the economy, with per capita growth rates increasing upwards of 1 percent for a one standard deviation increase in IPR protection. The level of IPR protection also appears to affect the structure of the economy, with high degrees of protection correlated with increased revenues in areas such as petroleum, chemical, and plastic manufacturing.
Privacy-Preserving Data Publish-Subscribe Service on Cloud-based Platforms

Data publish-subscribe service is an effective approach to share and filter data. Due to the huge volume and velocity of data generated daily, cloud systems are inevitably becoming the platform for data publication and subscription. However, the privacy becomes a challenging issue as the cloud server cannot be fully trusted by both data publishers and data subscribers. In this paper, we propose a privacy-preserving data publishsubscribe service for cloud-based platforms. Specifically, we first formulate the problem of privacy-preserving data publishsubscribe service by refining its security requirements on cloudbased platforms. Then, we propose a bi-policy attribute-based encryption (BP-ABE) scheme as the underlying technique that enables the encryptor to define access policies and the decryptor to define filtering policies. Based on BP-ABE, we also propose a Privacy-preserving Data Publish-Subscribe (PDPS) scheme on cloud-based platforms, which enables the cloud server to evaluate both subscription policy and access policy in a privacy-preserving way. The security analysis and performance evaluation show that the PDPS scheme is secure in standard model and efficient in practice.
Left ventricular dyssynchrony in patients with heart failure and preserved ejection fraction.

AIMS Mechanical dyssynchrony has been postulated to play a pathophysiologic role in heart failure with preserved ejection fraction (HFpEF). METHODS AND RESULTS We quantified left ventricular (LV) systolic dyssynchrony in 130 HFpEF patients with NYHA class II-IV symptoms, ejection fraction (EF) ≥45%, and NT-proBNP levels >400 pg/mL enrolled in the PARAMOUNT trial, and compared them to 40 healthy controls of similar age and gender. Dyssynchrony was assessed by 2D speckle tracking as standard deviation (SD) of time to peak longitudinal systolic strain in 12 ventricular segments and related to measures of systolic and diastolic function. Heart failure with preserved ejection fraction patients (62% women, mean age of 71 ± 9 years, body mass index of 30.2 ± 5.9 kg/m(2), systolic blood pressure 139 ± 15 mmHg) demonstrated significantly greater dyssynchrony than controls (SD of time to peak longitudinal strain; 90.6 ± 50.9 vs. 56.4 ± 33.5 ms, P < 0.001), even in the subset of patients (n = 63) with LVEF ≥55% and narrow QRS (≤100 ms). Among HFpEF patients, dyssynchrony was related to wider QRS interval, higher LV mass, and lower early diastolic tissue Doppler myocardial velocity (E'). Greater dyssynchrony remained significantly associated with worse diastolic function even after restricting the analysis to patients with EF≥55% and adjusting for age, gender, systolic blood pressure, LV mass index, and LVEF. CONCLUSION Heart failure with preserved EF is associated with greater mechanical dyssynchrony compared with healthy controls of similar age and gender. Within an HFpEF population, the severity of dyssynchrony is related to the width of QRS complex, LV hypertrophy, and diastolic dysfunction.
Oxidative Stress and Air Pollution Exposure

Air pollution is associated with increased cardiovascular and pulmonary morbidity and mortality. The mechanisms of air pollution-induced health effects involve oxidative stress and inflammation. As a matter of fact, particulate matter (PM), especially fine (PM2.5, PM < 2.5 μm) and ultrafine (PM0.1, PM < 0.1 μm) particles, ozone, nitrogen oxides, and transition metals, are potent oxidants or able to generate reactive oxygen species (ROS). Oxidative stress can trigger redox-sensitive pathways that lead to different biological processes such as inflammation and cell death. However, it does appear that the susceptibility of target organ to oxidative injury also depends upon its ability to upregulate protective scavenging systems. As vehicular traffic is known to importantly contribute to PM exposure, its intensity and quality must be strongly relevant determinants of the qualitative characteristics of PM spread in the atmosphere. Change in the composition of this PM is likely to modify its health impact.
Exercise: Why It is a Challenge for Both the Nonconscious and Conscious Mind

The epidemic of physical inactivity is an important societal and individual problem. Despite the well-documented health effects of physical activity, only 22% of the population exercises regularly enough to get the physiological and psychological benefits (S. N. Blair, 1993, Physical activity, physical fitness, and health. Research Quarterly for Exercise and Sport, Vol. 64, pp. 365–376.) Why does 78% fail to do so? The problem is largely psychological and attributable to the processes of nonconscious and conscious mind. This paper reviews research on how nonconscious and conscious processing affects human behavior in general and exercise behavior in particular. Although there generally is no question about the effect of the nonconscious mind on human behavior, “unconsciously operating motives” in and of themselves are incapable of igniting and sustaining this complex behavior—at least until the behavior has been repeated with regularity and long enough to become consistently prompted by situational cues (as is the case for 22% of the population). There is even some evidence to suggest that the nonconscious mind actually works against exercise by embracing cues and excuses for not exercising. A related problem for both the nonconscious and conscious mind, especially that of the occasional exerciser (54% of the population), is that exercise poses a threat to one's sense of freedom and choice (i.e., “you must do it or else”). The resultant psychological reactance leads to attempts to restore this freedom, but it is often accomplished by giving in to temptations (e.g., TV watching). Although people recognize fitness and health as important human conditions, they often pursue these goals by using exercise as a means toward another end (e.g., to lose weight). In doing so, they struggle cognitively with their need for autonomy while trying to balance it in interpersonal and leisure contexts. Such struggle depletes finite self-control resources and makes people more vulnerable to temptations. The net result is that both the nonconscious mind and the conscious mind fail to turn most people into rational thinkers and “self as doers,” who would do what is best for their health.
A Conceptual Modeling Method to Use Agents in Systems Analysis

Information systems research uses conceptual modelling to represent many aspects of a domain. The Entity-Relationship Diagram [4] was developed to deal with data modelling and the Data Flow Diagram [5] to handle how information was transferred and transformed in an organization. However, most of these diagrams do not explicitly represent all of the why, what, and how aspects of an information system functioning in a business. For example, the assumptions behind the processes that occur in a business, and the business context that an information system is operating under. It has been proposed by [20] that system analysts are in need of a new construct to fully represent the domains that information systems are situated in. He has proposed that the “agent” is that concept. He states that the autonomous nature of the agent makes it the perfect conceptualization of actors within an organization, which is essential in understanding the business context and assumptions. Unfortunately, no standard method for creating these agent models exist, and the definition of agent components (even the nature of an agent) is not clear [6]. It has not been disputed that an agent interacts with and changes its environment, but there is little consensus on how the agent achieves these changes. This confusion has led to various conflicting methodologies [1]. We propose that by conceptualizing the agent as a feedback system, we can begin to develop a standard method of describing agents in a business domain, which can then reconcile the disparate agent methodologies. A feedback system takes input from the environment, uses them to decide how to affect the environment, and takes the outcome of affecting the environment as input to the next round of actions [2]. Although many researchers have referred to agents as a system [18], no agent methodologies or definitions have defined their agent concepts in terms of a feedback system. We propose that by analyzing agents as a feedback system, we can better understand and represent business context and assumptions in conceptual modelling. We call such an agent representation a “conceptual agent”. Our research question is: what are the constructs of a conceptual agent, how can they be used in systems analysis, and how useful are these constructs in gathering requirements and developing and maintaining information systems? We call the resulting framework the “Conceptual Agent Model” or CAM. For the remaining of this paper, we will give background into using agents in conceptual modeling in Section 2. In Section 3, we will understand agents in terms of a feedback system. In Section 4, we will discuss the CAM framework, a methodology to use it, and some empirical studies to validate its usability, usefulness, and quality. We will conclude the work, discuss current progress, and future research plans in Section 5.
A robust Bayesian multisensor fusion algorithm for joint lane and pavement boundary detection

In this paper we propose to simultaneously detect lane and pavement boundaries by fusing information from both optical and radar images. The boundaries are described with concentric circular models, whose parameters are compatible and will result in better conditioned estimation problems than previous parabolic models. The optical and radar imaging processes are represented with Gaussian and log-normal probability densities, with which we successfully avoid the ad hoc weighting scheme carried on the two likelihood functions. The multisensor fusion boundary detection problem is posed in a Bayesian framework and a joint maximum a posteriori (MAP) estimate is employed to locate the lane and pavement boundaries. Experimental results have shown that the fusion algorithm outperforms single sensor based boundary detection algorithms in a variety of road scenarios. And it also yields better boundary detection results than the fusion algorithm that took advantage of existing prior and likelihood formulations.
Multihop Free-Space Optical Communications Over Strong Turbulence Channels

In this paper, we study the performance of multihop free-space optical (FSO) wireless systems over turbulence-induced fading channels. The analysis is carried out for systems employing amplify-and-forward (AF) or decode-and-forward (DF) relays and for turbulence channels which can be modeled by the Gamma-Gamma distribution. An exact analytical expression for the end-to-end outage probability of AF systems is obtained, while a closed-form expression of DF systems is derived. The average bit-error probability of a dual-hop FSO system employing a DF relay is studied as a special case. Numerical examples are also presented to illustrate the proposed analysis and to further investigate the effects of the turbulence severity on the multihop FSO systems' performance.
Features of Sjögren's syndrome in patients with primary biliary cirrhosis

Abstract. Twenty‐six consecutive patients with primary biliary cirrhosis (PBC) from northern Sweden were studied regarding the occurrence and features of Sjögren's syndrome (SS). In more than 50% of the patients the rose bengal dye test showed conjunctival and/or corneal staining. In six patients keratoconjunctivitis sicca (KCS) was present with positive rose bengal and Schirmer tests. In a further three patients only the results of the Schirmer tests were abnormal. Radiological findings of sialectasia were demonstrated in six patients, five of whom had KCS. Two of the seven patients who fulfilled our criteria for Sjögren's syndrome were HLA‐B8 positive. A high prevalence of increased immune globulins and rheumatic factor was found, but this did not correlate with the presence of Sjögren's syndrome. Some features of Sjögren's syndrome were found in 73% of PBC patients, and keratoconjunctivitis sicca and/or sialectasia were found in 27% of PBC patients. This constitutes a high frequency of secondary manifestations of the liver disease.
Efficacy and side effects of intermittent recombinant interferon‐α2a in chronic aggressive hepatitis C: With or without initial daily administration

To investigate the therapeutic effect and incidence of side effects of recombinant interferon‐α2a (IFN‐α) in chronic aggressive hepatitis C under stratification by administration mode, a study was conducted by assigning patients to either group A (daily consecutive administration of 9 million units (MU) IFN‐α for 2 weeks and, thereafter, 3 MU intermittently 3 times weekly for 22 weeks) or group B (exclusively intermittent administration; 9 MU IFN‐α twice weekly or 6 MU IFN‐α thrice weekly for 24 weeks). The 28 patients in group A received IFN‐α for 24 weeks up to a total dose of 324 MU and the 53 patients in group B received the same for 24 weeks up to a total dose of 432 MU. When recovery was defined as the absence of hepatitis C virus (HCV)‐RNA 6 months after the completion of treatment, the rate of recovery for group A was 32.1% and that for group B was 37.7%, the latter being higher but without significance. Side effects in groups A and B consisted of leucopenia occupying 14.3 and 7.5%, respectively, and thrombocytopenia occupying 42.9 and 11.3%, respectively; group B exhibited lower values for both side effects. No difference was detected between these groups in other side effects, including pyrexia, generalized malaise, arthralgia or psilosis. Intermittent administration from the outset permitted shortened duration of hospitalization and earlier rehabilitation. Intermittent administration of INF‐α is required when treating patients with chronic hepatitis C showing lower leucocyte or platelet counts.
Characterization of power quality disturbances using digital filtering techniques

This paper presents a characterization of the solar resource behavior for ten cities of Colombia. This study was made from solar radiation and ambient temperature data collected by the Instituto de Hidrología, Meteorología y Estudios Ambientales de Colombia IDEAM. According to the analyzes, we determined which of these ten cities are the best potential for developing solar energy projects.
Clinical applications of recombinant human BMPs: early experience and future development.

In 1965, Marshall R. Urist made the seminal discovery that the extracellular matrix of bone contains a substance that has the capacity to induce new bone formation when implanted into extraskeletal sites in a host 1. This substance, later named bone morphogenetic protein (BMP), has become the subject of extensive research aimed at developing therapeutic strategies for the restoration and treatment of skeletal conditions resulting from trauma, degenerative disease, or ablative surgery. By 1998, a team of investigators at Genetics Institute (now Wyeth Research, Cambridge, Massachusetts) characterized the molecular clones and activities associated with this protein and derived the amino acid sequence from a highly purified preparation obtained from bovine bone 2. This led to the isolation and expression of human complementary DNAs (cDNAs), recognized as members of the transforming growth factor-β supergene family. Over the course of the next fifteen years, investigators elucidated the molecular genetics of BMP biology, leading to the identification of fifteen individual human BMPs possessing varying degrees of cartilage and/or bone inductive activities and to the development of three therapeutic preparations, each for a specific clinical application. This article reviews the evidence upon which presently available therapeutic preparations of BMPs are based and suggests future applications likely to evolve from current investigations. It is currently estimated that approximately 1.5 million bone-grafting operations are performed annually in the United States 3. These procedures are done to enhance the healing of spinal fusions, internal fixation of fractures, and treatment of bone defects, and they are used in the treatment and reconstruction of maxillofacial conditions resulting from trauma or congenital anomalies. In most instances, autologous bone graft is the preferred material in these procedures because of its known osteogenic properties and complement of live cells. However, autologous bone graft is also known to possess two …
Serine Protease Variants Encoded by Echis ocellatus Venom Gland cDNA: Cloning and Sequencing Analysis

Envenoming by Echis saw-scaled viper is the leading cause of death and morbidity in Africa due to snake bite. Despite its medical importance, there have been few investigations into the toxin composition of the venom of this viper. Here, we report the cloning of cDNA sequences encoding four groups or isoforms of the haemostasis-disruptive Serine protease proteins (SPs) from the venom glands of Echis ocellatus. All these SP sequences encoded the cysteine residues scaffold that form the 6-disulphide bonds responsible for the characteristic tertiary structure of venom serine proteases. All the Echis ocellatus EoSP groups showed varying degrees of sequence similarity to published viper venom SPs. However, these groups also showed marked intercluster sequence conservation across them which were significantly different from that of previously published viper SPs. Because viper venom SPs exhibit a high degree of sequence similarity and yet exert profoundly different effects on the mammalian haemostatic system, no attempt was made to assign functionality to the new Echis ocellatus EoSPs on the basis of sequence alone. The extraordinary level of interspecific and intergeneric sequence conservation exhibited by the Echis ocellatus EoSPs and analogous serine proteases from other viper species leads us to speculate that antibodies to representative molecules should neutralise (that we will exploit, by epidermal DNA immunization) the biological function of this important group of venom toxins in vipers that are distributed throughout Africa, the Middle East, and the Indian subcontinent.
A 2.75mW wideband correlation-based transceiver for body-coupled communication

Electronic devices in contact or in close proximity to the human body can use its conductive properties to establish body coupled communication (BCC) between each other. This human centric communication paradigm can be used for wireless body-area networks to reduce the impact of interference on/from RF systems, to avoid the fading effect that the body has on radio systems and to enable power efficient, high data-rate wireless links.